From e46a043ecd9f9ef46d1d44393362bb7016454544 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2016 00:25:27 +0100 Subject: [PATCH 001/436] build-system/python: Make sure 'check' returns failures. * guix/build/python-build-system.scm (check): Wrap 'call-setuppy' in 'if' so that it actually fails when the tests fail. Print informational message when skipped. --- guix/build/python-build-system.scm | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/guix/build/python-build-system.scm b/guix/build/python-build-system.scm index 3f280b0ac0..dd07986b94 100644 --- a/guix/build/python-build-system.scm +++ b/guix/build/python-build-system.scm @@ -137,11 +137,15 @@ ;; (given with `package_dir`). This will by copied to the output, too, ;; so we need to remove. (let ((before (find-files "build" "\\.egg-info$" #:directories? #t))) - (call-setuppy test-target '() use-setuptools?) - (let* ((after (find-files "build" "\\.egg-info$" #:directories? #t)) - (inter (lset-difference eqv? after before))) - (for-each delete-file-recursively inter))) - #t)) + (if (call-setuppy test-target '() use-setuptools?) + (let* ((after (find-files "build" "\\.egg-info$" #:directories? #t)) + (inter (lset-difference eqv? after before))) + (for-each delete-file-recursively inter) + #t) + #f)) + (begin + (format #t "test suite not run~%") + #t))) (define (get-python-version python) (let* ((version (last (string-split python #\-))) From dcb0da7bff9dd35a65769e8f6a3b542306a115ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 01:19:07 +0100 Subject: [PATCH 002/436] gnu: python-py: Disable tests. * gnu/packages/python.scm (python-py, python2-py)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6d6d880bb8..fe96f0f392 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1625,6 +1625,12 @@ standard library.") (base32 "0561gz2w3i825gyl42mcq14y3dcgkapfiv5zv9a2bz15qxiijl56")))) (build-system python-build-system) + (arguments + ;; FIXME: "ImportError: 'test' module incorrectly imported from + ;; '/gnu/store/...-python-pytest-mimimal-3.0.5/lib/python3.5/site-packages'. + ;; Expected '/tmp/guix-build-python-py-1.4.31.drv-0/py-1.4.31/py'. + ;; Is this module globally installed?" + '(#:tests? #f)) (home-page "http://pylib.readthedocs.org/") (synopsis "Python library for parsing, I/O, instrospection, and logging") (description From 4fd129ee86b7f2f76fa705327925b7b6c54bb069 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 05:34:25 +0100 Subject: [PATCH 003/436] gnu: python-six: Fix test dependencies. * gnu/packages/python.scm (python-six, python2-six)[native-inputs]: Add python-py and python-pytest. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fe96f0f392..3f816bc1f0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -946,6 +946,9 @@ password storage.") (base32 "0snmb8xffb3vsma0z67i0h0w2g2dy0p3gsgh9gi4i0kgc5l8spqh")))) (build-system python-build-system) + (native-inputs + `(("python-py" ,python-py) + ("python-pytest" ,python-pytest))) (home-page "http://pypi.python.org/pypi/six/") (synopsis "Python 2 and 3 compatibility utilities") (description From bd10e677d1ff5650ea5a13c604a083824f12b238 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 09:50:08 +0100 Subject: [PATCH 004/436] gnu: python-coverage: Disable tests. * gnu/packages/python.scm (python-coverage, python2-coverage)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3f816bc1f0..bc0a82b3a3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2123,6 +2123,9 @@ have failed since the last commit or what tests are currently failing.") (base32 "01rbr4br4lsk0lwn8fb96zwd2xr4f0mg1w7iq3j11i8f5ig2nqs1")))) (build-system python-build-system) + (arguments + ;; FIXME: 95 tests failed, 539 passed, 6 skipped, 2 errors. + '(#:tests? #f)) (home-page "http://nedbatchelder.com/code/coverage") (synopsis "Code coverage measurement for Python") (description From 995cb99e4b9852c497d73a130430e5c96bb74ef7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 10:47:59 +0100 Subject: [PATCH 005/436] gnu: python-pygments: Disable tests. * gnu/packages/python.scm (python-pygments, python2-pygments)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bc0a82b3a3..65a8076363 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2782,6 +2782,9 @@ reStructuredText.") (base32 "0lagrwifsgn0s8bzqahpr87p7gd38xja8f06akscinp6hj89283k")))) (build-system python-build-system) + (arguments + ;; FIXME: Tests require sphinx, which depends on this. + '(#:tests? #f)) (home-page "http://pygments.org/") (synopsis "Syntax highlighting") (description From 03cb5f9edbe67c93d235060c877f6a135a418c9f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 12:01:52 +0100 Subject: [PATCH 006/436] gnu: python-sphinx: Disable tests. * gnu/packages/python.scm (python-sphinx, python2-sphinx)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 65a8076363..e9ec52271e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2808,6 +2808,9 @@ reStructuredText.") (base32 "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl")))) (build-system python-build-system) + (arguments + ;; FIXME: Missing dependencies. + '(#:tests? #f)) (propagated-inputs `(("python-jinja2" ,python-jinja2) ("python-docutils" ,python-docutils) From 3fe2c209e0e69660164b5484a2d9f9d946006e36 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 12:48:04 +0100 Subject: [PATCH 007/436] gnu: python-tornado: Disable tests. * gnu/packages/python.scm (python-tornado, python2-tornado)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e9ec52271e..28ead167d8 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5458,6 +5458,17 @@ It is written entirely in Python.") (sha256 (base32 "1gzgwayl6hmc9jfcl88bni4jcsk2jcca9dn1rvrfsvnijcjx7hn9")))) (build-system python-build-system) + (arguments + '(;; FIXME: Two tests error out with: + ;; AssertionError: b'Error in atexit._run_exitfuncs:\nFileNotF[44 chars]ry\n' != b'' + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; ;; 'setup.py test' hits an AssertionError on BSD-specific + ;; ;; "tornado/platform/kqueue.py". This is the supported method: + ;; (zero? (system* "python" "-m" "tornado.test"))))) + #:tests? #f)) (native-inputs `(("python-certifi" ,python-certifi))) (propagated-inputs From 97be1bc23128cf42c49867d984c43f6fea3820d6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 18:51:01 +0100 Subject: [PATCH 008/436] gnu: python-click: Fix tests. * gnu/packages/python.scm (python-click, python2-click)[arguments]: Replace 'check' with custom phase. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 28ead167d8..1a8a9a407c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2301,7 +2301,12 @@ is used by the Requests library to verify HTTPS requests.") (substitute* "click/_unicodefun.py" (("'locale'") (string-append "'" glibc "/bin/locale'")))) - #t))))) + #t)) + (replace 'check + (lambda _ + (zero? (system* "make" "test"))))))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "http://click.pocoo.org") (synopsis "Command line library for Python") (description From cff0ccf9dce5bb0c6c504909be7dfc581f3068a9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:07:30 +0100 Subject: [PATCH 009/436] gnu: python-requests: Disable tests. * gnu/packages/python.scm (python-requests, python2-requests, python-requests-2.7)[native-inputs]: Remove field. [arguments]: New field. Set #:tests? #f. --- gnu/packages/python.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1a8a9a407c..200ba30498 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2365,12 +2365,11 @@ installed with a newer @code{pip} or with wheel's own command line utility.") (sha256 (base32 "0zsqrzlybf25xscgi7ja4s48y2abf9wvjkn47wh984qgs1fq2xy5")))) + ;; TODO: unbundle urllib3 and chardet. (build-system python-build-system) - (native-inputs - `(("python-py" ,python-py) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-wheel" ,python-wheel))) + (arguments + ;; FIXME: Some tests require network access. + '(#:tests? #f)) (home-page "http://python-requests.org/") (synopsis "Python HTTP library") (description From c8cd850c87f50b476dc87166e09207426efd8409 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:15:21 +0100 Subject: [PATCH 010/436] gnu: python-xcffib: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-xcffib)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 200ba30498..6aee72cf70 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4230,15 +4230,15 @@ a front-end for C compilers or analysis tools.") ("python-six" ,python-six))) (arguments `(#:phases - (alist-cons-after - 'install 'install-doc - (lambda* (#:key outputs #:allow-other-keys) - (let ((doc (string-append (assoc-ref outputs "out") "/share" - "/doc/" ,name "-" ,version))) - (mkdir-p doc) - (copy-file "README.md" - (string-append doc "/README.md")))) - %standard-phases))) + (modify-phases %standard-phases + (add-after 'install 'install-doc + (lambda* (#:key outputs #:allow-other-keys) + (let ((doc (string-append (assoc-ref outputs "out") "/share" + "/doc/" ,name "-" ,version))) + (mkdir-p doc) + (copy-file "README.md" + (string-append doc "/README.md")) + #t)))))) (home-page "https://github.com/tych0/xcffib") (synopsis "XCB Python bindings") (description From e2816ac72d6225ecb5ab740b7313bfc28c9d7764 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:25:49 +0100 Subject: [PATCH 011/436] gnu: python-xcffib: Disable tests. * gnu/packages/python.scm (python-xcffib, python2-xcffib)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6aee72cf70..bed8124b55 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4229,7 +4229,9 @@ a front-end for C compilers or analysis tools.") `(("python-cffi" ,python-cffi) ; used at run time ("python-six" ,python-six))) (arguments - `(#:phases + `(;; FIXME: Tests cannot load libxcb.so.1 + #:tests? #f + #:phases (modify-phases %standard-phases (add-after 'install 'install-doc (lambda* (#:key outputs #:allow-other-keys) From 6734c7bae34888756eb40ed13a8c16f3e35cc53d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:28:27 +0100 Subject: [PATCH 012/436] gnu: python-cairocffi: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-cairocffi)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bed8124b55..37a595f7cb 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4278,24 +4278,24 @@ support for Python 3 and PyPy. It is based on cffi.") `(("python-xcffib" ,python-xcffib))) ; used at run time (arguments `(#:phases - (alist-cons-after - 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html"))) - (setenv "LD_LIBRARY_PATH" - (string-append (assoc-ref inputs "cairo") "/lib" ":" - (assoc-ref inputs "gdk-pixbuf") "/lib")) - (setenv "LANG" "en_US.UTF-8") - (mkdir-p html) - (for-each (lambda (file) - (copy-file (string-append "." file) - (string-append doc file))) - '("/README.rst" "/CHANGES" "/LICENSE")) - (system* "python" "setup.py" "build_sphinx") - (copy-recursively "docs/_build/html" html))) - %standard-phases))) + (modify-phases %standard-phases + (add-after 'install 'install-doc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "doc") "/share")) + (doc (string-append data "/doc/" ,name "-" ,version)) + (html (string-append doc "/html"))) + (setenv "LD_LIBRARY_PATH" + (string-append (assoc-ref inputs "cairo") "/lib" ":" + (assoc-ref inputs "gdk-pixbuf") "/lib")) + (setenv "LANG" "en_US.UTF-8") + (mkdir-p html) + (for-each (lambda (file) + (copy-file (string-append "." file) + (string-append doc file))) + '("/README.rst" "/CHANGES" "/LICENSE")) + (system* "python" "setup.py" "build_sphinx") + (copy-recursively "docs/_build/html" html) + #t)))))) (home-page "https://github.com/SimonSapin/cairocffi") (synopsis "Python bindings and object-oriented API for Cairo") (description From a792e1aa8dd6818f6fce942aa0efa9dc1076a99c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:30:21 +0100 Subject: [PATCH 013/436] gnu: python-cairocffi: Disable tests. * gnu/packages/python.scm (python-cairocffi, python2-cairocffi)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 37a595f7cb..31f0651d72 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4277,7 +4277,9 @@ support for Python 3 and PyPy. It is based on cffi.") (propagated-inputs `(("python-xcffib" ,python-xcffib))) ; used at run time (arguments - `(#:phases + `(;; FIXME: Tests cannot find 'libcairo.so.2'. + #:tests? #f + #:phases (modify-phases %standard-phases (add-after 'install 'install-doc (lambda* (#:key inputs outputs #:allow-other-keys) From 2b9e4bead983167aeca375a26d5ddf6a6a5877eb Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 13 Dec 2016 20:45:50 -0500 Subject: [PATCH 014/436] gnu: python-zope-schema: Build with python-zope-exceptions. * gnu/packages/python.scm (python-zope-schema, python2-zope-schema)[propagated-inputs]: Add python-zope-schema. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 31f0651d72..2f3d2b36ac 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7330,6 +7330,7 @@ internationalized messages within program source text.") (build-system python-build-system) (propagated-inputs `(("python-zope-event" ,python-zope-event) + ("python-zope-exceptions", python-zope-exceptions) ("python-zope-interface" ,python-zope-interface))) (native-inputs `(("python-zope-testing" ,python-zope-testing) From 9d3a15b4962612b8975e68a28f3b13d66b71c18d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 13 Dec 2016 20:51:26 -0500 Subject: [PATCH 015/436] gnu: python-sphinx-rtd-theme: Build with python-sphinx. * gnu/packages/python.scm (python-sphinx-rtd-theme, python2-sphinx-rtd-theme)[propagated-inputs]: Add python-sphinx. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 2f3d2b36ac..700e792143 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2843,6 +2843,8 @@ sources.") (base32 "19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g")))) (build-system python-build-system) + (propagated-inputs + `(("python-sphinx" ,python-sphinx))) (home-page "https://github.com/snide/sphinx_rtd_theme/") (synopsis "ReadTheDocs.org theme for Sphinx") (description "A theme for Sphinx used by ReadTheDocs.org.") From fb08c4fedc33bb8b7d8c89314b8e4da870d85438 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 10:18:33 +0100 Subject: [PATCH 016/436] gnu: python-psutil: Disable tests. * gnu/packages/python.scm (python-psutil, python2-psutil): Disable tests. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 700e792143..080d3fccc9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -437,6 +437,9 @@ instead of @command{python3}."))) (base32 "1w4r09fvn6kd80m5mx4ws1wz100brkaq6hzzpwrns8cgjzjpl6c6")))) (build-system python-build-system) + (arguments + ;; FIXME: some tests does not return and times out. + '(#:tests? #f)) (home-page "https://www.github.com/giampaolo/psutil") (synopsis "Library for retrieving information on running processes") (description From f6c1ef180459a525c1b38a5a7c37fec3cfb45ab9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 10:38:26 +0100 Subject: [PATCH 017/436] gnu: python-fixtures: Fix test suite. * gnu/packages/python.scm (python-fixtures, python2-fixtures): Replace 'check' with custom phase. [native-inputs]: Add python-mock. --- gnu/packages/python.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 080d3fccc9..ceb4896d34 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2068,10 +2068,18 @@ from git information. (base32 "0djxvdwm8s60dbfn7bhf40x6g818p3b3mlwijm1c3bqg7msn271y")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "python" "-m" "testtools.run" + "fixtures.test_suite"))))))) (propagated-inputs `(("python-six" ,python-six))) (native-inputs - `(("python-pbr-minimal" ,python-pbr-minimal) + `(("python-mock" ,python-mock) + ("python-pbr-minimal" ,python-pbr-minimal) ("python-testtools" ,python-testtools))) (home-page "https://launchpad.net/python-fixtures") (synopsis "Python test fixture library") From 90110ef95616f2fe71e2247aec636824676f0b54 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 10:46:47 +0100 Subject: [PATCH 018/436] gnu: python-testrepository: Disable tests. * gnu/packages/python.scm (python-testrepository, python2-testrepository): Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ceb4896d34..cea60b27e6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2105,6 +2105,9 @@ Python tests.") (base32 "1ssqb07c277010i6gzzkbdd46gd9mrj0bi0i8vn560n2k2y4j93m")))) (build-system python-build-system) + (arguments + ;; FIXME: Many tests are failing. + '(#:tests? #f)) (propagated-inputs `(("python-fixtures" ,python-fixtures) ("python-subunit" ,python-subunit) From 0d84e1ef22f46f27948887fcac56742dcde5fd23 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:19:11 +0100 Subject: [PATCH 019/436] gnu: python-pyflakes-0.8.1: Disable tests. * gnu/packages/python.scm (python-pyflakes-0.8.1, python2-pyflakes-0.8.1)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index cea60b27e6..a971e8bc3b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5721,7 +5721,10 @@ complexity of Python source code.") ".tar.gz")) (sha256 (base32 - "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z")))))) + "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z")))) + (arguments + ;; XXX Tests not compatible with Python 3.5. + '(#:tests? #f)))) (define-public python2-pyflakes-0.8.1 (package-with-python2 python-pyflakes-0.8.1)) From 73e3060d576effa1064bd89f23010ded6188ffd4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:21:50 +0100 Subject: [PATCH 020/436] gnu: python-pep8-1.5.7: Disable tests. * gnu/packages/python.scm (python-pep8-1.5.7, python2-pep8-1.5.7)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a971e8bc3b..ee5cbc5e77 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5702,7 +5702,10 @@ complexity of Python source code.") ".tar.gz")) (sha256 (base32 - "12b9bbdbwnspxgak14xg58c130x2n0blxzlms5jn2dszn8qj3d0m")))))) + "12b9bbdbwnspxgak14xg58c130x2n0blxzlms5jn2dszn8qj3d0m")))) + (arguments + ;; XXX Tests not compatible with Python 3.5. + '(#:tests? #f)))) (define-public python2-pep8-1.5.7 (package-with-python2 python-pep8-1.5.7)) From a717e8a698319424dfce58ce496d5bfb055753d8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:25:02 +0100 Subject: [PATCH 021/436] gnu: python-flake8-2.2.4: Disable tests. * gnu/packages/python.scm (python-flake8-2.2.4, python2-flake8-2.2.4)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ee5cbc5e77..6c58403dd6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5795,7 +5795,10 @@ complexity of Python source code.") (for-each delete-file-recursively (find-files "." "__pycache__" #:directories? #t)) (for-each delete-file (find-files "." "\\.pyc$")) - #t)))))) + #t)))) + (arguments + ;; XXX Fails with Python 3.5. + '(#:tests? #f)))) (define-public python2-flake8-2.2.4 (package-with-python2 python-flake8-2.2.4)) From 2ff4559b49b325252ef921be254f2ee800d212ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:27:11 +0100 Subject: [PATCH 022/436] gnu: python-hacking: Disable tests. * gnu/packages/openstack.scm (python-hacking, python2-hacking)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index e2672668d8..e4610c150b 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -113,6 +113,9 @@ manner.") (base32 "1a310k3dv04jg7zvmk37h2ql7y9kf4hvdxb74bjlwdxgmy6h4wap")))) (build-system python-build-system) + (arguments + ;; TODO: Requires unpackaged 'eventlet'. + '(#:tests? #f)) (propagated-inputs `(("python-flake8-2.2.4" ,python-flake8-2.2.4) ("python-mccabe-0.2.1" ,python-mccabe-0.2.1) From ea8907c5d5df89b26d67a7b067cb8c341714ed9b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:02:45 +0100 Subject: [PATCH 023/436] gnu: python-mox3: Disable tests. * gnu/packages/openstack.scm (python-mox3, python2-mox3)[arguments]: Disable tests. [native-inputs]: Add python-oslosphinx and python-sphinx. --- gnu/packages/openstack.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index e4610c150b..a91759faa0 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -149,9 +149,14 @@ guidelines}.") (base32 "0njmh40i1lg5mzn9hc2ax83adj6dli455j6xifilrw27c4wlkjzx")))) (build-system python-build-system) + (arguments + ;; TODO: Requires newer version of testtools (>=1.4.0). + '(#:tests? #f)) (native-inputs `(("python-fixtures" ,python-fixtures) + ("python-oslosphinx" ,python-oslosphinx) ("python-pbr" ,python-pbr) + ("python-sphinx" ,python-sphinx) ("python-testtools" ,python-testtools))) (home-page "http://www.openstack.org/") (synopsis "Mock object framework for Python") From 281cc11c8e33c1e1a558cc2bf4af924881f55c40 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:40:13 +0100 Subject: [PATCH 024/436] gnu: python-django-simple-math-captcha: Disable tests. * gnu/packages/django.scm (python-django-simple-math-captcha, python2-django-simple-math-captcha)[arguments]: Set #:tests? #f. --- gnu/packages/django.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index bbb2d71db1..93fc42f96f 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -106,6 +106,10 @@ to the @dfn{don't repeat yourself} (DRY) principle.") (base32 "0906hms6y6znjhpd0g4wmzv9vcla4brkdpsm4zha9zdj8g5vq2hd")))) (build-system python-build-system) + (arguments + ;; FIXME: Upstream uses a 'runtests.py' script that is not + ;; present in the pypi tarball. + '(#:tests? #f)) (propagated-inputs `(("python-django" ,python-django))) (home-page "https://github.com/alsoicode/django-simple-math-captcha") From 55ab64516bf8bcb27833479fb3c0df2a7ed06d6b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:43:36 +0100 Subject: [PATCH 025/436] gnu: python-django-filter: Fix test suite. * gnu/packages/django.scm (python-django-filter, python2-django-filter)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/django.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 93fc42f96f..415ee60a20 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -167,6 +167,12 @@ useful tools for testing Django applications and projects.") (base32 "0f78hmk8c903zwfzlsiw7ivgag81ymmb5hi73rzxbhnlg2v0l3fx")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "python" "runtests.py"))))))) (native-inputs `(("python-django" ,python-django) ("python-mock" ,python-mock))) From 63b02364aa259e58169b0c4af7e860f7b1ceebd2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:47:22 +0100 Subject: [PATCH 026/436] gnu: python-iso8601: Fix test dependencies. * gnu/packages/python.scm (python-iso8601, python2-iso8601)[native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6c58403dd6..9b7d5d99a0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6155,6 +6155,8 @@ and MAC network addresses.") (base32 "0c7gh3lsdjds262h0v1sqc66l7hqgfwbakn96qrhdbl0i3vm5yz8")))) (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://bitbucket.org/micktwomey/pyiso8601") (synopsis "Module to parse ISO 8601 dates") (description From 497355dc09449426ef4fda521433002ec93c4796 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:59:40 +0100 Subject: [PATCH 027/436] gnu: python-nbconvert: Disable tests. * gnu/packages/python.scm (python-nbconvert, python2-nbconvert)[arguments]: Set #:tests? #f. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9b7d5d99a0..540a988234 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6911,9 +6911,19 @@ functions to find and load entry points.") (base32 "0brclbb18l4nmd5qy3dl9wn05rjdh1fz4rmzdlfqacj12rcdvdgp")))) (build-system python-build-system) - ;; The "bdist_egg" target is disabled by default, causing the installation - ;; to fail. - (arguments `(#:configure-flags (list "bdist_egg"))) + (arguments + `(;; The "bdist_egg" target is disabled by default, causing the installation + ;; to fail. + #:configure-flags (list "bdist_egg") + ;; FIXME: 5 failures, 40 errors. + #:tests? #f)) + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; (zero? (system* "py.test" "-v"))))) + (native-inputs + `(("python-pytest" ,python-pytest))) (propagated-inputs `(("python-bleach" ,python-bleach) ("python-entrypoints" ,python-entrypoints) From bd100c7112b1717881ff6efcaa514be5cfeb5349 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 17:35:28 +0100 Subject: [PATCH 028/436] gnu: python-hypothesis: Don't propagate test inputs. * gnu/packages/python.scm (python-hypothesis, python2-hypothesis)[propagated-inputs]: Move everything from here ... [native-inputs]: ... to here. (python2-hypothesis)[native-inputs]: Append inherited native-inputs. --- gnu/packages/python.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 540a988234..cd6ed1c240 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8544,7 +8544,7 @@ Amazon Web Services (AWS) API.") (base32 "0qyqq9akm4vshhn8cngjc1qykcvsn7cz6dlm6njfsgpbraqrmbbw")))) (build-system python-build-system) - (propagated-inputs + (native-inputs `(("python-flake8" ,python-flake8) ("python-pytest" ,python-pytest))) (synopsis "Library for property based testing") @@ -8561,7 +8561,8 @@ seamlessly into your existing Python unit testing work flow.") (strip-python2-variant python-hypothesis)))) (package (inherit hypothesis) (native-inputs - `(("python2-enum34" ,python2-enum34)))))) + `(("python2-enum34" ,python2-enum34) + ,@(package-native-inputs hypothesis)))))) (define-public python-pytest-subtesthack (package From 30e0229a1713e77dc0397dfb4ee6af4ac6a00443 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 18:34:48 +0100 Subject: [PATCH 029/436] gnu: python-pyopenssl: Disable tests. * gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl)[arguments]: Set #:tests? #f. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index cd6ed1c240..ebe0194aa4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6585,11 +6585,16 @@ message digests and key derivation functions.") (base32 "0vji4yrfshs15xpczbhzhasnjrwcarsqg87n98ixnyafnyxs6ybp")))) (build-system python-build-system) + (arguments + ;; FIXME: Some tests fail with "NameError: name 'long' is not defined". + '(#:tests? #f)) (propagated-inputs `(("python-cryptography" ,python-cryptography) ("python-six" ,python-six))) (inputs `(("openssl" ,openssl))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/pyca/pyopenssl") (synopsis "Python wrapper module around the OpenSSL library") (description From da5ebd1007488209ba82ef02f0cb7f097f2b9106 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:18:26 +0100 Subject: [PATCH 030/436] gnu: python-biom-format: Fix tests. * gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3d84a44e4c..5f56551526 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -562,6 +562,8 @@ Python.") ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py))) + (native-inputs + `(("python-nose" ,python-nose))) (home-page "http://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description From 1b6d7c3f3f9a19cb899058a586afc0f16afc5e5a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:38:50 +0100 Subject: [PATCH 031/436] gnu: python2-fastlmm: Fix test requirements. * gnu/packages/python.scm (python2-fastlmm)[native-inputs]: Add python2-nose. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ebe0194aa4..77240ff36d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3290,7 +3290,8 @@ capabilities.") (native-inputs `(("unzip" ,unzip) ("python2-cython" ,python2-cython) - ("python2-mock" ,python2-mock))) + ("python2-mock" ,python2-mock) + ("python2-nose" ,python2-nose))) (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/") (synopsis "Perform genome-wide association studies on large data sets") (description From 52a75a83f970b62eb285067b454a1c25a8669491 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:45:46 +0100 Subject: [PATCH 032/436] gnu: python-jmespath: Fix tests. * gnu/packages/python.scm (python-jmespath, python2-jmespath)[native-inputs]: Add python-nose. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 77240ff36d..1bf3af100a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8468,6 +8468,8 @@ servers.") (base32 "0g9xvl69y7nr3w7ag4fsp6sm4fqf6vrqjw7504x2hzrrsh3ampq8")))) (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) (synopsis "JSON Matching Expressions") (description "JMESPath (pronounced “james path”) is a Python library that allows one to declaratively specify how to extract elements from a JSON From 877fdac9e3afba664b5c6f66858c98750aa98694 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:49:35 +0100 Subject: [PATCH 033/436] gnu: python-botocore: Disable tests. * gnu/packages/python.scm (python-botocore, python2-botocore): Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1bf3af100a..8e94b52429 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8492,6 +8492,9 @@ document.") (base32 "1zxczlwqy9bl27d9bc5x99mb5mcsxm350240lp5nx7014xb311lj")))) (build-system python-build-system) + (arguments + ;; FIXME: Many tests are failing. + '(#:tests? #f)) (propagated-inputs `(("python-dateutil" ,python-dateutil-2) ("python-docutils" ,python-docutils) From e91275256717a5325020a9a36749adbe759371d3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:50:44 +0100 Subject: [PATCH 034/436] gnu: python-inflection: Fix test requirements. * gnu/packages/python.scm (python-inflection, python2-inflection)[native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8e94b52429..0ee533d007 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10314,6 +10314,8 @@ datetime type.") (base32 "1jhnxgnw8y3mbzjssixh6qkc7a3afc4fygajhqrqalnilyvpzshq")))) (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "http://github.com/jpvanhal/inflection") (synopsis "Python string transformation library") (description From f620311a39a9a7dd8bd2637251e448824423a17f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:53:21 +0100 Subject: [PATCH 035/436] gnu: python-pyaml: Fix tests. * gnu/packages/python.scm (python-pyaml, python2-pyaml)[native-inputs]: Add python-unidecode. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0ee533d007..de11cd558d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10520,6 +10520,8 @@ addresses, and phone numbers.") (base32 "1f5m28vkh4ksq3d80d8mmd2z8wxvc3mgy2pmrv2751dm2xgznm4w")))) (build-system python-build-system) + (native-inputs + `(("python-unidecode" ,python-unidecode))) (propagated-inputs `(("python-pyyaml" ,python-pyyaml))) (home-page "https://github.com/mk-fg/pretty-yaml") From b7f3ea9532c0bf764228b3b7ecbd66d579a2517f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:01:36 +0100 Subject: [PATCH 036/436] gnu: python-fake-factory: Fix tests. * gnu/packages/python.scm (python-fake-factory, python2-fake-factory)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index de11cd558d..d6ea07de34 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10484,6 +10484,12 @@ parsing UK postcodes.") (base32 "0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "python" "-m" "unittest" "-v" "faker.tests"))))))) (native-inputs `(;; For testing ("python-email-validator" ,python-email-validator) From 6145b604629c071fba8b55b7e0e3a45ed68fa3cc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:07:38 +0100 Subject: [PATCH 037/436] gnu: python-clint: Fix tests. * gnu/packages/python.scm (python-clint, python2-clint)[native-inputs]: Add python-pytest. [arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d6ea07de34..17469036a3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8125,6 +8125,14 @@ Blog, News or Announcements section to a Sphinx website.") (base32 "1an5lkkqk1zha47198p42ji3m94xmzx1a03dn7866m87n4r4q8h5")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "py.test" "-v"))))))) + (native-inputs + `(("python-pytest" ,python-pytest))) (propagated-inputs `(("python-args" ,python-args))) (home-page "https://github.com/kennethreitz/clint") From ee4722411fb71f90deb63e7976207f84ecae7360 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:24:50 +0100 Subject: [PATCH 038/436] gnu: python-rdflib: Disable tests. * gnu/packages/rdf.scm (python-rdflib)[arguments]: Set #:tests? #f. [native-inputs]: Add python-nose. (python2-rdflib)[inputs]: Remove field. Use 'package-with-python2'. --- gnu/packages/rdf.scm | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm index 1dd23c28e3..97e6b881cc 100644 --- a/gnu/packages/rdf.scm +++ b/gnu/packages/rdf.scm @@ -315,6 +315,18 @@ ideal (e.g. in LV2 implementations or embedded applications).") (base32 "0kvaf332cqbi47rqzlpdx4mbkvw12mkrzkj8n9l19wk713d4py9w")))) (build-system python-build-system) + (arguments + '(;; FIXME: Three test failures. Try uncommenting the below next update. + #:tests? #f)) + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; ;; Run tests from the build directory so python3 only + ;; ;; sees the installed 2to3 version. + ;; (zero? (system* "nosetests" "--where=./build/src"))))) + (native-inputs + `(("python-nose" ,python-nose))) (propagated-inputs `(("python-html5lib" ,python-html5lib) ("python-isodate" ,python-isodate) @@ -329,12 +341,4 @@ powerful language for representing information.") "See LICENSE in the distribution.")))) (define-public python2-rdflib - (let ((base (package-with-python2 python-rdflib))) - (package - (inherit base) - (inputs - (append (package-inputs base) - `(("python2-nose" ,python2-nose)))) - (arguments - `(#:python ,python-2 - #:tests? #f))))) ; 3 tests fail, also outside Guix + (package-with-python2 python-rdflib)) From bfce8a344d446d7601c1a60adc7b13b66bc75030 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:59:56 +0100 Subject: [PATCH 039/436] gnu: python-jedi: Disable tests. * gnu/packages/python.scm (python-jedi, python2-jedi)[arguments]: Disable tests. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 17469036a3..90b0b575cc 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10650,6 +10650,11 @@ characters, mouse support, and auto suggestions.") (base32 "0c8x962ynpx001fdvp07m2q5jk4igkxbj3rmnydavphvlgxijk1v")))) (build-system python-build-system) + (arguments + ;; FIXME: One test fails (use "py.test" instead of 'setup.py test'). + '(#:tests? #f)) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/davidhalter/jedi") (synopsis "Autocompletion for Python that can be used for text editors") From 9026e6890a829fa2713cd1dcca407f19adf82802 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 23:01:40 +0100 Subject: [PATCH 040/436] gnu: python-scikit-image: Disable tests. * gnu/packages/python.scm (python-scikit-image, python2-scikit-image)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 90b0b575cc..9bcdb30820 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3060,6 +3060,9 @@ mining and data analysis.") (sha256 (base32 "0jz416fqvpahqyffw8plmszzfj669w8wvf3y9clnr5lr6a7md3kn")))) (build-system python-build-system) + (arguments + ;; TODO: Some tests require running X11 server. Disable them? + '(#:tests? #f)) ;; See DEPENDS.txt for the list of build and run time requiremnts (propagated-inputs `(("python-matplotlib" ,python-matplotlib) From 972cf9be524535fee3999021a68537039e204ee6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 10:02:11 +0100 Subject: [PATCH 041/436] gnu: python-ly: Disable tests. * gnu/packages/python.scm (python-ly): Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9bcdb30820..04ee836c6c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5991,6 +5991,9 @@ from an XML-based format.") (base32 "0g6n288l83sfwavxh1aryi0aqvsr3sp7v6f903mckwqa4scpky62")))) (build-system python-build-system) + (arguments + ;; FIXME: Some tests need network access. + '(#:tests? #f)) (synopsis "Tool and library for manipulating LilyPond files") (description "This package provides a Python library to parse, manipulate or create documents in LilyPond format. A command line program ly is also From 7b93d866708d1fae54aee86473ffde5bd64be055 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 10:12:38 +0100 Subject: [PATCH 042/436] gnu: snakemake: Update to 3.9.0. * gnu/packages/python.scm (snakemake): Update to 3.9.0. [source]: Use 'pypi-uri'. [arguments]: Disable tests. [home-page]: Update. --- gnu/packages/python.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 04ee836c6c..cbe770db39 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5306,17 +5306,18 @@ of the structure, dynamics, and functions of complex networks.") (define-public snakemake (package (name "snakemake") - (version "3.2.1") + (version "3.9.0") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/s/snakemake/snakemake-" - version ".tar.gz")) + (uri (pypi-uri "snakemake" version)) (sha256 - (base32 "0fi4b63sj60hvi7rfydvmz2icl4wj74djw5sn2gl8hxd02qw4b91")))) + (base32 "1d48ql0010v9ls6mac7fz6j391gm4h74a64hqgw89s0vfqgdyzdl")))) (build-system python-build-system) - (home-page "https://bitbucket.org/johanneskoester/snakemake") + (arguments + ;; TODO: Package missing test dependencies. + '(#:tests? #f)) + (home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home") (synopsis "Python-based execution environment for make-like workflows") (description "Snakemake aims to reduce the complexity of creating workflows by From 385871e5f7a69ed1c473501be22d0338984a932c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:12:13 +0100 Subject: [PATCH 043/436] gnu: python-zope-testrunner: Disable tests. * gnu/packages/python.scm (python-zope-testrunner, python2-zope-testrunner)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index cbe770db39..0646e9739b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7318,6 +7318,8 @@ forms, HTTP servers, regular expressions, and more.") (base32 "1r7iqknhh55y45f64mz5hghgvzx34h1i11k350s0avx6q8gznja1")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. (native-inputs `(("python-six" ,python-six) ;("python-zope-interface" ,python-zope-interface) From 22dba2eff978999a907dfa8b4e2da5cdbb357de4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:35:26 +0100 Subject: [PATCH 044/436] gnu: python-zope-interface: Disable tests. * gnu/packages/python.scm (python-zope-schema, python2-zope-schema)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0646e9739b..9e47d7cf1c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7380,6 +7380,8 @@ internationalized messages within program source text.") (base32 "1p943jdxb587dh7php4vx04qvn7b2877hr4qs5zyckvp5afhhank")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Tests can't find zope.event. (propagated-inputs `(("python-zope-event" ,python-zope-event) ("python-zope-exceptions", python-zope-exceptions) From 7e8b1bfa4b6e1003f2b80c049d89c70cc9e28d84 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:38:04 +0100 Subject: [PATCH 045/436] gnu: python-zope-configuration: Disable tests. * gnu/packages/python.scm (python-zope-configuration, python2-zope-configuration)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9e47d7cf1c..9afb37cdd1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7412,6 +7412,8 @@ defining data schemas.") (base32 "1x9dfqypgympnlm25p9m43xh4qv3p7d75vksv9pzqibrb4cggw5n")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. (propagated-inputs `(("python-zope-i18nmessageid" ,python-zope-i18nmessageid) ("python-zope-schema" ,python-zope-schema))) From 66b3aadb73af76c366803e1cd619a9d5d20571c1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:40:10 +0100 Subject: [PATCH 046/436] gnu: python-zope-proxy: Disable tests. * gnu/packages/python.scm (python-zope-proxy, python2-zope-proxy)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9afb37cdd1..47729db02b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7439,6 +7439,8 @@ Markup Language.") (base32 "0pqwwmvm1prhwv1ziv9lp8iirz7xkwb6n2kyj36p2h0ppyyhjnm4")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. (propagated-inputs `(("python-zope-interface" ,python-zope-interface))) (home-page "http://pypi.python.org/pypi/zope.proxy") From 40bb8e07aedb011de863657f6cec29d86d525375 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:42:39 +0100 Subject: [PATCH 047/436] gnu: python-zope-location: Disable tests. * gnu/packages/python.scm (python-zope-location, python2-zope-location)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 47729db02b..7109860f5b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7468,6 +7468,8 @@ brokering, etc.) for which the proxy is responsible.") (base32 "1nj9da4ksiyv3h8n2vpzwd0pb03mdsh7zy87hfpx72b6p2zcwg74")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. (propagated-inputs `(("python-zope-proxy" ,python-zope-proxy) ("python-zope-schema" ,python-zope-schema))) From a74f9b12ae3937cd75c4dba4715cf55387c507c8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:45:26 +0100 Subject: [PATCH 048/436] gnu: python-zope-security: Disable tests. * gnu/packages/python.scm (python-zope-security, python2-zope-security)[arguments]: Set #:tests? #f. [native-inputs]: Add python-six. --- gnu/packages/python.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7109860f5b..aca2f3c92d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7495,12 +7495,15 @@ Zope3, which are are special objects that have a structural location.") (base32 "14zmf684amc0x32kq05yxnhfqd1cmyhafkw05gn81rn90zjv6ssy")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Tests can't find zope.testrunner. (propagated-inputs `(("python-zope-i18nmessageid" ,python-zope-i18nmessageid) ("python-zope-proxy" ,python-zope-proxy) ("python-zope-schema" ,python-zope-schema))) - (native-inputs - `(("python-zope-component" ,python-zope-component) + (native-inputs + `(("python-six" ,python-six) + ("python-zope-component" ,python-zope-component) ("python-zope-configuration" ,python-zope-configuration) ("python-zope-location" ,python-zope-location) ("python-zope-testrunner" ,python-zope-testrunner) From a960e73fadda9e3d594775197a20f52177c96b43 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:11:53 +0100 Subject: [PATCH 049/436] gnu: python-twisted: Disable tests. * gnu/packages/python.scm (python-twisted, python2-twisted)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index aca2f3c92d..e640a777c4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10078,6 +10078,13 @@ to provide a high-level synchronous API on top of the libev event loop.") (base32 "0ydxrp9myw1mvsz3qfzx5579y5llmqa82pxvqchgp5syczffi450")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Some tests are failing. + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; (zero? (system* "./bin/trial" "twisted"))))) (propagated-inputs `(("python-zope-interface" ,python-zope-interface))) (home-page "https://twistedmatrix.com/") From 7917a1355456a924ca85992b4216cf6dc437873a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:17:29 +0100 Subject: [PATCH 050/436] gnu: python-termstyle: Fix tests. * gnu/packages/python.scm (python-termstyle)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e640a777c4..47d7c6a7d9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11940,6 +11940,12 @@ asynchronous messaging environments.") (base32 "17wzkkcqy5zc0g68xlad3kcv66iw14d2pwqc0h9420gak0vbhx7g")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "python" "test3.py"))))))) (home-page "http://github.com/gfxmonk/termstyle") (synopsis "Console text coloring for Python") (description "This package provides console text coloring for Python.") From 767c7e0ed1d9f8bec64fa5254570a1f2d75ce847 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:23:56 +0100 Subject: [PATCH 051/436] gnu: python-debtcollector: Disable tests. * gnu/packages/openstack.scm (python-debtcollector, python2-debtcollector)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index a91759faa0..7ffd9a2325 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -81,6 +81,8 @@ all the files it generates a report.") (base32 "0g4dfskaiy47rhsh4gh66l5vmdsrgq0qk68pl3ix1cj3ffvfndzv")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ;FIXME: Requires packaging python-doc8. (propagated-inputs `(("python-six" ,python-six) ("python-wrapt" ,python-wrapt))) From f30e53369bd64b572c1195a53a28d294da160336 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:31:31 +0100 Subject: [PATCH 052/436] gnu: python-oslo.context: Disable tests. * gnu/packages/openstack.scm (python-oslo.context, python2-oslo.context)[arguments]: Set #:tests? #f. [native-inputs]: Add python-coverage, python-hacking, python-mock, python-os-client-config, python-oslosphinx and python-sphinx. --- gnu/packages/openstack.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 7ffd9a2325..ad0c028af8 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -405,11 +405,19 @@ common features used in Tempest.") (base32 "0kvha0rs9295njyl2z6n6zm5dapi5mrl5zwjm0m6ldqrvccyf8c3")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Requires python-mock >= 1.2. (native-inputs `(("python-babel" ,python-babel) ("python-pbr" ,python-pbr) ;; Tests. - ("python-oslotest" ,python-oslotest))) + ("python-coverage" ,python-coverage) + ("python-hacking" ,python-hacking) + ("python-mock" ,python-mock) + ("python-os-client-config" ,python-os-client-config) + ("python-oslotest" ,python-oslotest) + ("python-oslosphinx" ,python-oslosphinx) + ("python-sphinx" ,python-sphinx))) (home-page "http://launchpad.net/oslo") (synopsis "Oslo context library") (description From bb56d9a18ce0f91131b202351a0496ad39103483 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:35:57 +0100 Subject: [PATCH 053/436] gnu: python-oslo.i18n: Disable tests. * gnu/packages/openstack.scm (python-oslo.i18n, python2-oslo.i18n)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index ad0c028af8..4bd44d005a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -441,6 +441,8 @@ pipeline and used by various modules such as logging.") (base32 "0bpb1c20sm8my650gl824nzaip83bfn8hr91s65k5ncmyh8hb6pl")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Circular dependency on python-oslo.config. (propagated-inputs `(("python-babel" ,python-babel) ("python-six" ,python-six))) From 130f68ec3bc2efb6895986435c2ff8043bbaa417 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:45:07 +0100 Subject: [PATCH 054/436] gnu: python-stevedore: Fix tests. * gnu/packages/openstack.scm (python-stevedore, python2-stevedore)[native-inputs]: Add python-discover, python-oslosphinx, python-sphinx and python-testrepository. --- gnu/packages/openstack.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 4bd44d005a..9c43ea9c6a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -292,10 +292,13 @@ portions of your testing code.") (native-inputs `(("python-pbr" ,python-pbr) ;; Tests + ("python-discover" ,python-discover) ("python-docutils" ,python-docutils) ("python-mock" ,python-mock) + ("python-oslosphinx" ,python-oslosphinx) ("python-oslotest" ,python-oslotest) - ("python-sphinx" ,python-sphinx))) + ("python-sphinx" ,python-sphinx) + ("python-testrepository" ,python-testrepository))) (home-page "https://github.com/dreamhost/stevedore") (synopsis "Manage dynamic plugins for Python applications") (description From d9184f4f76443011130944f7a2ca7fa75bad7aea Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:49:08 +0100 Subject: [PATCH 055/436] gnu: python-oslo.config: Disable tests. * gnu/packages/openstack.scm (python-oslo.config, python2-oslo.config)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 9c43ea9c6a..2a1313c4bd 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -375,6 +375,8 @@ common features used in Tempest.") (base32 "13r778jfb0fhna37c2pd1f2xipnsbd7zli7qhn96acrzymrwj5k1")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Requires packaging python-argparse. (propagated-inputs `(("python-netaddr" ,python-netaddr) ("python-six" ,python-six) From ad59ebda5350b94885475980dfdb1a6be8eda2d5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:50:55 +0100 Subject: [PATCH 056/436] gnu: python-oslo.utils: Disable tests. * gnu/packages/openstack.scm (python-oslo.utils, python2-oslo.utils)[arguments]: Set #:tests? #f. [native-inputs]: Add python-bandit and python-oslo.config. --- gnu/packages/openstack.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 2a1313c4bd..d05d9caf48 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -628,6 +628,8 @@ and better support for mocking results.") ;; phase. (delete-file "oslo_utils/tests/test_netutils.py"))))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Requires oslo.config >= 2.7.0. (propagated-inputs `(("python-debtcollector" ,python-debtcollector) ("python-oslo.i18n" ,python-oslo.i18n) @@ -641,6 +643,8 @@ and better support for mocking results.") `(("python-babel" ,python-babel) ("python-pbr" ,python-pbr) ;; Tests. + ("python-bandit" ,python-bandit) + ("python-oslo.config" ,python-oslo.config) ("python-oslotest" ,python-oslotest) ("python-mock" ,python-mock) ("python-mox3" ,python-mox3) From 5ae31b547cda78025a5a9f4d29b0cda511ec66d6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:55:54 +0100 Subject: [PATCH 057/436] gnu: python-oslo.serialization: Disable tests. * gnu/packages/openstack.scm (python-oslo.serialization, python2-oslo.serialization)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index d05d9caf48..97fdabffa7 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -521,6 +521,8 @@ handlers and support for context specific logging (like resource id’s etc).") (base32 "00s03krhf833gs76aw5ns32w9m1i4hx6x6d9g82m0j5wyqk0sci4")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Requires python-oslo.utils >= 3.2.0. (propagated-inputs `(("python-iso8601" ,python-iso8601) ("python-netaddr" ,python-netaddr) From 49910e6a7c14702502124efd70cc40227dc9df46 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 14:01:27 +0100 Subject: [PATCH 058/436] gnu: python-paramiko: Disable tests. * gnu/packages/python.scm (python-paramiko, python2-paramiko)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 47d7c6a7d9..4472e7832f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -540,6 +540,14 @@ John the Ripper).") (base32 "14k8z7ndc3zk5xivnm4d8lncchx475ll5izpf8vmfbq7rp9yp5rj")))) (build-system python-build-system) + (arguments + '(;; FIXME: One test fails with "EOFError not raised by connect". + #:tests? #f)) + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; (zero? (system* "python" "test.py"))))))) (propagated-inputs `(("python-pycrypto" ,python-pycrypto) ("python-ecdsa" ,python-ecdsa))) From 73b494a11de3eb59fdbcd73f2c90e74c4fc08924 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 15:22:16 +0100 Subject: [PATCH 059/436] gnu: python-oslo.log: Disable tests. * gnu/packages/openstack.scm (python-oslo.log, python2-oslo.log)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 97fdabffa7..080f283b2a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -484,6 +484,8 @@ in an application or library.") (base32 "1fhy6yvbd565nv4x4i3ppyrlbmz3yy9d0xsvw5nkqsa7g43nmf8z")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Requires oslo.utils >= 3.2.0. (propagated-inputs `(("python-debtcollector" ,python-debtcollector) ("python-oslo.config" ,python-oslo.config) From f959495ba06d77194d843ea729c39aaa8a168051 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 15:23:39 +0100 Subject: [PATCH 060/436] gnu: python-tempest-lib: Disable tests. * gnu/packages/openstack.scm (python-tempest-lib, python2-tempest-lib)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 080f283b2a..33a54e3ab9 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -328,7 +328,8 @@ extensions.") "1cpp2vwmawpd29hjsklsps181lq2ah91cl412qvpnz228nf9sqn5")))) (build-system python-build-system) (arguments - `(#:phases + `(#:tests? #f ; FIXME: Requires oslo.log >= 1.14.0. + #:phases (modify-phases %standard-phases (add-before 'check 'pre-check From c616b5d3b5aefc00485f03f756871a2d87714268 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 16:49:14 +0100 Subject: [PATCH 061/436] gnu: python-oauthlib: Fix tests. * gnu/packages/python.scm (python-oauthlib)[native-inputs]: Add python-mock. (python2-oauthlib)[native-inputs]: Inherit python-mock. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4472e7832f..55274783ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2536,6 +2536,7 @@ somewhat intelligeble.") (build-system python-build-system) (native-inputs `(("python-nose" ,python-nose) + ("python-mock" ,python-mock) ("python-cryptography" ,python-cryptography) ("python-pyjwt" ,python-pyjwt) ("python-blinker" ,python-blinker))) @@ -2552,7 +2553,6 @@ OAuth request-signing logic.") (package (inherit base) (native-inputs `(("python2-unittest2" ,python2-unittest2) - ("python2-mock" ,python2-mock) ,@(package-native-inputs base)))))) (define-public python-itsdangerous From bfba083684e80d2bc23e3c07205e3d63910e978f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 16:53:55 +0100 Subject: [PATCH 062/436] gnu: python-keystoneclient: Disable tests. * gnu/packages/openstack.scm (python-keystoneclient, python2-keystoneclient)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 33a54e3ab9..b3e3f08c23 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -677,6 +677,8 @@ handling.") (base32 "1w4csvkah67rfpxylxnvs2s3594i0f9isy8pf4gnsqs5zirvjaa4")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Many tests are failing. (native-inputs `(("python-sphinx" ,python-sphinx) ;; and some packages for the tests From 35d56b7b607f6de615d5e13eb05273c649ee4543 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:26:42 +0100 Subject: [PATCH 063/436] gnu: python-sqlalchemy-utils: Disable tests. * gnu/packages/python.scm (python-sqlalchemy-utils, python2-sqlalchemy-utils)[arguments]: Set #:tests? #f. [native-inputs]: Add python-dateutil-2, python-flexmock, python-pcycopg2 and python-pytz. --- gnu/packages/python.scm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 55274783ff..011483d897 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3988,11 +3988,22 @@ both of which are installed automatically if you install this library.") (base32 "1wghyvk73cmq3iqyg3fczw128fv2pan2v76m0xg1bw05h8fhvnk3")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Many tests require a running database server. + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; (zero? (system* "py.test" "sqlalchemy_utils" "tests"))))) (propagated-inputs `(("python-six" ,python-six) ("python-sqlalchemy" ,python-sqlalchemy))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-dateutil" ,python-dateutil-2) + ("python-flexmock" ,python-flexmock) + ("python-psycopg2" ,python-psycopg2) + ("python-pytest" ,python-pytest) + ("python-pytz" ,python-pytz))) (home-page "https://github.com/kvesteri/sqlalchemy-utils") (synopsis "Various utility functions for SQLAlchemy") (description From 6f976df6771a3eb90c3b16de45a861856bcde52e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:31:29 +0100 Subject: [PATCH 064/436] gnu: python-seaborn: Disable tests. * gnu/packages/python.scm (python-seaborn, python2-seaborn)[arguments]: Disable tests. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 011483d897..610785bc59 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5355,6 +5355,8 @@ Python style, together with a fast and comfortable execution environment.") (sha256 (base32 "0ibi3xsfm2kysph61mnfy0pf8d5rkgxgrdb0z9nbizgcgdsb5a0m")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; Tests requires a running X11 server. (propagated-inputs `(("python-pandas" ,python-pandas) ("python-matplotlib" ,python-matplotlib) From 444464ec28fe63a8162d6b7d8ef5b408082df91b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:42:22 +0100 Subject: [PATCH 065/436] gnu: python-rpy2: Fix tests. * gnu/packages/python.scm (python-rpy2, python2-rpy2)[arguments]: Replace check phase with custom post-install command. --- gnu/packages/python.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 610785bc59..f79073470a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3674,6 +3674,16 @@ operators such as union, intersection, and difference.") (base32 "0nhan2qvrw7b7gg5zddwa22kybdv3x1g26vkd7q8lvnkgzrs4dga")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key outputs inputs #:allow-other-keys) + ;; It's easier to run tests after install. + ;; Make installed package available for running the tests + (add-installed-pythonpath inputs outputs) + (zero? (system* "python" "-m" "rpy2.tests" "-v"))))))) (propagated-inputs `(("python-six" ,python-six))) (inputs From 9e378e6a5c0477cc0cb8cdbc06be8dd1fd4a8091 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:53:49 +0100 Subject: [PATCH 066/436] gnu: python-reportlab: Fix tests. * gnu/packages/pdf.scm (python-reportlab, python2-reportlab)[arguments]: Set #:test-target. --- gnu/packages/pdf.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 3f329c5426..1c04824ea6 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -628,6 +628,10 @@ using a stylus.") (base32 "0rz2pg04wnzjjm2f5a8ik9v8s54mv4xrjhv5liqjijqv6awh12gl")))) (build-system python-build-system) + (arguments + '(;; FIXME: There is one test failure, but it does not cause the + ;; build to fail. No time to investigate right now. + #:test-target "tests")) (propagated-inputs `(("python-pillow" ,python-pillow))) (home-page "http://www.reportlab.com") From 4eb385fb33a324ee87724d43131b40d0c371f72f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:11:43 +0100 Subject: [PATCH 067/436] gnu: python-pytest-xdist: Disable tests. * gnu/packages/python.scm (python-pytest-xdist, python2-pytest-xdist)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f79073470a..086890ec32 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1843,6 +1843,15 @@ same arguments.") (for-each delete-file (find-files "." "\\.pyc$")) #t)))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ;FIXME: Some tests are failing. + ;; #:phases + ;; (modify-phases %standard-phases + ;; (delete 'check) + ;; (add-after 'install 'check + ;; (lambda* (#:key inputs outputs #:allow-other-keys) + ;; (add-installed-pythonpath inputs outputs) + ;; (zero? (system* "py.test" "-v"))))) (native-inputs `(("unzip" ,unzip) ("python-setuptools-scm" ,python-setuptools-scm))) From 1f31a5e0bfd0287e5dcc6bcccd0e70474904e3cf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:19:34 +0100 Subject: [PATCH 068/436] gnu: python-pytest-django: Disable tests. * gnu/packages/django.scm (python-pytest-django, python2-pytest-django)[arguments]: Set #:tests? #f. --- gnu/packages/django.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 415ee60a20..106d18a8d7 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -135,7 +135,8 @@ with arguments to the field constructor.") "1mmc7zsz3dlhs6sx4sppkj1vgshabi362r1a8b8wpj1qfximpqcb")))) (build-system python-build-system) (arguments - `(#:phases + `(#:tests? #f ; FIXME: How to run tests? + #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-setuppy (lambda _ From 8bd5164b4ac1ec625cdbb45ddf8c539253c75b3d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:35:21 +0100 Subject: [PATCH 069/436] gnu: python-pystache: Disable tests for python3 variant. * gnu/packages/python.scm (python-pystache)[arguments]: Disable tests. [properties]: New field. Delay python2 variant. (python2-pystache)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 086890ec32..f99df753e5 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2710,15 +2710,26 @@ written in pure Python.") (base32 "0nmqsfmiw4arjxqkmf9z66ml950pcdjk6aq4gin4sywmzdjw5fzp")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Python 3 tests are failing. (home-page "http://defunkt.io/pystache/") (synopsis "Python logic-less template engine") (description "Pystache is a Python implementation of the framework agnostic, logic-free templating system Mustache.") - (license license:expat))) + (license license:expat) + (properties `((python2-variant . ,(delay python2-pystache)))))) (define-public python2-pystache - (package-with-python2 python-pystache)) + (package (inherit (package-with-python2 + (strip-python2-variant python-pystache))) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "python" "test_pystache.py"))))))))) (define-public python-joblib (package From 0a7020095185c6b5aaac42bc04449c39c3673e38 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:42:22 +0100 Subject: [PATCH 070/436] gnu: python-pyserial: Disable tests. * gnu/packages/python.scm (python-pyserial, python2-pyserial)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f99df753e5..81e085f2d7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10861,6 +10861,13 @@ relays publish about themselves.") (base32 "0k1nfdrxxkdlv4zgaqsdv8li0pj3gbh2pyxw8q2bsg6f9490amyn")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: 3/49 tests are failing. + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; (zero? (system* "python" "test/run_all_tests.py" "loop://"))))))) (home-page "https://github.com/pyserial/pyserial") (synopsis "Python Serial Port Bindings") From 810f89839cdbc8c73fdc40024465f1d12fdcaf4a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:06:12 +0100 Subject: [PATCH 071/436] gnu: python-pylast: Disable tests. * gnu/packages/music.scm (python-pylast, python2-pylast)[arguments]: Set #:tests? #f. --- gnu/packages/music.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 4297f846f9..8b1644ca4c 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2035,6 +2035,8 @@ detailed track info including timbre, pitch, rhythm and loudness information. (base32 "0bml11gfkxqd3i2jxkn5k2xllc4rvxjcyhs8an05gcyy1zp2bwvb")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Requires unpackaged python-flaky. (native-inputs `(("python-coverage" ,python-coverage) ("python-mock" ,python-mock) From 8653c1d5574d43bba0ecc7efbbdf0b0ee8264a6c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:09:18 +0100 Subject: [PATCH 072/436] gnu: python-py3status: Disable tests. * gnu/packages/python.scm (python-py3status)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 81e085f2d7..d438e5c6d4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9975,6 +9975,8 @@ to occurences in strings and comments.") (base32 "0i283z1pivmir61z8kbiycigc94l61v33ygzkhczf1ifq7cppyds")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; TODO: Requires many libraries not in Guix. (home-page "https://github.com/ultrabug/py3status") (synopsis "Extensible i3status wrapper written in Python") (description "py3status is an i3status wrapper which extends i3status From 15c37077bc3801317c9e40ee3552f6aac67baaa7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:47:47 +0100 Subject: [PATCH 073/436] gnu: python-hy: Fix test suite. * gnu/packages/python.scm (python-hy, python2-hy)[arguments]: Replace 'check' phase with custom command. [native-inputs]: Add python-coverage and python-nose. --- gnu/packages/python.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d438e5c6d4..c45afbc2ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8273,6 +8273,17 @@ with a new public API, and RPython support.") (base32 "1msqv747iz12r73mz4qvsmlwkddwjvrahlrk7ysrcz07h7dsscxs")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Tests require write access to HOME. + (setenv "HOME" "/tmp") + (zero? (system* "nosetests"))))))) + (native-inputs + `(("python-coverage" ,python-coverage) + ("python-nose" ,python-nose))) (propagated-inputs `(("python-astor" ,python-astor) ("python-clint" ,python-clint) From ad348f9f39434dfce5e778b678fba586a7cae670 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:50:12 +0100 Subject: [PATCH 074/436] gnu: python-gridmap: Disable tests. * gnu/packages/python.scm (python-gridmap, python2-gridmap)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c45afbc2ff..2dc2ba3b36 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4447,6 +4447,8 @@ Python language binding specification.") (sha256 (base32 "1gzjg2k6f14i1msm2b0ax8d9ds1hvk6qd5nlaivg8m4cxqp4cp1x")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: Requires python-cherrypy. (propagated-inputs `(("python-psutil" ,python-psutil) ("python-drmaa" ,python-drmaa) From 59f74825d60ec46d387edcc24f7d256d5c2c602d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:56:44 +0100 Subject: [PATCH 075/436] gnu: python-flask-restplus: Disable tests. * gnu/packages/python.scm (python-flask-restplus)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 2dc2ba3b36..91cee71d62 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12069,6 +12069,13 @@ asynchronous messaging environments.") (base32 "11his6ii5brpkhld0d5bwzjjw4q3vmplpd6fmgzjrvvklsbk0cf4")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: 35/882 tests failing. + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; (zero? (system* "nosetests"))))))) (propagated-inputs `(("python-aniso8601" ,python-aniso8601) ("python-flask" ,python-flask) From 22d7360b1660faeae42ca382b3dc3f999a56d3ca Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 00:54:48 +0100 Subject: [PATCH 076/436] gnu: Remove python-dateutil@1.5. * gnu/packages/python.scm (python-dateutil-2, python2-dateutil-2): Rename to ... (python-dateutil, python2-dateutil): ... this. Remove 1.5 version. (python-tzlocal, python2-tzlocal): Adjust variable name. (python-rst.linker, python2-rst.linker): Likewise. (pelican): Likewise. (python-matplotlib, python2-matplotlib): Likewise. (python-sqlalchemy-utils, python2-sqlalchemy-utils): Likewise. (python-icalendar, python2-icalendar): Likewise. (python-botocore, python2-botocore): Likewise. (python-vobject, python2-vobject): Likewise. (python-arrow, python2-arrow): Likewise. (python-fake-factory, python2-fake-factory): Likewise. (python-freezegun, python2-freezegun): Likewise. (python-aniso8601, python2-aniso8601): Likewise. * gnu/packages/jrnl.scm (jrnl): Likewise. * gnu/packages/calendar.scm (limnoria): Likewise. --- gnu/packages/calendar.scm | 2 +- gnu/packages/jrnl.scm | 2 +- gnu/packages/python.scm | 49 +++++++++++---------------------------- 3 files changed, 15 insertions(+), 38 deletions(-) diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index 447dcd698e..00e908109b 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -125,7 +125,7 @@ data units.") `(("sqlite" ,sqlite))) (propagated-inputs `(("python-configobj" ,python-configobj) - ("python-dateutil-2" ,python-dateutil-2) + ("python-dateutil" ,python-dateutil) ("python-icalendar" ,python-icalendar) ("python-tzlocal" ,python-tzlocal) ("python-urwid" ,python-urwid) diff --git a/gnu/packages/jrnl.scm b/gnu/packages/jrnl.scm index ef1f52956c..f26de0d4ab 100644 --- a/gnu/packages/jrnl.scm +++ b/gnu/packages/jrnl.scm @@ -48,7 +48,7 @@ ("python-pytz" ,python-pytz) ("python-tzlocal" ,python-tzlocal) ("python-six" ,python-six) - ("python-dateutil" , python-dateutil-2) + ("python-dateutil" ,python-dateutil) ("python-parsedatetime" ,python-parsedatetime))) (home-page "http://maebert.github.io/jrnl/") (synopsis "Personal journal application") diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 91cee71d62..57275ac5d2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -973,7 +973,7 @@ Python file, so it can be easily copied into your project.") (define-public python2-six (package-with-python2 python-six)) -(define-public python-dateutil-2 +(define-public python-dateutil (package (name "python-dateutil") (version "2.5.2") @@ -994,29 +994,6 @@ Python file, so it can be easily copied into your project.") datetime module, available in Python 2.3+.") (license license:bsd-3))) -(define-public python2-dateutil-2 - (package-with-python2 python-dateutil-2)) - -(define-public python-dateutil - (package - (name "python-dateutil") - (version "1.5") ; last version for python < 3 - (source - (origin - (method url-fetch) - (uri (string-append "http://labix.org/download/python-dateutil/" - "python-dateutil-" version ".tar.gz")) - (sha256 - (base32 - "0fqfglhy5khbvsipr3x7m6bcaqljh8xl5cw33vbfxy7qhmywm2n0")))) - (build-system python-build-system) - (home-page "https://dateutil.readthedocs.io/en/stable/") - (synopsis "Extensions to the standard datetime module") - (description - "The dateutil module provides powerful extensions to the standard -datetime module, available in Python 2.3+.") - (license license:psfl))) - (define-public python2-dateutil (package-with-python2 python-dateutil)) @@ -1062,7 +1039,7 @@ datetime module, available in Python 2.3+.") (propagated-inputs `(("python-numpy" ,python-numpy) ("python-pytz" ,python-pytz) - ("python-dateutil" ,python-dateutil-2))) + ("python-dateutil" ,python-dateutil))) (native-inputs `(("python-nose" ,python-nose) ("python-cython" ,python-cython))) @@ -2908,7 +2885,7 @@ sources.") "0bh4lnj2p1nh0wf5pgxgfbrp27xhb1rinahkb5j7s3qprq6qn0sr")))) (build-system python-build-system) (propagated-inputs - `(("python-dateutil" ,python-dateutil-2) + `(("python-dateutil" ,python-dateutil) ("python-six" ,python-six))) (native-inputs `(("python-setuptools-scm" ,python-setuptools-scm))) @@ -3002,7 +2979,7 @@ interested parties to subscribe to events, or \"signals\".") ("python-blinker" ,python-blinker) ("python-unidecode" ,python-unidecode) ("python-six" ,python-six) - ("python-dateutil-2" ,python-dateutil-2))) + ("python-dateutil" ,python-dateutil))) (home-page "http://getpelican.com/") (arguments `(;; XXX Requires a lot more packages to do unit tests :P @@ -3530,7 +3507,7 @@ transcendental functions).") ("python-pygobject" ,python-pygobject) ("gobject-introspection" ,gobject-introspection) ("python-tkinter" ,python "tk") - ("python-dateutil" ,python-dateutil-2) + ("python-dateutil" ,python-dateutil) ("python-numpy" ,python-numpy-bootstrap) ("python-pillow" ,python-pillow) ("python-pytz" ,python-pytz) @@ -4029,7 +4006,7 @@ both of which are installed automatically if you install this library.") `(("python-six" ,python-six) ("python-sqlalchemy" ,python-sqlalchemy))) (native-inputs - `(("python-dateutil" ,python-dateutil-2) + `(("python-dateutil" ,python-dateutil) ("python-flexmock" ,python-flexmock) ("python-psycopg2" ,python-psycopg2) ("python-pytest" ,python-pytest) @@ -8140,7 +8117,7 @@ processes across test runs.") "01v2f3swd5s72x65cdihw83dx1z799b4i49a6ncg7vqmcm20wapd")))) (build-system python-build-system) (propagated-inputs - `(("python-dateutil-2" ,python-dateutil-2) + `(("python-dateutil" ,python-dateutil) ("python-pytz" ,python-pytz))) (synopsis "Python library for parsing iCalendar files") (description "The icalendar package is a parser/generator of iCalendar @@ -8588,7 +8565,7 @@ document.") ;; FIXME: Many tests are failing. '(#:tests? #f)) (propagated-inputs - `(("python-dateutil" ,python-dateutil-2) + `(("python-dateutil" ,python-dateutil) ("python-docutils" ,python-docutils) ("python-jmespath" ,python-jmespath))) (native-inputs @@ -9352,7 +9329,7 @@ introspection of @code{zope.interface} instances in code.") '(;; The test suite relies on some non-portable Windows interfaces. #:tests? #f)) (propagated-inputs - `(("python-dateutil-2" ,python-dateutil-2) + `(("python-dateutil" ,python-dateutil) ("python-pyicu" ,python-pyicu))) (synopsis "Parse and generate vCard and vCalendar files") (description "Vobject is intended to be a full featured Python package for @@ -10392,7 +10369,7 @@ objects, patterned after the Mocha library for Ruby.") ("python-chai" ,python-chai) ("python-simplejson" ,python-simplejson))) (propagated-inputs - `(("python-dateutil" ,python-dateutil-2))) + `(("python-dateutil" ,python-dateutil))) (home-page "https://github.com/crsmithdev/arrow/") (synopsis "Dates and times for Python") (description @@ -10597,7 +10574,7 @@ parsing UK postcodes.") ("python-mock" ,python-mock) ("python-ukpostcodeparser" ,python-ukpostcodeparser))) (propagated-inputs - `(("python-dateutil" ,python-dateutil-2) + `(("python-dateutil" ,python-dateutil) ("python-six" ,python-six))) (home-page "https://github.com/joke2k/faker") (synopsis "Python package that generates fake data") @@ -11202,7 +11179,7 @@ List. Forked from and using the same API as the publicsuffix package.") ("python-coverage" ,python-coverage))) (propagated-inputs `(("python-six" ,python-six) - ("python-dateutil-2" ,python-dateutil-2))) + ("python-dateutil" ,python-dateutil))) (arguments `(#:phases (modify-phases %standard-phases ;; The tests are normally executed via `make test`, but the PyPi @@ -11785,7 +11762,7 @@ useful as a validator for JSON data.") "1k5mjg9iqbjfslb5prrsfz7dhlvi6s35p1jxq8dm87w1b7dn5i2g")))) (build-system python-build-system) (propagated-inputs - `(("python-dateutil-2" ,python-dateutil-2))) + `(("python-dateutil" ,python-dateutil))) (home-page "https://bitbucket.org/nielsenb/aniso8601") (synopsis From 01fb9f6638bf6a77e5323ed63b3462976aa318f0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 01:07:41 +0100 Subject: [PATCH 077/436] gnu: python-axolotl: Remove workaround for bug #20765. * gnu/packages/python.scm (python-axolotl, python2-axolotl)[arguments]: Remove #:configure-flags. --- gnu/packages/python.scm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 57275ac5d2..326f5ee1b3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11959,10 +11959,7 @@ python-axolotl.") (lambda _ (for-each delete-file-recursively '("axolotl/tests" "build/lib/axolotl/tests")) - #t))) - ;; Prevent creation of the egg. This works around - ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765 - #:configure-flags '("--root=/"))) + #t))))) (propagated-inputs `(("python-axolotl-curve25519" ,python-axolotl-curve25519) ("python-dateutil" ,python-dateutil) From ed11804309a1fba077ae44bde83bc84c5f2b1b12 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:10:58 +0100 Subject: [PATCH 078/436] gnu: python-pexpect: Update to 4.2.1. * gnu/packages/python.scm (python-pexpect, python2-pexpect): Update to 4.2.1. [source]: Use 'pypi-uri'. [arguments]: Add 'prepare-tests' phase to patch paths and delete network test. [native-inputs]: Add python-pytest, man-db and which. [propagated-inputs]: Add python-ptyprocess. --- gnu/packages/python.scm | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 326f5ee1b3..52f242df33 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -74,6 +74,7 @@ #:use-module (gnu packages libevent) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) + #:use-module (gnu packages man) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) @@ -4444,21 +4445,39 @@ cluster without needing to write any wrapper code yourself.") (define-public python-pexpect (package (name "python-pexpect") - (version "3.3") + (version "4.2.1") (source (origin (method url-fetch) - (uri (string-append "https://pypi.python.org/packages/source/p/" - "pexpect/pexpect-" version ".tar.gz")) + (uri (pypi-uri "pexpect" version)) (sha256 - (base32 "1fp5gm976z7ghm8jw57463rj19cv06c8zw842prgyg788f6n3snz")))) + (base32 "14ls7k99pwvl21zqv65kzrhccv50j89m5ij1hf0slmsvlxjj84rx")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases + (add-before 'check 'prepare-tests + (lambda _ + (substitute* (find-files "tests") + (("/bin/ls") (which "ls")) + (("/bin/echo") (which "echo")) + (("/bin/which") (which "which")) + ;; Many tests try to use the /bin directory which + ;; is not present in the build environment. + ;; Use one that's non-empty and unlikely to change. + (("/bin'") "/dev'")) + ;; XXX: Socket connection test gets "Connection reset by peer". + ;; Why does it not work? Delete for now. + (delete-file "tests/test_socket.py") + #t)) (replace 'check (lambda _ (zero? (system* "nosetests"))))))) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-nose" ,python-nose) + ("python-pytest" ,python-pytest) + ("man-db" ,man-db) + ("which" ,which))) + (propagated-inputs + `(("python-ptyprocess" ,python-ptyprocess))) (home-page "http://pexpect.readthedocs.org/") (synopsis "Controlling interactive console applications") (description From 58f5fae7c40f1bca9adfe63c2e6a134f89da0c0c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:14:54 +0100 Subject: [PATCH 079/436] gnu: python-widgetsnbextension: Fix tests. * gnu/packages/python.scm (python-widgetsnbextension, python2-widgetsnbextension)[native-inputs]: Add python-certifi. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 52f242df33..10f295fe93 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7086,7 +7086,8 @@ interactive computing.") (propagated-inputs `(("python-notebook" ,python-notebook))) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-certifi" ,python-certifi) + ("python-nose" ,python-nose))) (home-page "http://ipython.org") (synopsis "IPython HTML widgets for Jupyter") (description "This package provides interactive HTML widgets for Jupyter From 80ce42bdbf3f795ba6b91cebd472261b1e141a4a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:16:23 +0100 Subject: [PATCH 080/436] gnu: python-argcomplete: Fix tests. * gnu/packages/python.scm (python-argcomplete, python2-argcomplete)[native-inputs]: Add python-pexpect and tcsh. --- gnu/packages/python.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 10f295fe93..90c9ecd413 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -87,6 +87,7 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages readline) #:use-module (gnu packages sdl) + #:use-module (gnu packages shells) #:use-module (gnu packages statistics) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -12150,6 +12151,9 @@ specs from your Flask-Restful projects.") (base32 "11bwiw6j0nilgz81xnw6f1npyga3prp8asjqrm87cdr3ria5l03x")))) (build-system python-build-system) + (native-inputs + `(("python-pexpect" ,python-pexpect) + ("tcsh" ,tcsh))) (home-page "https://github.com/kislyuk/argcomplete") (synopsis "Shell tab completion for Python argparse") (description "argcomplete provides extensible command line tab completion From 154d207c435a5a16d44bcb98dbb31c124dc87574 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:45:49 +0100 Subject: [PATCH 081/436] gnu: python-apsw: Fix tests. * gnu/packages/python.scm (python-apsw, python2-apsw)[arguments]: Use 'modify-phases'. Add installed PYTHONPATH before running tests. --- gnu/packages/python.scm | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 90c9ecd413..7e7e54f54f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5155,13 +5155,12 @@ implementation of D-Bus.") `(("sqlite" ,sqlite))) (arguments `(#:phases - ;; swap check and install phases - (alist-cons-after - 'install 'check - (assoc-ref %standard-phases 'check) - (alist-delete - 'check - %standard-phases)))) + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (zero? (system* "python" "setup.py" "test"))))))) (home-page "https://github.com/rogerbinns/apsw/") (synopsis "Another Python SQLite Wrapper") (description "APSW is a Python wrapper for the SQLite From d281be18bca2437ff27f8c045c5dd5a3e5b77e57 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 04:26:32 +0100 Subject: [PATCH 082/436] gnu: clipper: Fix test dependency. * gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5f56551526..3a7bffba79 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1562,6 +1562,7 @@ databases.") ("python-scipy" ,python2-scipy))) (native-inputs `(("python-mock" ,python2-mock) ; for tests + ("python-nose" ,python2-nose) ; for tests ("python-pytz" ,python2-pytz))) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") From aaffb9c97b8daae7dd81547e8b808ac73fd65f4f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 04:27:35 +0100 Subject: [PATCH 083/436] gnu: deeptools: Fix test dependency. * gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3a7bffba79..e160015b1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2002,6 +2002,7 @@ trees (phylogenies) and characters.") ("python-pybigwig" ,python2-pybigwig))) (native-inputs `(("python-mock" ,python2-mock) ;for tests + ("python-nose" ,python2-nose) ;for tests ("python-pytz" ,python2-pytz))) ;for tests (home-page "https://github.com/fidelram/deepTools") (synopsis "Tools for normalizing and visualizing deep-sequencing data") From 1c10a1d75c78afc85f5709743b1ac5f83e1897f4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:08:57 +0100 Subject: [PATCH 084/436] gnu: idr: Disable tests. * gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f. --- gnu/packages/bioinformatics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e160015b1f..fc75fd1abd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2879,7 +2879,8 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) (build-system python-build-system) (arguments - `(#:phases + `(#:tests? #f ; FIXME: "ImportError: No module named 'utility'" + #:phases (modify-phases %standard-phases (add-after 'install 'wrap-program From b7a820fc97485a7bdf7703d3b627871d6a6be6c6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:11:20 +0100 Subject: [PATCH 085/436] gnu: idr: Correct inputs. * gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ... [propagated-inputs]: ... to here. Add python-sympy. --- gnu/packages/bioinformatics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fc75fd1abd..a2191d060b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2900,8 +2900,9 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") (wrap-program (string-append out "/bin/idr") `("PYTHONPATH" ":" prefix (,path)))) #t))))) - (inputs + (propagated-inputs `(("python-scipy" ,python-scipy) + ("python-sympy" ,python-sympy) ("python-numpy" ,python-numpy) ("python-matplotlib" ,python-matplotlib))) (native-inputs From 14386fc7d9192b35a81dedb7616a44651807ee19 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:16:39 +0100 Subject: [PATCH 086/436] gnu: idr: Remove explicit wrapper. This is now done implicitly. * gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases. --- gnu/packages/bioinformatics.scm | 22 +--------------------- 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a2191d060b..3fb9bbc35d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2879,27 +2879,7 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) (build-system python-build-system) (arguments - `(#:tests? #f ; FIXME: "ImportError: No module named 'utility'" - #:phases - (modify-phases %standard-phases - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (python-version (string-take (string-take-right - (assoc-ref inputs "python") 5) 3)) - (path (string-join - (map (lambda (name) - (string-append (assoc-ref inputs name) - "/lib/python" python-version - "/site-packages")) - '("python-scipy" - "python-numpy" - "python-matplotlib")) - ":"))) - (wrap-program (string-append out "/bin/idr") - `("PYTHONPATH" ":" prefix (,path)))) - #t))))) + `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'" (propagated-inputs `(("python-scipy" ,python-scipy) ("python-sympy" ,python-sympy) From 58a35665d98386d98e7fbb84812d2b2282990eca Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 15:59:23 +0100 Subject: [PATCH 087/436] gnu: Add python-mpmath. * gnu/packages/python.scm (python-mpmath, python2-mpmath): New variables. --- gnu/packages/python.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7e7e54f54f..0414e889fe 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5406,6 +5406,36 @@ and statistical routines from scipy and statsmodels.") (propagated-inputs `(("python2-pytz" ,python2-pytz) ,@(package-propagated-inputs base)))))) +(define-public python-mpmath + (package + (name "python-mpmath") + (version "0.19") + (source (origin + (method url-fetch) + (uri (string-append "http://mpmath.org/files/mpmath-" + version ".tar.gz")) + (sha256 + (base32 + "08ijsr4ifrqv3cjc26mkw0dbvyygsa99in376hr4b96ddm1gdpb8")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? + (system* "python" "mpmath/tests/runtests.py" "-local"))))))) + (home-page "http://mpmath.org") + (synopsis "Arbitrary-precision floating-point arithmetic in python") + (description + "@code{mpmath} can be used as an arbitrary-precision substitute for +Python's float/complex types and math/cmath modules, but also does much +more advanced mathematics.") + (license license:bsd-3))) + +(define-public python2-mpmath + (package-with-python2 python-mpmath)) + (define-public python-sympy (package (name "python-sympy") From 52f622ef9fd315945f37de921c9d46997d176692 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 16:47:13 +0100 Subject: [PATCH 088/436] gnu: python-sympy: Update to 1.0. * gnu/packages/python.scm (python-sympy, python2-sympy): Update to 1.0. [propagated-inputs]: Add python-mpmath. --- gnu/packages/python.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0414e889fe..18a8b58873 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5439,7 +5439,7 @@ more advanced mathematics.") (define-public python-sympy (package (name "python-sympy") - (version "0.7.6") + (version "1.0") (source (origin (method url-fetch) @@ -5447,8 +5447,10 @@ more advanced mathematics.") "https://github.com/sympy/sympy/releases/download/sympy-" version "/sympy-" version ".tar.gz")) (sha256 - (base32 "19yp0gy4i7p4g6l3b8vaqkj9qj7yqb5kqy0qgbdagpzgkdz958yz")))) + (base32 "1bpzjwr9hrr7w88v4vgnj9lr6vxcldc94si13n8xpr1rv08d5b1y")))) (build-system python-build-system) + (propagated-inputs + `(("python-mpmath" ,python-mpmath))) (home-page "http://www.sympy.org/") (synopsis "Python library for symbolic mathematics") (description From 0d9087597467c3e34cf614a5475bfb0ea75b133b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:28:49 +0100 Subject: [PATCH 089/436] gnu: multiqc: Fix test dependencies. * gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3fb9bbc35d..e37226b275 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7843,6 +7843,8 @@ replacement for strverscmp.") (base32 "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy")))) (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) (propagated-inputs `(("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) From 329553482d0632e35b3c0028548b004f8cb32aec Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:39:07 +0100 Subject: [PATCH 090/436] gnu: ptpython: Disable tests. * gnu/packages/python.scm (ptpython, ptpython2)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 18a8b58873..fece7cdb75 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10798,6 +10798,8 @@ characters, mouse support, and auto suggestions.") (base32 "1mmbiyzf0n8hm7z2a562x7w5cbl6jc0zsk6vp40q1z4cyblv1k13")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; FIXME: No tests in pypi tarball. (propagated-inputs `(("python-docopt" ,python-docopt) ("python-jedi" ,python-jedi) From 7c6bf660d8a455090f4c140c5b2849f1b58f2fe3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 14:32:34 +0100 Subject: [PATCH 091/436] gnu: python-pyopenssl: Enable tests. * gnu/packages/patches/python-pyopenssl-skip-network-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl)[source]: Use it. [arguments]: Replace 'check' with custom phase. --- gnu/local.mk | 1 + .../python-pyopenssl-skip-network-test.patch | 50 +++++++++++++++++++ gnu/packages/python.scm | 13 +++-- 3 files changed, 61 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/python-pyopenssl-skip-network-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index a06f359435..89d1e83b4b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -815,6 +815,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-configobj-setuptools.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ + %D%/packages/patches/python-pyopenssl-skip-network-test.patch \ %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \ %D%/packages/patches/qemu-CVE-2016-8576.patch \ %D%/packages/patches/qemu-CVE-2016-8577.patch \ diff --git a/gnu/packages/patches/python-pyopenssl-skip-network-test.patch b/gnu/packages/patches/python-pyopenssl-skip-network-test.patch new file mode 100644 index 0000000000..a24eaf69a0 --- /dev/null +++ b/gnu/packages/patches/python-pyopenssl-skip-network-test.patch @@ -0,0 +1,50 @@ +This test tries connecting to an external server which is not supported +in the build environment. See discussion at: + +https://lists.gnu.org/archive/html/guix-devel/2016-12/msg00650.html + +diff --git a/tests/test_ssl.py b/tests/test_ssl.py +index ee849fd..60048b8 100644 +--- a/tests/test_ssl.py ++++ b/tests/test_ssl.py +@@ -1180,40 +1180,6 @@ class ContextTests(TestCase, _LoopbackMixin): + TypeError, context.load_verify_locations, None, None, None + ) + +- @pytest.mark.skipif( +- platform == "win32", +- reason="set_default_verify_paths appears not to work on Windows. " +- "See LP#404343 and LP#404344." +- ) +- def test_set_default_verify_paths(self): +- """ +- :py:obj:`Context.set_default_verify_paths` causes the +- platform-specific CA certificate locations to be used for +- verification purposes. +- """ +- # Testing this requires a server with a certificate signed by one +- # of the CAs in the platform CA location. Getting one of those +- # costs money. Fortunately (or unfortunately, depending on your +- # perspective), it's easy to think of a public server on the +- # internet which has such a certificate. Connecting to the network +- # in a unit test is bad, but it's the only way I can think of to +- # really test this. -exarkun +- +- # Arg, verisign.com doesn't speak anything newer than TLS 1.0 +- context = Context(SSLv23_METHOD) +- context.set_default_verify_paths() +- context.set_verify( +- VERIFY_PEER, +- lambda conn, cert, errno, depth, preverify_ok: preverify_ok) +- +- client = socket() +- client.connect(("encrypted.google.com", 443)) +- clientSSL = Connection(context, client) +- clientSSL.set_connect_state() +- clientSSL.do_handshake() +- clientSSL.send(b"GET / HTTP/1.0\r\n\r\n") +- self.assertTrue(clientSSL.recv(1024)) +- + def test_set_default_verify_paths_signature(self): + """ + :py:obj:`Context.set_default_verify_paths` takes no arguments and diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fece7cdb75..dce46cec34 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6672,11 +6672,18 @@ message digests and key derivation functions.") (uri (pypi-uri "pyOpenSSL" version)) (sha256 (base32 - "0vji4yrfshs15xpczbhzhasnjrwcarsqg87n98ixnyafnyxs6ybp")))) + "0vji4yrfshs15xpczbhzhasnjrwcarsqg87n98ixnyafnyxs6ybp")) + (patches + (search-patches "python-pyopenssl-skip-network-test.patch")))) (build-system python-build-system) (arguments - ;; FIXME: Some tests fail with "NameError: name 'long' is not defined". - '(#:tests? #f)) + '(#:phases + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (zero? (system* "py.test" "-v"))))))) (propagated-inputs `(("python-cryptography" ,python-cryptography) ("python-six" ,python-six))) From 752eb9e0d86931de9eb42d1a60069e48ac1fbfd8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 15:33:13 +0100 Subject: [PATCH 092/436] gnu: python2-kombu: Disable tests. * gnu/packages/python.scm (python2-kombu)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index dce46cec34..8af6965b1e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9165,6 +9165,10 @@ RabbitMQ messaging server is the most popular implementation.") (strip-python2-variant python-kombu)))) (package (inherit kombu) + (arguments `(;; FIXME: 'TestTransport.test_del_sync' fails on python2. + ;; It works fine on the python3 variant. + #:tests? #f + ,@(package-arguments kombu))) (native-inputs `(("python2-unittest2" ,python2-unittest2) ,@(package-native-inputs kombu)))))) From ee94ca11a1d695871c11cd5cf521089d5bcdb34f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 16:15:41 +0100 Subject: [PATCH 093/436] gnu: python-beautifulsoup4: Fix python2 variant. This is a followup to 5f37f0b66e301210698ab0c0af24453c826ba18a. * gnu/packages/python.scm (python-beautifulsoup4)[properties]: New field. Delay python2 variant. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8af6965b1e..9388534c98 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5232,7 +5232,8 @@ screen-scraping projects. It offers Pythonic idioms for navigating, searching, and modifying a parse tree, providing a toolkit for dissecting a document and extracting what you need. It automatically converts incoming documents to Unicode and outgoing documents to UTF-8.") - (license license:expat))) + (license license:expat) + (properties `((python2-variant . ,(delay python2-beautifulsoup4)))))) (define-public python2-beautifulsoup4 (package From cdc2bb50b29422e8edfb00cabb5edd632f6ebe07 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 18:15:47 +0100 Subject: [PATCH 094/436] gnu: pbtranscript-tofu: Disable tests. * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f. --- gnu/packages/bioinformatics.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e37226b275..50b0bfaa03 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3572,6 +3572,9 @@ the phenotype as it models the data.") (build-system python-build-system) (arguments `(#:python ,python-2 + ;; FIXME: Tests fail with "No such file or directory: + ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" + #:tests? #f #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-directory From 39d0de3375071b240f6a4d617e48d8449bc50e5e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2016 12:19:41 +0100 Subject: [PATCH 095/436] gnu: asciinema: Fix test requirements. * gnu/packages/terminals.scm (asciinema)[native-inputs]: Add python-requests. --- gnu/packages/terminals.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index efedba480f..79da6c7127 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -164,6 +164,9 @@ insert mode and command mode where keybindings have different functions.") (string-append "'" ncurses "/bin/tput'")))) #t))))) (inputs `(("ncurses" ,ncurses))) + (native-inputs + ;; For tests. + `(("python-requests" ,python-requests))) (home-page "https://asciinema.org") (synopsis "Terminal session recorder") (description From 7b6ff42aa3cf9398213d3c1f0e5f87c45a9730df Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 18 Dec 2016 00:44:09 +0100 Subject: [PATCH 096/436] gnu: git-annex-remote-hubic: Fix python-dateutil dependency. This is a followup to 22d7360b1660faeae42ca382b3dc3f999a56d3ca. * gnu/packages/version-control.scm (git-annex-remote-hubic)[propagated-inputs]: Change python-dateutil-2 to python-dateutil. --- gnu/packages/version-control.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 7918b90ca6..cc958281c7 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1172,7 +1172,7 @@ Mercurial, Bazaar, Darcs, CVS, Fossil, and Veracity.") `(;; for the tests ("python2-six" ,python2-six))) (propagated-inputs - `(("python2-dateutil" ,python2-dateutil-2) + `(("python2-dateutil" ,python2-dateutil) ("python2-futures" ,python2-futures) ("python2-rauth" ,python2-rauth) ("python2-swiftclient" ,python2-swiftclient))) From 1c1b67a3c91cd46241dee9c556d326e11b1d9ce2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2016 01:05:52 +0100 Subject: [PATCH 097/436] gnu: thefuck: Correct inputs and disable tests. * gnu/packages/admin.scm (thefuck)[arguments]: Set #:tests? #f. [inputs]: Move everything to ... [propagated-inputs]: ... here. Remove duplicate [inputs] and python-setuptools. [native-inputs]: Add python-pytest, python-pytest-mock and python-mock. --- gnu/packages/admin.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 69c04dc139..6e913d2cd0 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1697,15 +1697,26 @@ throughput (in the same interval).") (base32 "04q2cn8c83f6z6wn1scla1ilrpi5ssjc64987hvmwfvwvb82bvkp")))) (build-system python-build-system) - (inputs + (arguments + '(#:tests? #f)) + ;; FIXME: 10 test failures. Some require newer pytest (> 2.9.2). + ;; Others need more work. Un-comment the below to run the tests. + ;; #:phases + ;; (modify-phases %standard-phases + ;; (replace 'check + ;; (lambda _ + ;; ;; Some tests need write access to $HOME. + ;; (setenv "HOME" "/tmp") + ;; (zero? (system* "py.test" "-v"))))))) + (propagated-inputs `(("python-colorama" ,python-colorama) ("python-decorator" ,python-decorator) ("python-psutil" ,python-psutil) ("python-six" ,python-six))) - (inputs - ;; Requires setuptools >= 17.1 due to some features used, while our - ;; python currently only includes 12.0. TODO: Remove this input. - `(("python-setuptools" ,python-setuptools))) + (native-inputs + `(("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-mock" ,python-pytest-mock))) (home-page "https://github.com/nvbn/thefuck") (synopsis "Correct mistyped console command") (description From c0b12a606b6af07e739b8326e032774245f38297 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2016 04:13:59 +0100 Subject: [PATCH 098/436] gnu: sshoot: Fix tests. * gnu/packages/vpn.scm (sshoot)[arguments]: Add 'patch-paths' phase. --- gnu/packages/vpn.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index a32ac206ac..9a08ad4f41 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -247,6 +247,14 @@ DNS domain name queries.") (base32 "0a92lk8790dpp9j64vb6p4sazax0x3nby01lnfll7mxs1hx6n27q")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda _ + (substitute* "sshoot/tests/test_manager.py" + (("/bin/sh") (which "sh"))) + #t))))) (inputs `(("python-argcomplete" ,python-argcomplete) ("python-prettytable" ,python-prettytable) From a25b6880f1398ad36aea1d0e4e4105936a8b7e70 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2016 17:01:48 +0100 Subject: [PATCH 099/436] gnu: python-efl: Disable tests. * gnu/packages/enlightenment.scm (python-efl, python2-efl)[arguments]: Add phase to set test environment. And set #:tests? #f. --- gnu/packages/enlightenment.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index 77814960ee..5ec3ec5a88 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -253,7 +253,17 @@ embedded systems.") (lambda _ (setenv "CFLAGS" (string-append "-I" (assoc-ref %build-inputs "python-dbus") - "/include/dbus-1.0"))))))) + "/include/dbus-1.0")) + #t)) + (add-before 'check 'set-environment + (lambda _ + ;; Some tests require write access to HOME. + (setenv "HOME" "/tmp") + #t))) + ;; FIXME: Some tests require a running D-Bus server or a network + ;; connection and should be disabled. Other test failures looks + ;; legitimate. Disabled for now, needs work! + #:tests? #f)) (native-inputs `(("pkg-config" ,pkg-config) ("python-cython" ,python-cython))) From 9a8acd00da3ad44ac6ef423f3d9cba87645cc022 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 13 Jan 2017 22:58:54 +0100 Subject: [PATCH 100/436] gnu: python-sphinx: Update to 1.4.8. * gnu/packages/python.scm (python-sphinx)[version]: Update to 1.4.8. [source]: Use pypi-uri. [propagated-inputs]: Add python-imagesize, python-sphinx-alabaster-theme, python-babel, python-snowballstemmer, python-six. [properties]: Add python2-variant. (python2-sphinx)[native-inputs]: Add python2-mock. [propagated-inputs]: Add python2-pytz. --- gnu/packages/python.scm | 29 ++++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bfd003ba3e..c540d7b5a0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2945,33 +2945,44 @@ reStructuredText.") (define-public python-sphinx (package (name "python-sphinx") - (version "1.2.3") + (version "1.4.8") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/S/Sphinx/Sphinx-" - version ".tar.gz")) + (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl")))) + "0zvh8wwhm6gy21rr0cg42znsy4zzv2mnsxxk9gmn5y1ycn7rgbs1")))) (build-system python-build-system) (arguments ;; FIXME: Missing dependencies. '(#:tests? #f)) (propagated-inputs - `(("python-jinja2" ,python-jinja2) + `(("python-imagesize" ,python-imagesize) + ("python-sphinx-alabaster-theme" + ,python-sphinx-alabaster-theme) + ("python-babel" ,python-babel) + ("python-snowballstemmer" ,python-snowballstemmer) ("python-docutils" ,python-docutils) - ("python-pygments" ,python-pygments))) + ("python-jinja2" ,python-jinja2) + ("python-pygments" ,python-pygments) + ("python-six" ,python-six))) (home-page "http://sphinx-doc.org/") (synopsis "Python documentation generator") (description "Sphinx is a tool that makes it easy to create documentation for Python projects or other documents consisting of multiple reStructuredText sources.") - (license license:bsd-3))) + (license license:bsd-3) + (properties `((python2-variant . ,(delay python2-sphinx)))))) (define-public python2-sphinx - (package-with-python2 python-sphinx)) + (let ((base (package-with-python2 (strip-python2-variant python-sphinx)))) + (package + (inherit base) + (native-inputs `(("python2-mock" ,python2-mock) + ,@(package-native-inputs base))) + (propagated-inputs `(("python2-pytz" ,python2-pytz) + ,@(package-propagated-inputs base)))))) (define-public python-sphinx-rtd-theme (package From 42b7009a004178332f761c64c4363549e5743714 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 14 Jan 2017 22:03:54 +0100 Subject: [PATCH 101/436] gnu: python-matplotlib: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-matplotlib)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 102 ++++++++++++++++++++-------------------- 1 file changed, 50 insertions(+), 52 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c540d7b5a0..40b65012d3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3723,62 +3723,60 @@ transcendental functions).") ("texinfo" ,texinfo))) (arguments `(#:phases - (alist-cons-before - 'build 'configure-environment - (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((cairo (assoc-ref inputs "cairo")) - (gtk+ (assoc-ref inputs "gtk+"))) - ;; Setting these directories in the 'basedirlist' of 'setup.cfg' - ;; has not effect. - (setenv "LD_LIBRARY_PATH" - (string-append cairo "/lib:" gtk+ "/lib")) - (setenv "HOME" (getcwd)) - (call-with-output-file "setup.cfg" - (lambda (port) - (format port "[directories]~% + (modify-phases %standard-phases + (add-before 'build 'configure-environment + (lambda* (#:key outputs inputs #:allow-other-keys) + (let ((cairo (assoc-ref inputs "cairo")) + (gtk+ (assoc-ref inputs "gtk+"))) + ;; Setting these directories in the 'basedirlist' of 'setup.cfg' + ;; has not effect. + (setenv "LD_LIBRARY_PATH" + (string-append cairo "/lib:" gtk+ "/lib")) + (setenv "HOME" (getcwd)) + (call-with-output-file "setup.cfg" + (lambda (port) + (format port "[directories]~% basedirlist = ~a,~a~% [rc_options]~% backend = TkAgg~%" - (assoc-ref inputs "tcl") - (assoc-ref inputs "tk")))))) - (alist-cons-after - 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (info (string-append data "/info")) - (html (string-append doc "/html"))) - ;; Make installed package available for building the - ;; documentation - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "doc" - ;; Produce pdf in 'A4' format. - (substitute* (find-files "." "conf\\.py") - (("latex_paper_size = 'letter'") - "latex_paper_size = 'a4'")) - (mkdir-p html) - (mkdir-p info) - ;; The doc recommends to run the 'html' target twice. - (system* "python" "make.py" "html") - (system* "python" "make.py" "html") - (copy-recursively "build/html" html) - (system* "python" "make.py" "latex") - (system* "python" "make.py" "texinfo") - (symlink (string-append html "/_images") - (string-append info "/matplotlib-figures")) - (with-directory-excursion "build/texinfo" - (substitute* "matplotlib.texi" - (("@image\\{([^,]*)" all file) - (string-append "@image{matplotlib-figures/" file))) + (assoc-ref inputs "tcl") + (assoc-ref inputs "tk"))))))) + (add-after 'install 'install-doc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "doc") "/share")) + (doc (string-append data "/doc/" ,name "-" ,version)) + (info (string-append data "/info")) + (html (string-append doc "/html"))) + ;; Make installed package available for building the + ;; documentation + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "doc" + ;; Produce pdf in 'A4' format. + (substitute* (find-files "." "conf\\.py") + (("latex_paper_size = 'letter'") + "latex_paper_size = 'a4'")) + (mkdir-p html) + (mkdir-p info) + ;; The doc recommends to run the 'html' target twice. + (system* "python" "make.py" "html") + (system* "python" "make.py" "html") + (copy-recursively "build/html" html) + (system* "python" "make.py" "latex") + (system* "python" "make.py" "texinfo") (symlink (string-append html "/_images") - "./matplotlib-figures") - (system* "makeinfo" "--no-split" - "-o" "matplotlib.info" "matplotlib.texi")) - (copy-file "build/texinfo/matplotlib.info" - (string-append info "/matplotlib.info")) - (copy-file "build/latex/Matplotlib.pdf" - (string-append doc "/Matplotlib.pdf"))))) - %standard-phases)))) + (string-append info "/matplotlib-figures")) + (with-directory-excursion "build/texinfo" + (substitute* "matplotlib.texi" + (("@image\\{([^,]*)" all file) + (string-append "@image{matplotlib-figures/" file))) + (symlink (string-append html "/_images") + "./matplotlib-figures") + (system* "makeinfo" "--no-split" + "-o" "matplotlib.info" "matplotlib.texi")) + (copy-file "build/texinfo/matplotlib.info" + (string-append info "/matplotlib.info")) + (copy-file "build/latex/Matplotlib.pdf" + (string-append doc "/Matplotlib.pdf"))))))))) (home-page "http://matplotlib.org") (synopsis "2D plotting library for Python") (description From 84e0f8c1ed48614a636f4462ec50d52597624861 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 14 Jan 2017 22:05:35 +0100 Subject: [PATCH 102/436] gnu: python-matplotlib: Fix reST markup error. * gnu/packages/python.scm (python-matplotlib)[arguments]: Fix reST markup error. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 40b65012d3..a5220e05e7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3755,6 +3755,9 @@ backend = TkAgg~%" (substitute* (find-files "." "conf\\.py") (("latex_paper_size = 'letter'") "latex_paper_size = 'a4'")) + (substitute* "users/intro.rst" + ;; Fix reST markup error (see ) + (("[[][*][]]") "[#]")) (mkdir-p html) (mkdir-p info) ;; The doc recommends to run the 'html' target twice. From fdcbf10b700e58c5d527254c2624a9b624f32cfc Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 14 Jan 2017 22:33:46 +0100 Subject: [PATCH 103/436] gnu: python-matplotlib: Make sure that phases end with #t. * gnu/packages/python.scm (python-matplotlib)[arguments]: Make sure that phases end with #t. --- gnu/packages/python.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a5220e05e7..6518006aa2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3740,7 +3740,8 @@ basedirlist = ~a,~a~% [rc_options]~% backend = TkAgg~%" (assoc-ref inputs "tcl") - (assoc-ref inputs "tk"))))))) + (assoc-ref inputs "tk")))) + #t))) (add-after 'install 'install-doc (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((data (string-append (assoc-ref outputs "doc") "/share")) @@ -3779,7 +3780,8 @@ backend = TkAgg~%" (copy-file "build/texinfo/matplotlib.info" (string-append info "/matplotlib.info")) (copy-file "build/latex/Matplotlib.pdf" - (string-append doc "/Matplotlib.pdf"))))))))) + (string-append doc "/Matplotlib.pdf"))) + #t)))))) (home-page "http://matplotlib.org") (synopsis "2D plotting library for Python") (description From d1ba1d6bfd05bbf7e5855d43a2bdfcb0a9742cc9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 17 Jan 2017 21:56:31 +0100 Subject: [PATCH 104/436] gnu: python-requests: Update to 2.12.4. * gnu/packages/python.scm (python-requests, python2-requests): Update to 2.12.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6518006aa2..7f72ed13da 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2467,13 +2467,13 @@ installed with a newer @code{pip} or with wheel's own command line utility.") (define-public python-requests (package (name "python-requests") - (version "2.9.1") + (version "2.12.4") (source (origin (method url-fetch) (uri (pypi-uri "requests" version)) (sha256 (base32 - "0zsqrzlybf25xscgi7ja4s48y2abf9wvjkn47wh984qgs1fq2xy5")))) + "0d5fwxmw4ibynk3imph3n4n84m0n3ib1vj339fxhkqri0qd4767d")))) ;; TODO: unbundle urllib3 and chardet. (build-system python-build-system) (arguments From c9a1812527f97ca2963dad6be9a9792120cdb99b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 17 Jan 2017 23:13:19 +0100 Subject: [PATCH 105/436] gnu: Add python-geventhttpclient. * gnu/packages/python.scm (python-geventhttpclient, python2-geventhttpclient): New variables. --- gnu/packages/python.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7f72ed13da..9a44b5881a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10487,6 +10487,51 @@ to provide a high-level synchronous API on top of the libev event loop.") (define-public python2-gevent (package-with-python2 python-gevent)) +(define-public python-geventhttpclient + (package + (name "python-geventhttpclient") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "geventhttpclient" version)) + (sha256 + (base32 + "07d0q3wzmml75227r6y6mrl5a0zpf4v9gj0ni5rhbyzmaj4az1xx")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete pre-compiled files. + (for-each delete-file (find-files "src/geventhttpclient" + ".*\\.pyc")) + #t)))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-network-tests + (lambda _ + (delete-file "src/geventhttpclient/tests/test_client.py") + #t)) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (zero? (system* "py.test" "src/geventhttpclient/tests" "-v"))))))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-certifi" ,python-certifi) + ("python-gevent" ,python-gevent) + ("python-six" ,python-six))) + (home-page "https://github.com/gwik/geventhttpclient") + (synopsis "HTTP client library for gevent") + (description "@code{python-geventhttpclient} is a high performance, +concurrent HTTP client library for python using @code{gevent}.") + (license license:expat))) + +(define-public python2-geventhttpclient + (package-with-python2 python-geventhttpclient)) + (define-public python-twisted (package (name "python-twisted") From c227458ac84273c12c254827e3311e9df2798767 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:05 +0100 Subject: [PATCH 106/436] gnu: python-sphinx: Update to 1.5.1 and enable tests. * gnu/packages/python.scm (python-sphinx): Update to 1.5.1. [arguments]: New field. [native-inputs]: Add graphviz, python-html5lib, python-mock, python-nose, python-requests. (python2-sphinx)[native-inputs]: Add python2-enum34. --- gnu/packages/python.scm | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9a44b5881a..75c3bc8574 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -67,6 +67,7 @@ #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) @@ -2945,18 +2946,23 @@ reStructuredText.") (define-public python-sphinx (package (name "python-sphinx") - (version "1.4.8") + (version "1.5.1") (source (origin (method url-fetch) (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "0zvh8wwhm6gy21rr0cg42znsy4zzv2mnsxxk9gmn5y1ycn7rgbs1")))) + "1i8p9idnli4gr0y4x67yakbdk5w6a0xjzhrg6bg51y9d1fi7fslf")))) (build-system python-build-system) (arguments - ;; FIXME: Missing dependencies. - '(#:tests? #f)) + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Requires Internet access. + (delete-file "tests/test_build_linkcheck.py") + (zero? (system* "make" "test"))))))) (propagated-inputs `(("python-imagesize" ,python-imagesize) ("python-sphinx-alabaster-theme" @@ -2967,6 +2973,12 @@ reStructuredText.") ("python-jinja2" ,python-jinja2) ("python-pygments" ,python-pygments) ("python-six" ,python-six))) + (native-inputs + `(("graphviz" ,graphviz) + ("python-html5lib" ,python-html5lib) + ("python-mock" ,python-mock) + ("python-nose" ,python-nose) + ("python-requests" ,python-requests))) (home-page "http://sphinx-doc.org/") (synopsis "Python documentation generator") (description "Sphinx is a tool that makes it easy to create documentation @@ -2980,6 +2992,7 @@ sources.") (package (inherit base) (native-inputs `(("python2-mock" ,python2-mock) + ("python2-enum34" ,python2-enum34) ,@(package-native-inputs base))) (propagated-inputs `(("python2-pytz" ,python2-pytz) ,@(package-propagated-inputs base)))))) From 376c4619cf8ad683fba5d04513a5298c0a77cfdb Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:04 +0100 Subject: [PATCH 107/436] gnu: python-mox3: Remove python-oslosphinx dependency (since the tests don't run anyway). * gnu/packages/openstack.scm (python-mox3)[native-inputs]: Remove python-oslosphinx. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index b3e3f08c23..2500590b2f 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -152,11 +152,11 @@ guidelines}.") "0njmh40i1lg5mzn9hc2ax83adj6dli455j6xifilrw27c4wlkjzx")))) (build-system python-build-system) (arguments - ;; TODO: Requires newer version of testtools (>=1.4.0). + ;; TODO: Resolve dependency cycle and re-enable. '(#:tests? #f)) (native-inputs `(("python-fixtures" ,python-fixtures) - ("python-oslosphinx" ,python-oslosphinx) + ; TODO re-add ("python-oslosphinx" ,python-oslosphinx) ("python-pbr" ,python-pbr) ("python-sphinx" ,python-sphinx) ("python-testtools" ,python-testtools))) From b585e361844e0ab527d10880698ee0489347b1c6 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:01 +0100 Subject: [PATCH 108/436] gnu: Add python-fastimport. * gnu/packages/python.scm (python-fastimport, python2-fastimport): New variables. --- gnu/packages/python.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 75c3bc8574..b0601da4db 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10545,6 +10545,27 @@ concurrent HTTP client library for python using @code{gevent}.") (define-public python2-geventhttpclient (package-with-python2 python-geventhttpclient)) +(define-public python-fastimport + (package + (name "python-fastimport") + (version "0.9.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fastimport" version)) + (sha256 + (base32 "1aqjsin4rmqm7ln4j0p73fzxifws6c6ikgyhav7r137m2ixsxl43")))) + (build-system python-build-system) + (home-page "https://github.com/jelmer/python-fastimport") + (synopsis "VCS fastimport parser and generator in Python") + (description "This package provides a parser for and generator of the Git +@url{https://www.kernel.org/pub/software/scm/git/docs/git-fast-import.html,fastimport} +format.") + (license license:gpl2+))) + +(define-public python2-fastimport + (package-with-python2 python-fastimport)) + (define-public python-twisted (package (name "python-twisted") From d83d87225980cec4926aec03280ad3533b778281 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:02 +0100 Subject: [PATCH 109/436] gnu: Add python-dulwich. * gnu/packages/python.scm (python-dulwich, python2-dulwich): New variables. --- gnu/packages/python.scm | 46 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b0601da4db..7c4996ce4b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12734,3 +12734,49 @@ Features: @item Compiles templates into optimized, yet readable, Python code. @end enumerate") (license (license:x11-style "file://LICENSE")))) + +(define-public python-dulwich + (package + (name "python-dulwich") + (version "0.16.3") + (source + (origin + (method url-fetch) + (uri (list (string-append "https://www.dulwich.io/releases/" + "dulwich-" version ".tar.gz") + (pypi-uri "dulwich" version))) + (sha256 + (base32 "0fl47vzfgc3w3rmhn8naii905cjqcp0vc68iyvymxp7567hh6als")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'fix-tests + (lambda* (#:key inputs #:allow-other-keys) + ;; The tests use Popen with a custom environment which doesn't + ;; include PATH. + (substitute* "dulwich/tests/compat/utils.py" + (("'git'") (string-append "'" + (which "git") + "'"))) + (substitute* '("dulwich/tests/test_repository.py" + "dulwich/tests/test_hooks.py") + (("#!/bin/sh") (string-append "#!" (which "sh")))) + (setenv "TEST_RUNNER" "unittest") + (setenv "PYTHONHASHSEED" "random") + #t))))) + (propagated-inputs + `(("python-fastimport" ,python-fastimport))) + (native-inputs + `(("python-mock" ,python-mock) + ("python-geventhttpclient" ,python-geventhttpclient) + ("git" ,git))) + (home-page "https://www.dulwich.io/") + (synopsis "Git implementation in Python") + (description "Dulwich is an implementation of the Git file formats and +protocols written in pure Python.") + ;; Can be used with either license. + (license (list license:asl2.0 license:gpl2+)))) + +(define-public python2-dulwich + (package-with-python2 python-dulwich)) From 7adb90311f8ce5e44c5bd1ecba28dcb26bfabebe Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:00 +0100 Subject: [PATCH 110/436] gnu: python-testtools: Update to 1.4.0. * gnu/packages/python.scm (python-testtools): Update to 1.4.0. [source]: Use pypi-uri. [arguments]: New field. --- gnu/packages/python.scm | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7c4996ce4b..80d03f6b0a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1983,17 +1983,36 @@ subprocess and see the output as well as any file modifications.") (define-public python-testtools (package (name "python-testtools") - (version "1.0.0") + (version "1.4.0") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/t/testtools/testtools-" - version ".tar.gz")) + (uri (pypi-uri "testtools" version)) (sha256 (base32 - "1dyml28ykpl5jb9khdmcdvhy1cxqingys6qvj2k04fzlaj6z3bbx")))) + "1vw8yljnd75d396hhw6s2hrf4cclzy845ifd5am0lxsl235z3i8c")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-module-imports + (lambda _ + (substitute* "setup.py" + (("'unittest2>=0.8.0',") "")) + (substitute* '("testtools/testcase.py" + "testtools/testsuite.py" + "testtools/run.py" + "testtools/tests/test_run.py" + "testtools/tests/test_testsuite.py" + "testtools/tests/test_deferredruntest.py") + ;; unittest2 is a backport of Python2.7 features to Python 2.4. + (("import unittest2 as unittest") "import unittest") + (("import unittest2") "import unittest as unittest2") + (("from unittest2 import") "from unittest import")) + (substitute* "testtools/tests/test_testresult.py" + ;; NUL in source code is not allowed (raises ValueError). + (("\\x00\\x04") "\\x04")) + #t))))) (propagated-inputs `(("python-mimeparse" ,python-mimeparse) ("python-extras" ,python-extras))) From c8d7e063d0b576615fb481e0abc55c0aeab609b8 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:03 +0100 Subject: [PATCH 111/436] gnu: Add python-reno. * gnu/packages/openstack.scm (python-reno, python-reno2): New variables. --- gnu/packages/openstack.scm | 42 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 2500590b2f..5bb83095a0 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -19,6 +19,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages openstack) + #:use-module (gnu packages gnupg) #:use-module (gnu packages python) #:use-module (gnu packages ssh) #:use-module (gnu packages tls) @@ -550,6 +551,47 @@ in transmittable and storable formats, such as JSON and MessagePack.") (define-public python2-oslo.serialization (package-with-python2 python-oslo.serialization)) +(define-public python-reno + (package + (name "python-reno") + (version "2.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "reno" version)) + (sha256 + (base32 "1i2wnn5fnm3jm5774pahg000q0lma5i913hml91bbbm2mybphndd")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'init-git + (lambda _ + ;; reno expects a git repo + (zero? (system* "git" "init"))))))) + (propagated-inputs + `(("python-babel" ,python-babel) + ("python-dulwich" ,python-dulwich) + ("python-pyyaml" ,python-pyyaml) + ("python-six" ,python-six))) + (native-inputs + `(("python-testtools" ,python-testtools) + ("python-pbr" ,python-pbr) + ("python-testscenarios" ,python-testscenarios) + ("python-testrepository" ,python-testrepository) + ("python-mock" ,python-mock) + ("python-oslotest" ,python-oslotest) + ("gnupg" ,gnupg) + ("git" ,git))) + (home-page "http://docs.openstack.org/developer/reno/") + (synopsis "Release notes manager") + (description "Reno is a tool for storing release notes in a git repository +and building documentation from them.") + (license asl2.0))) + +(define-public python2-reno + (package-with-python2 python-reno)) + (define-public python-oslosphinx (package (name "python-oslosphinx") From 16ca6aaac867862ea6d84c5888bfc59099f335a0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 19 Jan 2017 16:59:28 +0100 Subject: [PATCH 112/436] gnu: python-scipy: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-scipy)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 104 +++++++++++++++++++--------------------- 1 file changed, 50 insertions(+), 54 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 80d03f6b0a..6d1a04ce88 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3946,13 +3946,18 @@ functions.") (outputs '("out" "doc")) (arguments `(#:phases - (alist-cons-before - 'build 'configure-openblas - (lambda* (#:key inputs #:allow-other-keys) - (call-with-output-file "site.cfg" - (lambda (port) - (format port - "[blas] + (modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "scipy/integrate/tests/test_quadpack.py" + (("libm.so") "libm.so.6")) + #t) + (add-before 'build 'configure-openblas + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "site.cfg" + (lambda (port) + (format port + "[blas] libraries = openblas library_dirs = ~a/lib include_dirs = ~a/include @@ -3962,53 +3967,44 @@ include_dirs = ~a/include library_dirs = ~a/lib atlas_libs = openblas " - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas")))) - #t) - (alist-cons-after - 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html")) - (pyver ,(string-append "PYVER="))) - ;; Make installed package available for building the - ;; documentation - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "doc" - ;; Fix generation of images for mathematical expressions. - (substitute* (find-files "source" "conf\\.py") - (("pngmath_use_preview = True") - "pngmath_use_preview = False")) - (mkdir-p html) - (system* "make" "html" pyver) - (system* "make" "latex" "PAPER=a4" pyver) - (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver) - (copy-file "build/latex/scipy-ref.pdf" - (string-append doc "/scipy-ref.pdf")) - (with-directory-excursion "build/html" - (for-each (lambda (file) - (let* ((dir (dirname file)) - (tgt-dir (string-append html "/" dir))) - (install-file file html))) - (find-files "." ".*")))))) - ;; Tests can only be run after the library has been installed and not - ;; within the source directory. - (alist-cons-after - 'install 'check - (lambda _ - (with-directory-excursion "/tmp" - (zero? (system* "python" "-c" "import scipy; scipy.test()")))) - (alist-delete - 'check - (alist-cons-after - 'unpack 'fix-tests - (lambda _ - (substitute* "scipy/integrate/tests/test_quadpack.py" - (("libm.so") "libm.so.6")) - #t) - %standard-phases))))))) + (assoc-ref inputs "openblas") + (assoc-ref inputs "openblas") + (assoc-ref inputs "openblas")))) + #t) + (delete 'check) + (add-after 'install 'install-doc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "doc") "/share")) + (doc (string-append data "/doc/" ,name "-" ,version)) + (html (string-append doc "/html")) + (pyver ,(string-append "PYVER="))) + ;; Make installed package available for building the + ;; documentation + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "doc" + ;; Fix generation of images for mathematical expressions. + (substitute* (find-files "source" "conf\\.py") + (("pngmath_use_preview = True") + "pngmath_use_preview = False")) + (mkdir-p html) + (system* "make" "html" pyver) + (system* "make" "latex" "PAPER=a4" pyver) + (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver) + (copy-file "build/latex/scipy-ref.pdf" + (string-append doc "/scipy-ref.pdf")) + (with-directory-excursion "build/html" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append html "/" dir))) + (install-file file html))) + (find-files "." ".*")))) + #t))) + (add-after 'install-doc 'check + (lambda _ + ;; Tests can only be run after the library has been installed and not + ;; within the source directory. + (with-directory-excursion "/tmp" + (zero? (system* "python" "-c" "import scipy; scipy.test()")))))))))) (home-page "http://www.scipy.org/") (synopsis "The Scipy library provides efficient numerical routines") (description "The SciPy library is one of the core packages that make up From db967b646292e3517fc11f98ea0d4c19fd2191a9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 19 Jan 2017 17:46:48 +0100 Subject: [PATCH 113/436] gnu: python-scipy: Fix expression after changing to 'modify-phases'. This is a followup to 16ca6aaac867862ea6d84c5888bfc59099f335a0. * gnu/packages/python.scm (python-scipy)[arguments]: Fix parens. --- gnu/packages/python.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6d1a04ce88..007c18206e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3951,7 +3951,7 @@ functions.") (lambda _ (substitute* "scipy/integrate/tests/test_quadpack.py" (("libm.so") "libm.so.6")) - #t) + #t)) (add-before 'build 'configure-openblas (lambda* (#:key inputs #:allow-other-keys) (call-with-output-file "site.cfg" @@ -3970,7 +3970,7 @@ atlas_libs = openblas (assoc-ref inputs "openblas") (assoc-ref inputs "openblas") (assoc-ref inputs "openblas")))) - #t) + #t)) (delete 'check) (add-after 'install 'install-doc (lambda* (#:key inputs outputs #:allow-other-keys) @@ -4004,7 +4004,7 @@ atlas_libs = openblas ;; Tests can only be run after the library has been installed and not ;; within the source directory. (with-directory-excursion "/tmp" - (zero? (system* "python" "-c" "import scipy; scipy.test()")))))))))) + (zero? (system* "python" "-c" "import scipy; scipy.test()")))))))) (home-page "http://www.scipy.org/") (synopsis "The Scipy library provides efficient numerical routines") (description "The SciPy library is one of the core packages that make up From a50e03014177d2f00b5b85d3e1c295406f842016 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 20 Jan 2017 19:03:08 +0100 Subject: [PATCH 114/436] gnu: python-scipy, python-matplotlib: Fix build after Sphinx update. * gnu/packages/python.scm (python-sphinx-1.2.3, python2-sphinx-1.2.3): New variables. (python-matplotlib)[native-inputs]: Change 'python-sphinx' to 'python-sphinx-1.2.3'. (python2-matplotlib)[native-inputs]: New field. (python-scipy)[native-inputs]: Change 'python-sphinx' to 'python-sphinx-1.2.3'. (python2-scipy)[native-inputs]: New field. --- gnu/packages/python.scm | 36 +++++++++++++++++++++++++++++++++--- 1 file changed, 33 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 007c18206e..fd423d3112 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3016,6 +3016,24 @@ sources.") (propagated-inputs `(("python2-pytz" ,python2-pytz) ,@(package-propagated-inputs base)))))) +;; This is needed for python-matplotlib@1.4 and python-scipy@0.16, at least. +;; Try removing this when they are updated. +(define-public python-sphinx-1.2.3 + (package (inherit python-sphinx) + (version "1.2.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "Sphinx" version)) + (sha256 + (base32 + "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl")))) + ;; XXX: "'NoneType' object has no attribute 'split'". + (arguments '(#:tests? #f)))) + +(define-public python2-sphinx-1.2.3 + (package (inherit (package-with-python2 + (strip-python2-variant python-sphinx-1.2.3))))) + (define-public python-sphinx-rtd-theme (package (name "python-sphinx-rtd-theme") @@ -3747,7 +3765,7 @@ transcendental functions).") ("tk" ,tk))) (native-inputs `(("pkg-config" ,pkg-config) - ("python-sphinx" ,python-sphinx) + ("python-sphinx" ,python-sphinx-1.2.3) ("python-numpydoc" ,python-numpydoc) ("python-nose" ,python-nose) ("python-mock" ,python-mock) @@ -3831,6 +3849,10 @@ toolkits.") (package (inherit matplotlib) ;; Make sure to use special packages for Python 2 instead ;; of those automatically rewritten by package-with-python2. + (native-inputs + `(("python2-sphinx" ,python2-sphinx-1.2.3) + ,@(fold alist-delete (package-native-inputs matplotlib) + '("python-sphinx")))) (propagated-inputs `(("python2-pycairo" ,python2-pycairo) ("python2-pygobject-2" ,python2-pygobject-2) @@ -3938,7 +3960,7 @@ functions.") ("openblas" ,openblas))) (native-inputs `(("python-nose" ,python-nose) - ("python-sphinx" ,python-sphinx) + ("python-sphinx" ,python-sphinx-1.2.3) ("python-numpydoc" ,python-numpydoc) ("gfortran" ,gfortran) ("texlive" ,texlive) @@ -4013,7 +4035,15 @@ routines such as routines for numerical integration and optimization.") (license license:bsd-3))) (define-public python2-scipy - (package-with-python2 python-scipy)) + (let ((scipy (package-with-python2 + (strip-python2-variant python-scipy)))) + (package (inherit scipy) + ;; Make sure to use special packages for Python 2 instead + ;; of those automatically rewritten by package-with-python2. + (native-inputs + `(("python2-sphinx" ,python2-sphinx-1.2.3) + ,@(fold alist-delete (package-native-inputs scipy) + '("python-sphinx"))))))) (define-public python-socksipy-branch (package From 97b62eb0bfcf5eb7e1e5a320f779839d13052ad0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 13 Feb 2017 22:58:03 +0100 Subject: [PATCH 115/436] gnu: python-trollius-redis: Disable tests. * gnu/packages/python.scm (python-trollius-redis, python2-trollius-redis)[arguments]: New field. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1492e0f369..13dc698341 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8488,6 +8488,8 @@ minimal and fast API targetting the following uses: (base32 "0k3vypszmgmaipgw9xscvgm79h2zd6p6ci8gdp5sxl6g5kbqr9fy")))) (build-system python-build-system) + ;; TODO: Tests require packaging 'hiredis'. + (arguments '(#:tests? #f)) (home-page "https://github.com/benjolitz/trollius-redis") (synopsis "Port of asyncio-redis to trollius") (description "@code{trollius-redis} is a Redis client for Python From bb6043fe9f0198c1e253ae2a8adeea1337830265 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:01:59 +0100 Subject: [PATCH 116/436] gnu: python-pygit2: Skip tests requiring network access. * gnu/packages/python.scm (python-pygit2, python2-pygit2)[source](patches): New field. * gnu/packages/patches/python-pygit2-disable-network-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + .../python-pygit2-disable-network-tests.patch | 64 +++++++++++++++++++ gnu/packages/python.scm | 4 +- 3 files changed, 68 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-pygit2-disable-network-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8615d12b08..0b9b5b1a1e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -861,6 +861,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-configobj-setuptools.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ + %D%/packages/patches/python-pygit2-disable-network-tests.patch \ %D%/packages/patches/python-pyopenssl-skip-network-test.patch \ %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch \ %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \ diff --git a/gnu/packages/patches/python-pygit2-disable-network-tests.patch b/gnu/packages/patches/python-pygit2-disable-network-tests.patch new file mode 100644 index 0000000000..e46d244807 --- /dev/null +++ b/gnu/packages/patches/python-pygit2-disable-network-tests.patch @@ -0,0 +1,64 @@ +Disable tests trying to look up remote servers. + +diff --git a/test/test_credentials.py b/test/test_credentials.py +index 92482d9..9a281e5 100644 +--- a/test/test_credentials.py ++++ b/test/test_credentials.py +@@ -68,39 +68,5 @@ class CredentialCreateTest(utils.NoRepoTestCase): + self.assertEqual((username, None, None, None), cred.credential_tuple) + + +-class CredentialCallback(utils.RepoTestCase): +- def test_callback(self): +- class MyCallbacks(pygit2.RemoteCallbacks): +- @staticmethod +- def credentials(url, username, allowed): +- self.assertTrue(allowed & GIT_CREDTYPE_USERPASS_PLAINTEXT) +- raise Exception("I don't know the password") +- +- url = "https://github.com/github/github" +- remote = self.repo.create_remote("github", url) +- +- self.assertRaises(Exception, lambda: remote.fetch(callbacks=MyCallbacks())) +- +- def test_bad_cred_type(self): +- class MyCallbacks(pygit2.RemoteCallbacks): +- @staticmethod +- def credentials(url, username, allowed): +- self.assertTrue(allowed & GIT_CREDTYPE_USERPASS_PLAINTEXT) +- return Keypair("git", "foo.pub", "foo", "sekkrit") +- +- url = "https://github.com/github/github" +- remote = self.repo.create_remote("github", url) +- self.assertRaises(TypeError, lambda: remote.fetch(callbacks=MyCallbacks())) +- +-class CallableCredentialTest(utils.RepoTestCase): +- +- def test_user_pass(self): +- credentials = UserPass("libgit2", "libgit2") +- callbacks = pygit2.RemoteCallbacks(credentials=credentials) +- +- url = "https://bitbucket.org/libgit2/testgitrepository.git" +- remote = self.repo.create_remote("bb", url) +- remote.fetch(callbacks=callbacks) +- + if __name__ == '__main__': + unittest.main() +diff --git a/test/test_repository.py b/test/test_repository.py +index cfdf01e..c0d8de4 100644 +--- a/test/test_repository.py ++++ b/test/test_repository.py +@@ -538,13 +538,6 @@ class CloneRepositoryTest(utils.NoRepoTestCase): + self.assertTrue('refs/remotes/custom_remote/master' in repo.listall_references()) + self.assertIsNotNone(repo.remotes["custom_remote"]) + +- def test_clone_with_credentials(self): +- repo = clone_repository( +- "https://bitbucket.org/libgit2/testgitrepository.git", +- self._temp_dir, callbacks=pygit2.RemoteCallbacks(credentials=pygit2.UserPass("libgit2", "libgit2"))) +- +- self.assertFalse(repo.is_empty) +- + def test_clone_with_checkout_branch(self): + # create a test case which isolates the remote + test_repo = clone_repository('./test/data/testrepo.git', diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 13dc698341..c9cf347373 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3580,7 +3580,9 @@ association studies (GWAS) on extremely large data sets.") (uri (pypi-uri "pygit2" version)) (sha256 (base32 - "0wf5rp0fvrw7j3j18dvwjq6xqlbm611wd55aphrfpps0v1gxh3ny")))) + "0wf5rp0fvrw7j3j18dvwjq6xqlbm611wd55aphrfpps0v1gxh3ny")) + (patches + (search-patches "python-pygit2-disable-network-tests.patch")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six) From 23015b4fb4dd7964d37165687ca1fa6dc796a4f4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:15:27 +0100 Subject: [PATCH 117/436] gnu: python-oslosphinx: Disable tests. * gnu/packages/openstack.scm (python-oslosphinx, python2-oslosphinx)[arguments]: New field. --- gnu/packages/openstack.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 5bb83095a0..6f7e843e9d 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -604,6 +604,9 @@ and building documentation from them.") (base32 "0cz8ym4i1n4rgljlqhyhfkpgdmid7nkb909k8r8nk186m9cmpla2")))) (build-system python-build-system) + ;; FIXME: Incompatible sphinx version. + (arguments + '(#:tests? #f)) (propagated-inputs `(("python-requests" ,python-requests))) (native-inputs From 019ccdb6c88cb19a6db3b1a4394cd2c2bfcd30c0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:22:06 +0100 Subject: [PATCH 118/436] gnu: python-openid-cla: Disable tests. * gnu/packages/python.scm (python-openid-cla, python2-openid-cla)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c9cf347373..1c3415988a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5611,6 +5611,7 @@ another XPath engine to find the matching elements in an XML or HTML document.") (base32 "102hy2qisvjxp5s0v9lvwqi4f2dk0dhns40vjgn008yxc7k0h3cr")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (home-page "https://github.com/puiterwijk/python-openid-cla/") (synopsis "Implementation of the OpenID CLA extension for python-openid") (description "@code{openid-cla} is an implementation of the OpenID From ac72d3d2cca1381a807493763b2e80db5307fdb1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:38:04 +0100 Subject: [PATCH 119/436] gnu: python-openid-teams: Disable tests. * gnu/packages/python.scm (python-openid-teams, python2-openid-teams)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1c3415988a..18e55bf6b2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5633,6 +5633,7 @@ contributor license agreement extension for python-openid.") (base32 "05zrh78alav24rxkbqlpbad6d3x2nljk6z6j7kflxf3vdqa7w969")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (home-page "https://github.com/puiterwijk/python-openid-teams/") (synopsis "Implementation of the OpenID teams extension for python-openid") (description From e435af5c2a9318a65dd4f240c33ba77870e6086d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:48:53 +0100 Subject: [PATCH 120/436] gnu: python-mako: Fix tests. * gnu/packages/python.scm (python-mako, python2-mako)[native-inputs]: Add PYTHON-PYTEST. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 18e55bf6b2..85704d3eee 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9271,7 +9271,8 @@ available in Django, but is a standalone package.") `(("python-markupsafe" ,python-markupsafe))) (native-inputs `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) (home-page "http://www.makotemplates.org/") (synopsis "Templating language for Python") (description "Mako is a templating language for Python that compiles From 619bfd811eb778998101cf3d72d7fba9447813e3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 16:09:49 +0100 Subject: [PATCH 121/436] gnu: awscli: Explicitly disable tests. * gnu/packages/python.scm (awscli)[arguments]: New field. [native-inputs]: Remove. --- gnu/packages/python.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 85704d3eee..421291d7de 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9108,12 +9108,9 @@ interface to the Amazon Web Services (AWS) API.") ("python-s3transfer" ,python-s3transfer) ("python-docutils" ,python-docutils) ("python-rsa" ,python-rsa))) - (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-sphinx" ,python-sphinx) - ("python-tox" ,python-tox) - ("python-wheel" ,python-wheel))) + (arguments + ;; FIXME: The 'pypi' release does not contain tests. + '(#:tests? #f)) (home-page "https://aws.amazon.com/cli/") (synopsis "Command line client for AWS") (description "AWS CLI provides a unified command line interface to the From fe2ba3a888f78669cc4abe6a9bf2db73c390a4c8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:28:03 +0100 Subject: [PATCH 122/436] gnu: python-tabulate: Disable tests. * gnu/packages/python.scm (python-tabulate)[arguments]: New field. [native-inputs]: Remove. [source]: Remove test substitution snippet. --- gnu/packages/python.scm | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 421291d7de..87066fc88e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10824,18 +10824,12 @@ It uses LR parsing and does extensive error checking.") (uri (pypi-uri "tabulate" version)) (sha256 (base32 - "1inqhspd4frxnp08c32yndr0lc4px1xfkqah184i5w09gkhvi843")) - ;; Fix tests - (modules '((guix build utils))) - (snippet '(substitute* '("test/test_cli.py" - "test/test_input.py" - "test/test_output.py" - "test/test_regression.py") - (("from common") "from nose.tools"))))) + "1inqhspd4frxnp08c32yndr0lc4px1xfkqah184i5w09gkhvi843")))) (build-system python-build-system) - (native-inputs - `(;; For testing - ("python-nose" ,python-nose))) + (arguments + ;; FIXME: The pypi release tarball is missing a 'test/common.py' + ;; and the latest release is not tagged in the upstream repository. + '(#:tests? #f)) (home-page "https://bitbucket.org/astanin/python-tabulate") (synopsis "Pretty-print tabular data") (description From 2010af55b98b1cbe6295b7f8b066fed04696a4ba Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:39:15 +0100 Subject: [PATCH 123/436] gnu: python-requests-mock: Update to 1.3.0. * gnu/packages/openstack.scm (python-requests-mock, python2-requests-mock): Update to 1.3.0. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 6f7e843e9d..1e8a840e9a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -245,14 +245,14 @@ tested on Python version 3.2, 2.7 and 2.6.") (define-public python-requests-mock (package (name "python-requests-mock") - (version "1.0.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (pypi-uri "requests-mock" version)) (sha256 (base32 - "0gcjjwsckhqixyffflc54i59x41jnbb37bli077vabii1bjmkin6")))) + "0jr997dvk6zbmhvbpcv3rajrgag69mcsm1ai3w3rgk2jdh6rg1mx")))) (build-system python-build-system) (propagated-inputs `(("python-requests" ,python-requests) From e2cb140efb43a56b1cdf2253564490a0f5be26ff Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:51:17 +0100 Subject: [PATCH 124/436] gnu: python-sphinxcontrib-programoutput: Disable tests. * gnu/packages/python.scm (python-sphinxcontrib-programoutput, python2-sphinxcontrib-programoutput)[arguments]: New field. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 87066fc88e..5c6dda0fbf 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9763,6 +9763,9 @@ programmatically interfacing with your system's $EDITOR.") (base32 "098as6z1s0gb4dh5xcr1fd2vpm91zj93jzvgawspxf5s4hqs0xhp")))) (build-system python-build-system) + (arguments + ;; FIXME: Many tests are failing and the upstream is gone. + '(#:tests? #f)) (propagated-inputs `(("python-sphinx" ,python-sphinx))) (synopsis "Sphinx extension to include program output") From 3d2a544c6901622ca30c507028532734f0f52040 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:03:05 +0100 Subject: [PATCH 125/436] gnu: python-sphinxcontrib-newsfeed: Disable tests. * gnu/packages/python.scm (python-sphinxcontrib-newsfeed python2-sphinxcontrib-newsfeed)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5c6dda0fbf..a80daeea73 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8642,6 +8642,7 @@ files for use with Python.") (sha256 (base32 "1d7gam3mn8v4in4p16yn3v10vps7nnaz6ilw99j4klij39dqd37p")))) + (arguments '(#:tests? #f)) ; No tests. (build-system python-build-system) (propagated-inputs `(("python-sphinx" ,python-sphinx))) From 9893cff37695dbe99eb3d776d405f90607e86d37 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:05:56 +0100 Subject: [PATCH 126/436] gnu: python-sphinx-rtd-theme: Disable tests. * gnu/packages/python.scm (python-sphinx-rtd-theme, python2-sphinx-rtd-theme)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a80daeea73..196fe2c833 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3050,6 +3050,7 @@ sources.") (base32 "19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (propagated-inputs `(("python-sphinx" ,python-sphinx))) (home-page "https://github.com/snide/sphinx_rtd_theme/") From 5b3c3d4b5a7a775a407b97f044c93cc151b3103f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:08:11 +0100 Subject: [PATCH 127/436] gnu: python-sphinx-repoze-autointerface: Disable tests. * gnu/packages/python.scm (python-sphinx-repoze-autointerface, python2-sphinx-repoze-autointerface)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 196fe2c833..315d741b7f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9790,6 +9790,7 @@ commands into documents, helping you to keep your command examples up to date.") (base32 "08ycivzf7bh4a1zcyp31hbyqs1b2c9r26raa3vxjwwmbfqr3iw4f")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (propagated-inputs `(("python-sphinx" ,python-sphinx) ("python-zope-interface" ,python-zope-interface))) From a31e2f1a56ed0495698ad0355db7f6caef3cc8b3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:11:05 +0100 Subject: [PATCH 128/436] gnu: python-sphinx-cloud-sptheme: Explicitly disable tests. * gnu/packages/python.scm (python-sphinx-cloud-sptheme, python2-sphinx-cloud-sptheme)[arguments]: New field. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 315d741b7f..39fd58716e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12240,6 +12240,8 @@ English stemmer.") (base32 "0zm9ap4p5dzln8f1m2immadaxv2xpg8jg4w53y52rhfl7pdb58vy")))) (build-system python-build-system) + ;; FIXME: The 'pypi' release archive does not contain tests. + (arguments '(#:tests? #f)) (native-inputs `(("python-sphinx" ,python-sphinx))) (home-page "https://bitbucket.org/ecollins/cloud_sptheme") From 6925cd788b5a36481dd261c78fb954a9825e3041 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:23:01 +0100 Subject: [PATCH 129/436] gnu: python-qrcode: Disable tests. * gnu/packages/python.scm (python-qrcode, python2-qrcode)[arguments]: New field. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 39fd58716e..5bcdc6d0c7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12995,6 +12995,9 @@ a file-like object from which an arbitrarly-sized key can be read.") (base32 "0kljfrfq0c2rmxf8am57333ia41kd0snbm2rnqbdy816hgpcq5a1")))) (build-system python-build-system) + (arguments + ;; FIXME: Tests require packaging 'pymaging'. + '(#:tests? #f)) (propagated-inputs `(("python-lxml" ,python-lxml) ; for SVG output ("python-pillow" ,python-pillow) ; for PNG output From a1e3ed6e8b57c1920d01e357fb2a8e545d4acc33 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 18 Feb 2017 16:43:37 +0100 Subject: [PATCH 130/436] gnu: python-pbr: Support python-sphinx>=1.2.1. * gnu/packages/patches/python-pbr-fix-man-page-support.patch: New file. * gnu/packages/python.scm (python-pbr-minimal): Use the new patch file. --- .../python-pbr-fix-man-page-support.patch | 28 +++++++++++++++++++ gnu/packages/python.scm | 3 +- 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-pbr-fix-man-page-support.patch diff --git a/gnu/packages/patches/python-pbr-fix-man-page-support.patch b/gnu/packages/patches/python-pbr-fix-man-page-support.patch new file mode 100644 index 0000000000..b9036f5b01 --- /dev/null +++ b/gnu/packages/patches/python-pbr-fix-man-page-support.patch @@ -0,0 +1,28 @@ +See: https://bugs.launchpad.net/oslosphinx/+bug/1661861 +diff -ur orig/pbr-1.10.0/pbr/builddoc.py pbr-1.10.0/pbr/builddoc.py +--- orig/pbr-1.10.0/pbr/builddoc.py 2016-05-23 21:38:18.000000000 +0200 ++++ pbr-1.10.0/pbr/builddoc.py 2017-02-18 14:01:37.424434317 +0100 +@@ -138,7 +138,8 @@ + sphinx_config.init_values(warnings.warn) + else: + sphinx_config.init_values() +- if self.builder == 'man' and len(sphinx_config.man_pages) == 0: ++ if self.builder == 'man' and len( ++ getattr(sphinx_config, 'man_pages', '')) == 0: + return + app = application.Sphinx( + self.source_dir, self.config_dir, +diff -ur orig/pbr-1.10.0/pbr/util.py pbr-1.10.0/pbr/util.py +--- orig/pbr-1.10.0/pbr/util.py 2016-05-23 21:38:18.000000000 +0200 ++++ pbr-1.10.0/pbr/util.py 2017-02-18 15:36:32.951196795 +0100 +@@ -211,7 +211,9 @@ + parser.read(path) + config = {} + for section in parser.sections(): +- config[section] = dict(parser.items(section)) ++ config[section] = dict() ++ for k, value in parser.items(section): ++ config[section][k.replace('-', '_')] = value + + # Run setup_hooks, if configured + setup_hooks = has_get_option(config, 'global', 'setup_hooks') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5bcdc6d0c7..93e18b2fb9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2130,7 +2130,8 @@ protocol.") (uri (pypi-uri "pbr" version)) (sha256 (base32 - "177kd9kbv1hvf2ban7l3x9ymzbi1md4hkaymwbgnz7ihf312hr0q")))) + "177kd9kbv1hvf2ban7l3x9ymzbi1md4hkaymwbgnz7ihf312hr0q")) + (patches (search-patches "python-pbr-fix-man-page-support.patch")))) (build-system python-build-system) (arguments `(#:tests? #f)) From 9c4810b47cdf2aeccfbb99a6af427c6c2777c46e Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 18 Feb 2017 16:49:03 +0100 Subject: [PATCH 131/436] gnu: python-oslosphinx: Update to 4.10.0. * gnu/packages/openstack.scm (python-oslosphinx): Update to 4.10.0. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 1e8a840e9a..fe0dd11eb3 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -595,14 +595,14 @@ and building documentation from them.") (define-public python-oslosphinx (package (name "python-oslosphinx") - (version "4.3.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (pypi-uri "oslosphinx" version)) (sha256 (base32 - "0cz8ym4i1n4rgljlqhyhfkpgdmid7nkb909k8r8nk186m9cmpla2")))) + "09mxqyabi68f3s3arvdhlhq0mn38vf74jbsfcg84151hcj6czhnl")))) (build-system python-build-system) ;; FIXME: Incompatible sphinx version. (arguments From 27693b1e34347c4e2e4d12283c8c825ec6332716 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 18 Feb 2017 18:12:34 +0100 Subject: [PATCH 132/436] gnu: python-oslosphinx: Re-enable tests. * gnu/packages/openstack.scm (python-oslosphinx): Re-enable tests. --- gnu/packages/openstack.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index fe0dd11eb3..381480b786 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -604,9 +604,15 @@ and building documentation from them.") (base32 "09mxqyabi68f3s3arvdhlhq0mn38vf74jbsfcg84151hcj6czhnl")))) (build-system python-build-system) - ;; FIXME: Incompatible sphinx version. (arguments - '(#:tests? #f)) + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Note: Upstream tests would have also built the release notes. + ;; That only would work if we were in a git checkout. + ;; Therefore, we don't do it here. + (zero? (system* "python" "setup.py" "build_sphinx"))))))) (propagated-inputs `(("python-requests" ,python-requests))) (native-inputs From a10b9810c6abfca006c8f2e0c2f8a4c60753c338 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:55:48 +0100 Subject: [PATCH 133/436] gnu: python-sphinx: Propagate python-requests. * gnu/packages/python.scm (python-sphinx)[native-inputs]: Move PYTHON-REQUESTS to ... [propagated-inputs]: ... here. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 93e18b2fb9..fff9a666a6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2994,13 +2994,13 @@ reStructuredText.") ("python-docutils" ,python-docutils) ("python-jinja2" ,python-jinja2) ("python-pygments" ,python-pygments) + ("python-requests" ,python-requests) ("python-six" ,python-six))) (native-inputs `(("graphviz" ,graphviz) ("python-html5lib" ,python-html5lib) ("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-requests" ,python-requests))) + ("python-nose" ,python-nose))) (home-page "http://sphinx-doc.org/") (synopsis "Python documentation generator") (description "Sphinx is a tool that makes it easy to create documentation From 8ef8de799fcbc7b1a04be0d33e1183c766d0f893 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 21:40:08 +0100 Subject: [PATCH 134/436] gnu: duplicity: Fix tests. * gnu/packages/backup.scm (duplicity)[native-inputs]: Add PAR2CMDLINE. [arguments]: Move /bin/sh substitution to 'patch-source' phase and add one file. --- gnu/packages/backup.scm | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 8dbe32ebdd..809d54a646 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -67,6 +67,7 @@ (build-system python-build-system) (native-inputs `(("util-linux" ,util-linux) ;setsid command, for the tests + ("par2cmdline" ,par2cmdline) ("python-pexpect" ,python2-pexpect) ("mock" ,python2-mock))) (propagated-inputs @@ -83,16 +84,18 @@ #:test-target "test" #:phases (modify-phases %standard-phases - (add-before - 'build 'patch-source ; embed gpg store name - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "duplicity/gpginterface.py" - (("self.call = 'gpg'") - (string-append "self.call = '" (assoc-ref inputs "gnupg") "/bin/gpg'"))))) + (add-before 'build 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + ;; embed gpg store name + (substitute* "duplicity/gpginterface.py" + (("self.call = 'gpg'") + (string-append "self.call = '" (assoc-ref inputs "gnupg") "/bin/gpg'"))) + (substitute* '("testing/functional/__init__.py" + "testing/overrides/bin/lftp") + (("/bin/sh") (which "sh"))) + #t)) (add-before 'check 'check-setup (lambda* (#:key inputs #:allow-other-keys) - (substitute* "testing/functional/__init__.py" - (("/bin/sh") (which "sh"))) (setenv "HOME" (getcwd)) ;gpg needs to write to $HOME (setenv "TZDIR" ;some timestamp checks need TZDIR (string-append (assoc-ref inputs "tzdata") From fffcd8b829d1fbd8bdb6af85385033224c576cec Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 22:19:08 +0100 Subject: [PATCH 135/436] gnu: python-pbkdf2: Fix tests. * gnu/packages/python.scm (python-pbkdf2)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fff9a666a6..70aa8cd665 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12967,6 +12967,15 @@ protocols written in pure Python.") (base32 "0yb99rl2mbsaamj571s1mf6vgniqh23v98k4632150hjkwv9fqxc")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) "/build/lib:" + (getenv "PYTHONPATH"))) + (zero? (system* "python" "test/test_pbkdf2.py"))))))) (propagated-inputs `(("python-pycrypto" ,python-pycrypto))) ; optional (home-page "http://www.dlitz.net/software/python-pbkdf2/") From d296d30013587722b37aeb0be114e00b15564f3f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 23:55:37 +0100 Subject: [PATCH 136/436] gnu: python-flask-wtf: Drop failing test. * gnu/packages/python.scm (python-flask-wtf, python2-flask-wtf)[arguments]: Add phase to delete file that needs network access. --- gnu/packages/python.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 70aa8cd665..635feb489c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9922,6 +9922,16 @@ presume or force a developer to use a particular tool or library.") (base32 "04l5743j2dici46038sqlzvf0xzpg8rf7s9ld2x24xv7f4idg990")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-before 'check 'drop-failing-test + (lambda _ + ;; FIXME: This file tries resolving an external server, which + ;; fails. Try to patch out the offending section instead of + ;; deleting the whole thing. + (delete-file "tests/test_recaptcha.py") + #t))))) (propagated-inputs `(("python-flask-babel" ,python-flask-babel) ("python-babel" ,python-babel) From 2c1cad7ad2f95685be889bdf662ffdf8df87d5cf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 23:59:51 +0100 Subject: [PATCH 137/436] gnu: python-flake8-polyfill: Enable tests. * gnu/packages/python.scm (python-flake8-polyfill, python2-flake8-polyfill)[native-inputs]: Add PYTHON-FLAKE8, PYTHON-MOCK, PYTHON-PYCODESTYLE and PYTHON-PYTEST. New field. [arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 635feb489c..89d8c5cb06 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6250,6 +6250,20 @@ complexity of Python source code.") (base32 "02gn2wxvh9vnf7m7dld7ca4l60mg5c370hv3swwppkngwaqmcw67")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) "/build/lib:" + (getenv "PYTHONPATH"))) + (zero? (system* "py.test" "-v"))))))) + (native-inputs + `(("python-flake8" ,python-flake8) + ("python-mock" ,python-mock) + ("python-pycodestyle" ,python-pycodestyle) + ("python-pytest" ,python-pytest))) (home-page "https://gitlab.com/pycqa/flake8-polyfill") (synopsis "Polyfill package for Flake8 plugins") (description From 9200fe14f70506474cfc178dc8c1066bf00a5e7e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 17 Feb 2017 00:57:11 +0000 Subject: [PATCH 138/436] gnu: python-scipy: Declare python2-variant. This is a followup to a50e03014177d2f00b5b85d3e1c295406f842016. * gnu/packages/python.scm (python-scipy)[properties]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 89d8c5cb06..e7553bb82b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4036,6 +4036,7 @@ atlas_libs = openblas (description "The SciPy library is one of the core packages that make up the SciPy stack. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.") + (properties `((python2-variant . ,(delay python2-scipy)))) (license license:bsd-3))) (define-public python2-scipy From 4d25c486a5565e2b3fed1be53bc8b8278204f86e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 17 Feb 2017 02:37:58 +0100 Subject: [PATCH 139/436] gnu: python-scikit-learn: Fix test failure. * gnu/packages/python.scm (python-scikit-learn, python2-scikit-learn)[arguments]: Use 'modify-phases'. Move 'check' phase after 'install' and incorporate 'set-HOME' phase. --- gnu/packages/python.scm | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e7553bb82b..e2bf5f73da 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3210,11 +3210,20 @@ and is very extensible.") (build-system python-build-system) (arguments `(#:phases - (alist-cons-before - 'check 'set-HOME - ;; some tests require access to "$HOME" - (lambda _ (setenv "HOME" "/tmp")) - %standard-phases))) + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + ;; Running tests from the source directory requires + ;; an "inplace" build with paths relative to CWD. + ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing + ;; Use the installed version instead. + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + ;; some tests require access to "$HOME" + (setenv "HOME" "/tmp") + ;; Step out of the source directory just to be sure. + (chdir "..") + (zero? (system* "nosetests" "-v" "sklearn"))))))) (inputs `(("openblas" ,openblas))) (native-inputs From dc027d401471955a3edd17cdd810357c6c01ca41 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 17 Feb 2017 07:09:46 +0100 Subject: [PATCH 140/436] gnu: python-pyicu: Fix build. * gnu/packages/python.scm (python-pyicu, python2-pyicu)[arguments]: New field. Add phase to delete locale-dependent test. --- gnu/packages/python.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e2bf5f73da..8353ca178f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1288,6 +1288,15 @@ Python 3.3+.") (base32 "16rmxy9y0qhqqna2v49i7nzwm09as699rbyvh4raw7w602w55c3k")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-before 'check 'delete-failing-test + (lambda _ + ;; XXX: These tests require locales that are unavailable + ;; in the build environment. + (delete-file "test/test_DateTimeParserGenerator.py") + #t))))) (inputs `(("icu4c" ,icu4c))) (home-page "http://pyicu.osafoundation.org/") From ab4ccc8fcfaf2215d4b33b1376147e4c2c70426a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 14 Feb 2017 21:48:30 +0200 Subject: [PATCH 141/436] daemon: Ensure proper alignment on the stack. * nix/libstore/build.cc (startBuilder): When calling 'clone', increase the step to 16 and ensure it aligns properly on the stack. --- nix/libstore/build.cc | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index cebc404d1c..9b7bb5391c 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -26,6 +26,7 @@ #include #include #include +#include #include #include @@ -2008,7 +2009,11 @@ void DerivationGoal::startBuilder() char stack[32 * 1024]; int flags = CLONE_NEWPID | CLONE_NEWNS | CLONE_NEWIPC | CLONE_NEWUTS | SIGCHLD; if (!fixedOutput) flags |= CLONE_NEWNET; - pid = clone(childEntry, stack + sizeof(stack) - 8, flags, this); + + /* Ensure proper alignment on the stack. On aarch64, it has to be 16 + bytes. */ + pid = clone(childEntry, (char *)(((uintptr_t)stack + 16) & ~0xf), + flags, this); if (pid == -1) throw SysError("cloning builder process"); } else From f578a412607edc60c1140076dca6cda7f18cedef Mon Sep 17 00:00:00 2001 From: ng0 Date: Sun, 19 Feb 2017 12:03:31 +0000 Subject: [PATCH 142/436] gnu: usbredir: Use correct url. * gnu/packages/spice.scm (usbredir)[source]: Update repository URL. Signed-off-by: Ben Woodcroft --- gnu/packages/spice.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm index e775174e23..363a5e8fc5 100644 --- a/gnu/packages/spice.scm +++ b/gnu/packages/spice.scm @@ -66,7 +66,7 @@ (source (origin (method git-fetch) (uri (git-reference - (url "http://cgit.freedesktop.org/spice/usbredir") + (url "https://anongit.freedesktop.org/git/spice/usbredir.git") (commit commit))) (sha256 (base32 From 05d80f0c5482be00ae6891d8add62f308eb0b600 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 20 Feb 2017 23:30:24 -0500 Subject: [PATCH 143/436] gnu: imagemagick: Update to 6.9.7-9. * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.7-9. --- gnu/packages/imagemagick.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index a58e83d725..8918b658f2 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -46,14 +46,14 @@ ;; The 7 release series has an incompatible API, while the 6 series is still ;; maintained. Don't update to 7 until we've made sure that the ImageMagick ;; users are ready for the 7-series API. - (version "6.9.7-7") + (version "6.9.7-9") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "02x463z31j449pfm8czb7jlpkd3nx4a3yyjxq3bhpjfq13i20d62")))) + "1fqvi6h96mfbyw292awiwsqs449sjmw6i9ib53c66nnq1zchw7l3")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch") From f769c1d77a3c0450d90ecb007de43420b91b205f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 23 Jan 2017 02:33:00 -0500 Subject: [PATCH 144/436] gnu: lcms: Specify 'cpe-name'. * gnu/packages/ghostscript.scm (lcms)[properties]: New field. --- gnu/packages/ghostscript.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/ghostscript.scm b/gnu/packages/ghostscript.scm index a00448a8c6..2c7b86c042 100644 --- a/gnu/packages/ghostscript.scm +++ b/gnu/packages/ghostscript.scm @@ -57,7 +57,8 @@ focus on accuracy and performance. It uses the International Color Consortium standard (ICC), approved as ISO 15076-1.") (license license:x11) - (home-page "http://www.littlecms.com/"))) + (home-page "http://www.littlecms.com/") + (properties '((cpe-name . "little_cms_color_engine"))))) (define lcms/fixed (package From 4995ae75409bfcf319a2d21f03176162c7b0d575 Mon Sep 17 00:00:00 2001 From: Andy Wingo Date: Tue, 21 Feb 2017 08:17:29 +0100 Subject: [PATCH 145/436] gnu: guile-next: Update to 2.1.7. * gnu/packages/guile.scm (guile-next): Update to 2.1.7. --- gnu/packages/guile.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 54f2ed27b6..6d8f30ebd4 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -233,7 +233,7 @@ without requiring the source code to be rewritten.") (define-public guile-next (package (inherit guile-2.0) (name "guile-next") - (version "2.1.5") + (version "2.1.7") (replacement #f) (source (origin (method url-fetch) @@ -241,7 +241,7 @@ without requiring the source code to be rewritten.") version ".tar.xz")) (sha256 (base32 - "0r9y4hw17dlxahik4zsccfb2f3p2a07wqndfm251bgmam9hln6gi")) + "0qf2664bglv5rrj4c99cc7gry7v9x0sqdyzgfg8zi8gm5wbcmqda")) (modules '((guix build utils))) ;; Remove the pre-built object files. Instead, build everything From 2178b580cbb7d7c4648d4fb26edb4d2412aecf96 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 21 Feb 2017 15:53:17 +0100 Subject: [PATCH 146/436] gnu: feh: Update to 2.18.2. * gnu/packages/image-viewers.scm (feh): Update to 2.18.2. --- gnu/packages/image-viewers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 05d39ba877..c3f6de8057 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -43,7 +43,7 @@ (define-public feh (package (name "feh") - (version "2.18") + (version "2.18.2") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -51,7 +51,7 @@ name "-" version ".tar.bz2")) (sha256 (base32 - "036lgv81d0vmrnmh1z1x360nr5avb2sk5jb1h3g5n6jijm8vzblx")))) + "09f5rfzls4h5jcrp7ylwbiljp5qzc2nbw9p2csv0pnlaixj69gil")))) (build-system gnu-build-system) (arguments '(#:phases (alist-delete 'configure %standard-phases) From 025519fa955cd554dd9c868b996b1dc6ba54f4a7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 21 Feb 2017 15:59:10 +0100 Subject: [PATCH 147/436] gnu: diffoscope: Update to 77. * gnu/packages/package-management.scm (diffoscope): Update to 77. [arguments]: Remove obsolete colordiff substitution. Adjust 'xxd' substitution to source path renames. Fix test failure by making it required. --- gnu/packages/package-management.scm | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 8291740998..388368e2d3 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -445,13 +445,13 @@ transactions from C or Python.") (define-public diffoscope (package (name "diffoscope") - (version "63") + (version "77") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "12q5d2nszql1g4jf2ss863v0wpvvhrkaivqzhy6af9m9zwvw0p0k")))) + "0wrb6pl88611frxj19kq3vikhbld40fy1ncrskb1iayxsmbfcbn9")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -464,12 +464,7 @@ transactions from C or Python.") (("'python-magic',") "")))) (add-after 'unpack 'embed-tool-references (lambda* (#:key inputs #:allow-other-keys) - (substitute* "diffoscope/difference.py" - (("@tool_required\\('colordiff'\\)") "") - (("\\[\"colordiff\"") - (string-append "[\"" (which "colordiff") "\""))) - (substitute* "diffoscope/comparators/utils.py" - (("@tool_required\\('xxd'\\)") "") + (substitute* "diffoscope/comparators/utils/compare.py" (("\\['xxd',") (string-append "['" (which "xxd") "',"))) (substitute* "diffoscope/comparators/elf.py" From 0ef7ea66b9d10e70a6e09a0e0e13811ceb99ee65 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 20 Feb 2017 02:08:27 +0100 Subject: [PATCH 148/436] gnu: dlib: Update to 19.2. * gnu/packages/machine-learning.scm (dlib): Update to 19.2. [arguments]: Enable previously failing tests. Fix truthiness of some phases. [source]: End snippet on #t. --- gnu/packages/machine-learning.scm | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 8f1f8ee53b..7ed12e677a 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -504,20 +504,21 @@ and a QP solver.") (define-public dlib (package (name "dlib") - (version "19.1") + (version "19.2") (source (origin (method url-fetch) (uri (string-append "http://dlib.net/files/dlib-" version ".tar.bz2")) (sha256 (base32 - "0p2pvcdalc6jhb6r99ybvjd9x74sclr0ngswdg9j2xl5pj7knbr4")) + "0jh840b3ynlqsvbpswzg994yk539zbhx2sk6lybd23qyd2b8zgi8")) (modules '((guix build utils))) (snippet '(begin ;; Delete ~13MB of bundled dependencies. (delete-file-recursively "dlib/external") - (delete-file-recursively "docs/dlib/external"))))) + (delete-file-recursively "docs/dlib/external") + #t)))) (build-system cmake-build-system) (arguments `(#:phases @@ -532,8 +533,7 @@ and a QP solver.") (add-after 'disable-asserts 'disable-failing-tests (lambda _ ;; One test times out on MIPS, so we need to disable it. - ;; The rest is known to fail on non-x86_64 platforms in the current release. - ;; Some have been fixed in git; this list should be readjusted next update. + ;; Others are flaky on some platforms. (let* ((system ,(or (%current-target-system) (%current-system))) (disabled-tests (cond @@ -543,15 +543,14 @@ and a QP solver.") ((string-prefix? "armhf" system) '("learning_to_track" "max_cost_assignment")) ((string-prefix? "i686" system) - '("optimization" "matrix2" "mpc")) + '("optimization")) (else '())))) - ;; The following test fails due a bug in openblas < 0.2.18. - (append! disabled-tests '("empirical_map")) (for-each (lambda (test) (substitute* "dlib/test/makefile" - (((string-append "SRC \\+= " test "\\.cpp")) "")) #t) - disabled-tests)))) + (((string-append "SRC \\+= " test "\\.cpp")) ""))) + disabled-tests) + #t))) (replace 'check (lambda _ ;; No test target, so we build and run the unit tests here. @@ -562,7 +561,9 @@ and a QP solver.") (zero? (system* "./dtest" "--runall"))))))) (add-after 'install 'delete-static-library (lambda* (#:key outputs #:allow-other-keys) - (delete-file (string-append (assoc-ref outputs "out") "/lib/libdlib.a"))))))) + (delete-file (string-append (assoc-ref outputs "out") + "/lib/libdlib.a")) + #t))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs From 53a55c9c867919827efca190cea532561417485e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 21 Feb 2017 18:59:45 -0500 Subject: [PATCH 149/436] gnu: curl: Update replacement to 7.53.0 [fixes CVE-2017-2629]. * gnu/packages/curl.scm (curl-7.52.1): Replace variable with ... (curl-7.53.0): ... new variable. (curl)[replacement]: Update to 7.53.0. --- gnu/packages/curl.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 7329d870de..13e0686519 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -40,7 +40,7 @@ (define-public curl (package (name "curl") - (replacement curl-7.52.1) + (replacement curl-7.53.0) (version "7.50.3") (source (origin (method url-fetch) @@ -121,15 +121,15 @@ tunneling, and so on.") "See COPYING in the distribution.")) (home-page "https://curl.haxx.se/"))) -(define curl-7.52.1 +(define curl-7.53.0 (package (inherit curl) (source - (let ((version "7.52.1")) + (let ((version "7.53.0")) (origin (method url-fetch) (uri (string-append "https://curl.haxx.se/download/curl-" version ".tar.lzma")) (sha256 (base32 - "0r937wplchjxifxqqcjxd9rzp6l9rqqdfjn41x1y4djrh95nsa24"))))))) + "1k0i31xygb804c61llhin5wbpcscg4gfqmbxcfkpdr1alwh7igrq"))))))) From aaf1bdc3497bb76b22019ded6b0846d02833e79e Mon Sep 17 00:00:00 2001 From: Christopher Allan Webber Date: Tue, 21 Feb 2017 11:20:02 +0100 Subject: [PATCH 150/436] gnu: Add guile-fibers. * gnu/packages/guile.scm (guile-fibers): New variable. --- gnu/packages/guile.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 6d8f30ebd4..293579b1be 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2016 Adonay "adfeno" Felipe Nogueira ;;; Copyright © 2016 Amirouche ;;; Copyright © 2016 Jan Nieuwenhuizen +;;; Copyright © 2017 Andy Wingo ;;; ;;; This file is part of GNU Guix. ;;; @@ -1655,6 +1656,38 @@ library for GNU Guile based on the actor model. Note that 8sync is only available for Guile 2.2 (guile-next in Guix).") (license license:lgpl3+))) +(define-public guile-fibers + (package + (name "guile-fibers") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (string-append "https://wingolog.org/pub/fibers/fibers-" + version ".tar.gz")) + (sha256 + (base32 + "0vjkg72ghgdgphzbjz9ig8al8271rq8974viknb2r1rg4lz92ld0")))) + (build-system gnu-build-system) + (native-inputs + `(("texinfo" ,texinfo) + ("pkg-config" ,pkg-config))) + (inputs + `(("guile" ,guile-next))) + (synopsis "Lightweight concurrency facility for Guile") + (description + "Fibers is a Guile library that implements a a lightweight concurrency +facility, inspired by systems like Concurrent ML, Go, and Erlang. A fiber is +like a \"goroutine\" from the Go language: a lightweight thread-like +abstraction. Systems built with Fibers can scale up to millions of concurrent +fibers, tens of thousands of concurrent socket connections, and many parallel +cores. The Fibers library also provides Concurrent ML-like channels for +communication between fibers. + +Note that Fibers makes use of some Guile 2.1/2.2-specific features and +is not available for Guile 2.0.") + (home-page "https://github.com/wingo/fibers") + (license license:lgpl3+))) + (define-public guile-git (let ((revision "0") (commit "969514aa7224217bc3c1a4c5312a9469ac5f13d5")) From 7031b9a76364e3e28ee6a50325daf23240899447 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 22 Feb 2017 06:26:33 +0100 Subject: [PATCH 151/436] gnu: libass: Update to 0.13.6. * gnu/packages/video.scm (libass): Update to 0.13.6. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 7eff842e0d..72e4dd6b1f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -294,7 +294,7 @@ designed to encode video or images into an H.265 / HEVC encoded bitstream.") (define-public libass (package (name "libass") - (version "0.13.4") + (version "0.13.6") (source (origin (method url-fetch) (uri (string-append @@ -302,7 +302,7 @@ designed to encode video or images into an H.265 / HEVC encoded bitstream.") version "/libass-" version ".tar.xz")) (sha256 (base32 - "1dlzkjybnpl2fkvyjq0qblb7qw12cs893bs7zj3rvf8ij342yjnq")))) + "0b9cj5xfsa7zwlk5m146fhv102v51iqs3rapq0n2xrz30k8p9a7q")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) From bc5d2620b63cf3ddce945c8015884748eadfc829 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 22 Feb 2017 06:04:02 +0100 Subject: [PATCH 152/436] gnu: mpv: Update to 0.24.0. * gnu/packages/video.scm (mpv): Update to 0.24.0. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 72e4dd6b1f..985ff6c691 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -837,7 +837,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.") (define-public mpv (package (name "mpv") - (version "0.23.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (string-append @@ -845,7 +845,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.") ".tar.gz")) (sha256 (base32 - "1629v5l0rmphxra7chmfm7bnn59zc1mp529b9m2zqzaqf1czxvla")) + "059zblcj98fhrns1rwa66mf4km68czpam4nnk8q9qny31bx58654")) (file-name (string-append name "-" version ".tar.gz")))) (build-system waf-build-system) (native-inputs From 7db818c945cc8d3fe4c75e44d5ceb1dfd6d38cbe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 22 Feb 2017 06:53:43 +0100 Subject: [PATCH 153/436] gnu: ola: Update to 0.10.3. * gnu/packages/lighting.scm (ola): Update to 0.10.3. --- gnu/packages/lighting.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lighting.scm b/gnu/packages/lighting.scm index e70b276fd7..5f816dc54b 100644 --- a/gnu/packages/lighting.scm +++ b/gnu/packages/lighting.scm @@ -36,7 +36,7 @@ (define-public ola (package (name "ola") - (version "0.10.2") + (version "0.10.3") (source (origin (method url-fetch) (uri (string-append @@ -45,7 +45,7 @@ (patches (search-patches "ola-readdir-r.patch")) (sha256 (base32 - "09zx1c8nkj29shfdzkahrh9397m3mwnsy0gj7jrb63f89f3n2vlq")))) + "1yf1yy9n64n73zjq2bwc0gik0dd3n05297hdrrma2qvb0imzm5h1")))) (build-system gnu-build-system) (native-inputs `(("bison" ,bison) From c762d09e89746025bc38299a933e7e6aa611b8b6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 22 Feb 2017 07:39:05 +0100 Subject: [PATCH 154/436] gnu: bash-completion: Update to 2.5. * gnu/packages/bash.scm (bash-completion): Update to 2.5. --- gnu/packages/bash.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm index c121fd84d6..c3b94391e1 100644 --- a/gnu/packages/bash.scm +++ b/gnu/packages/bash.scm @@ -281,7 +281,7 @@ can apply to a patch-level 0 Bash." (define-public bash-completion (package (name "bash-completion") - (version "2.4") + (version "2.5") (source (origin (method url-fetch) (uri (string-append @@ -289,7 +289,7 @@ can apply to a patch-level 0 Bash." version "/" name "-" version ".tar.xz")) (sha256 (base32 - "1xlhd09sb2w3bw8qaypxgkr0782w082mcbx8zf7yzjgy0996pxy0")) + "1kwmii1z1ljx5i4z702ynsr8jgrq64bj9w9hl3n2aa2kcl659fdh")) (patches (search-patches "bash-completion-directories.patch")))) (build-system gnu-build-system) From 6983b8a8264044c46fbd5c90a11152e2d2303e6b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 22 Feb 2017 10:09:03 +0100 Subject: [PATCH 155/436] gnu: strace: Update to 4.16. * gnu/packages/linux.scm (strace): Update to 4.16. [arguments]: Add phase to patch /bin/sh reference. New field. [home-page]: Update to redirected URL. --- gnu/packages/linux.scm | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index cdeb8e92c7..5342c7f92e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -811,17 +811,25 @@ images more compressible.") (define-public strace (package (name "strace") - (version "4.7") + (version "4.16") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/strace/strace/" version "/strace-" version ".tar.xz")) (sha256 (base32 - "158iwk0pl2mfw93m1843xb7a2zb8p6lh0qim07rca6f1ff4dk764")))) + "1vzhmpcy989i4k12q4cc438yal2ghhm6x7ychscjbhcf2yspqj4q")))) (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-/bin/sh + (lambda _ + (substitute* "strace.c" + (("/bin/sh") (which "sh"))) + #t))))) (native-inputs `(("perl" ,perl))) - (home-page "http://strace.sourceforge.net/") + (home-page "https://strace.io/") (synopsis "System call tracer for Linux") (description "strace is a system call tracer, i.e. a debugging tool which prints out a From c0185d8e84047f4e209dbc217bbece9921aaf745 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 22 Feb 2017 10:31:59 +0100 Subject: [PATCH 156/436] gnu: nginx: Update to 1.11.10. * gnu/packages/web.scm (nginx): Update to 1.11.10. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index b5bb887352..116ccf231b 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -130,14 +130,14 @@ and its related documentation.") (define-public nginx (package (name "nginx") - (version "1.11.9") + (version "1.11.10") (source (origin (method url-fetch) (uri (string-append "https://nginx.org/download/nginx-" version ".tar.gz")) (sha256 (base32 - "0j2pcara9ir2xj3m2mjzf7wz46mdy51c0kal61cp0ldm2qgvf8nw")))) + "0gak6pcsn1m8fsz0g95z4b72nn12ivy35vlxrmagfcvnn2mkr2vp")))) (build-system gnu-build-system) (inputs `(("pcre" ,pcre) ("openssl" ,openssl) From 052f75da754b1d6aae00049f732a3bb549147e0f Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Tue, 21 Feb 2017 18:53:19 +0100 Subject: [PATCH 157/436] gnu: python-pygame: Update to 1.9.3. * gnu/packages/game-development.scm (python-pygame)[version]: Update to 1.9.3. [source]: Use pypi-uri. [inputs]: Add freetype. [arguments]: Use python-3 instead of python-2. Provide path to freetype library in 'set-library-paths' phase. Remove "src/movie.c" dummy substitution. (python2-pygame): New variable. --- gnu/packages/game-development.scm | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 619c2f1bc2..908ce48347 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -526,18 +526,16 @@ interface (API).") (define-public python-pygame (package (name "python-pygame") - (version "1.9.1") + (version "1.9.3") (source (origin (method url-fetch) - (uri (string-append "http://pygame.org/ftp/pygame-" - version "release.tar.gz")) + (uri (pypi-uri "pygame" version)) (sha256 (base32 - "0cyl0ww4fjlf289pjxa53q4klyn55ajvkgymw0qrdgp4593raq52")))) + "1hlydiyygl444bq5m5g8n3jsxsgrdyxlm42ipmfbw36wkf0j243m")))) (build-system python-build-system) (arguments - `(#:python ,python-2 - #:tests? #f ; Tests require pygame to be installed first. + `(#:tests? #f ; Tests require pygame to be installed first. #:phases (modify-phases %standard-phases ;; Set the paths to the dependencies manually because @@ -553,6 +551,7 @@ interface (API).") (smpeg-ref (assoc-ref inputs "libsmpeg")) (png-ref (assoc-ref inputs "libpng")) (jpeg-ref (assoc-ref inputs "libjpeg")) + (freetype-ref (assoc-ref inputs "freetype")) (v4l-ref (assoc-ref inputs "v4l-utils")) (out-ref (assoc-ref outputs "out"))) (substitute* "Setup.in" @@ -582,9 +581,14 @@ interface (API).") (("JPEG = -ljpeg") (string-append "JPEG = -I" jpeg-ref "/include -L" jpeg-ref "/lib -ljpeg"))) + + (substitute* "Setup.in" + (("FREETYPE = -lfreetype") + (string-append "FREETYPE = -I" freetype-ref "/include/freetype2 -L" + freetype-ref "/lib -lfreetype"))) + (substitute* "Setup.in" (("^pypm") "#pypm")) - (substitute* "src/movie.c") ;; Create a path to a header file provided by v4l-utils. (system* "mkdir" "linux") (system* "ln" "--symbolic" @@ -592,7 +596,8 @@ interface (API).") "linux/videodev.h") (system* "ln" "--symbolic" "Setup.in" "Setup"))))))) (inputs - `(("sdl" ,sdl) + `(("freetype" ,freetype) + ("sdl" ,sdl) ("sdl-image" ,sdl-image) ("sdl-mixer" ,sdl-mixer) ("sdl-ttf" ,sdl-ttf) @@ -619,3 +624,6 @@ to create fully featured games and multimedia programs in the python language.") license:psfl license:public-domain license:lgpl2.1+)))) + +(define-public python2-pygame + (package-with-python2 python-pygame)) From f59a20cb6ccbde86a4b06428c9dbfe43ef813983 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Tue, 21 Feb 2017 20:06:43 +0100 Subject: [PATCH 158/436] gnu: xonsh: Update to 0.5.5. * gnu/packages/shells.scm (xonsh): Update to 0.5.5. --- gnu/packages/shells.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 5aada54340..2ea23acd33 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -342,14 +342,14 @@ ksh, and tcsh.") (define-public xonsh (package (name "xonsh") - (version "0.5.3") + (version "0.5.5") (source (origin (method url-fetch) (uri (pypi-uri "xonsh" version)) (sha256 (base32 - "1pb1am26wl21g798lpl091j95900py7jj4g98rs9qkhywiln4z4q")) + "1wa5g1gxk4aw8jazp3fqmr7mlkdmnva83x28i9xd3s99lv0qb3dd")) (modules '((guix build utils))) (snippet `(begin From 8923441951133c33ab0ef5ae1031559eba3268fd Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 22 Feb 2017 12:06:44 -0500 Subject: [PATCH 159/436] gnu: linux-libre@4.1, linux-libre@4.4, linux-libre@4.9: Fix CVE-2017-6074. * gnu/packages/linux.scm (linux-libre-4.1, linux-libre-4.4, linux-libre-4.9): Add patch for CVE-2017-6074. --- gnu/packages/linux.scm | 36 +++++++++++++++++++++++++++++++++--- 1 file changed, 33 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5342c7f92e..a6c564b275 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -351,19 +351,49 @@ It has been modified to remove all non-free binary blobs.") (make-linux-libre "4.9.11" "1gypfg2984zr4z7hihnl3bbpxnk1mrqbynb6xd8ad2v2z04aw13q" %intel-compatible-systems - #:configuration-file kernel-config)) + #:configuration-file kernel-config + #:patches + (list %boot-logo-patch + (origin + (method url-fetch) + (uri "\ +https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=5edabca9d4cff7f1f2b68f0bac55ef99d9798ba4") + (file-name "linux-libre-CVE-2017-6074.patch") + (sha256 + (base32 + "1x40slfz1qxgiaznyy13bwlh34450pkyyrkljpyjlx6c4mrzb1jj")))))) (define-public linux-libre-4.4 (make-linux-libre "4.4.50" "0c157kk0vgrb1fsyy4q3czqdg4npgql82n6p303afy8ylh2w6d3l" %intel-compatible-systems - #:configuration-file kernel-config)) + #:configuration-file kernel-config + #:patches + (list %boot-logo-patch + (origin + (method url-fetch) + (uri "\ +https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=5edabca9d4cff7f1f2b68f0bac55ef99d9798ba4") + (file-name "linux-libre-CVE-2017-6074.patch") + (sha256 + (base32 + "1x40slfz1qxgiaznyy13bwlh34450pkyyrkljpyjlx6c4mrzb1jj")))))) (define-public linux-libre-4.1 (make-linux-libre "4.1.38" "165kmzglhg63hn7y4q7r6cb2dpsljxiq1czvgyx0bkd1vd2bcvsa" %intel-compatible-systems - #:configuration-file kernel-config)) + #:configuration-file kernel-config + #:patches + (list %boot-logo-patch + (origin + (method url-fetch) + (uri "\ +https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=5edabca9d4cff7f1f2b68f0bac55ef99d9798ba4") + (file-name "linux-libre-CVE-2017-6074.patch") + (sha256 + (base32 + "1x40slfz1qxgiaznyy13bwlh34450pkyyrkljpyjlx6c4mrzb1jj")))))) (define-public linux-libre-arm-generic (make-linux-libre %linux-libre-version From 93d32da9f8bba815b1effe6358904b5e1f9c73ff Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 21 Feb 2017 14:57:02 -0500 Subject: [PATCH 160/436] services: guix: Support using an HTTP proxy. * gnu/services/base.scm ()[http-proxy]: New field. (guix-shepherd-service): Use 'http-proxy' in #:environment-variables. * doc/guix.texi (Base Services)[guix-configuration]: Document it. --- doc/guix.texi | 4 ++++ gnu/services/base.scm | 13 +++++++++---- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 6cdb5e592b..19a31c659a 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8611,6 +8611,10 @@ are written. @item @code{lsof} (default: @var{lsof}) The lsof package to use. +@item @code{http-proxy} (default: @code{#f}) +The HTTP proxy used for downloading fixed-output derivations and +substitutes. + @end table @end deftp diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 57601eab85..0fb7bd721c 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016 Alex Kost ;;; Copyright © 2015, 2016 Mark H Weaver ;;; Copyright © 2015 Sou Bunnbu -;;; Copyright © 2016 Leo Famulari +;;; Copyright © 2016, 2017 Leo Famulari ;;; Copyright © 2016 David Craven ;;; Copyright © 2016 Ricardo Wurmus ;;; @@ -1114,7 +1114,9 @@ failed to register hydra.gnu.org public key: ~a~%" status)))))))) (log-file guix-configuration-log-file ;string (default "/var/log/guix-daemon.log")) (lsof guix-configuration-lsof ; - (default lsof))) + (default lsof)) + (http-proxy guix-http-proxy ;string | #f + (default #f))) (define %default-guix-configuration (guix-configuration)) @@ -1125,7 +1127,7 @@ failed to register hydra.gnu.org public key: ~a~%" status)))))))) (($ guix build-group build-accounts authorize-key? keys use-substitutes? substitute-urls extra-options - log-file lsof) + log-file lsof http-proxy) (list (shepherd-service (documentation "Run the Guix daemon.") (provision '(guix-daemon)) @@ -1142,7 +1144,10 @@ failed to register hydra.gnu.org public key: ~a~%" status)))))))) ;; Add 'lsof' (for the GC) to the daemon's $PATH. #:environment-variables - (list (string-append "PATH=" #$lsof "/bin")) + (list (string-append "PATH=" #$lsof "/bin") + #$@(if http-proxy + (list (string-append "http_proxy=" http-proxy)) + '())) #:log-file #$log-file)) (stop #~(make-kill-destructor))))))) From 937b71dfce3cc203c30cb882095c4c590edd43a3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 23 Feb 2017 13:47:03 +0100 Subject: [PATCH 161/436] gnu: slop: Update to 5.3.21. * gnu/packages/xdisorg.scm (slop): Update to 5.3.21. [arguments]: Specify -std=gnu++11 in #:configure-flags. [inputs]: Drop LIBX11, LIBXRANDR, IMLIB2 and GLEW. Add GLM. --- gnu/packages/xdisorg.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index a1c89a5caa..d94455f834 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) + #:use-module (gnu packages maths) #:use-module (gnu packages m4) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) @@ -437,7 +438,7 @@ of the screen selected by mouse.") (define-public slop (package (name "slop") - (version "4.3.21") + (version "5.3.21") (source (origin (method url-fetch) (uri (string-append @@ -446,15 +447,14 @@ of the screen selected by mouse.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0z0p4a3p5mc6fjh5f8js9ppb0maxyvfxpiw2n6nqc5nim1kv6bim")))) + "0qlyksiaknd40jabra0fv71k4qc4y6dgxihjmmv9a1g4hdmmqklb")))) (build-system cmake-build-system) - (arguments '(#:tests? #f)) ; no "check" target + (arguments + '(#:configure-flags '("-DCMAKE_CXX_FLAGS=-std=gnu++11") + #:tests? #f)) ; no "check" target (inputs - `(("libx11" ,libx11) - ("libxrandr" ,libxrandr) + `(("glm" ,glm) ("libxext" ,libxext) - ("imlib2" ,imlib2) - ("glew" ,glew) ("mesa" ,mesa))) (home-page "https://github.com/naelstrof/slop") (synopsis "Select a region and print its bounds to stdout") From 2b7d10d2db9f5e2dc2afb0d8711ce67e0a63229b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 23 Feb 2017 14:06:19 +0100 Subject: [PATCH 162/436] gnu: maim: Update to 4.4.47. * gnu/packages/xdisorg.scm (maim): Update to 4.4.47. [arguments]: Remove obsolete 'patch-source' phase. [inputs]: Remove LIBX11 and IMLIB2. Add GLM, LIBJPEG-TURBO, LIBPNG, LIBXCOMPOSITE, MESA and ZLIB. --- gnu/packages/xdisorg.scm | 29 +++++++++++------------------ 1 file changed, 11 insertions(+), 18 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index d94455f834..8aa4c38db4 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -469,7 +469,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "3.4.47") + (version "4.4.47") (source (origin (method url-fetch) (uri (string-append @@ -478,27 +478,20 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0kfp7k55bxc5h6h0wv8bwmsc5ny66h9ra2z4dzs4yzszq16544pv")))) + "0bfq2p158b26s913afbh6vvs4mhxs897q9zwb0hhifyx8i85863i")))) (build-system cmake-build-system) (arguments - '(#:tests? #f ; no "check" target - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-source - (lambda* (#:key inputs #:allow-other-keys) - (let ((slop (string-append (assoc-ref inputs "slop") - "/bin/slop"))) - ;; "slop" command is hardcoded in the source; replace it - ;; with the full file name. - (substitute* "src/main.cpp" - (("^( +slopcommand.*)\"slop\"" all front) - (string-append front "\"" slop "\""))))))))) + '(#:tests? #f)) ; no "check" target (inputs - `(("libx11" ,libx11) - ("libxrandr" ,libxrandr) + `(("glm" ,glm) + ("libjpeg" ,libjpeg-turbo) + ("libpng" ,libpng) + ("libxcomposite" ,libxcomposite) ("libxfixes" ,libxfixes) - ("imlib2" ,imlib2) - ("slop" ,slop))) + ("libxrandr" ,libxrandr) + ("mesa" ,mesa) + ("slop" ,slop) + ("zlib" ,zlib))) (home-page "https://github.com/naelstrof/maim") (synopsis "Screenshot utility for X Window System") (description From 94b28aed1e4f151997cb2bc70df20f0eea11ee1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= Date: Wed, 22 Feb 2017 20:51:59 +0100 Subject: [PATCH 163/436] gnu: prosody: Update to 0.9.12. * gnu/packages/messaging.scm (prosody): Update to 0.9.12. [inputs]: Change lua5.1-sec-0.5 to lua5.1-sec. * gnu/packages/lua.scm (lua5.1-sec-0.5): Remove variable. Signed-off-by: Marius Bakke --- gnu/packages/lua.scm | 12 ------------ gnu/packages/messaging.scm | 7 +++---- 2 files changed, 3 insertions(+), 16 deletions(-) diff --git a/gnu/packages/lua.scm b/gnu/packages/lua.scm index 5016732b7a..e3ab3561cb 100644 --- a/gnu/packages/lua.scm +++ b/gnu/packages/lua.scm @@ -283,18 +283,6 @@ communication. It takes an already established TCP connection and creates a secure session between the peers.") (license (package-license lua-5.1)))) -(define-public lua5.1-sec-0.5 - (package - (inherit lua5.1-sec) - (version "0.5.1") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/brunoos/luasec/archive/" - "luasec-" version ".tar.gz")) - (sha256 - (base32 - "01llf5bcrjmqqy6m65avqkajz7h79rvkka6rd131kwr10n75yp3d")))))) - (define-public lua-lgi (package (name "lua-lgi") diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 9345e24263..0ffc031c85 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -495,14 +495,14 @@ end-to-end encryption support; XML console.") (define-public prosody (package (name "prosody") - (version "0.9.10") + (version "0.9.12") (source (origin (method url-fetch) (uri (string-append "https://prosody.im/downloads/source/" "prosody-" version ".tar.gz")) (sha256 (base32 - "0bv6s5c0iizz015hh1lxlwlw1iwvisywajm2rcrbdfyrskzfwdj8")))) + "139yxqpinajl32ryrybvilh54ddb1q6s0ajjhlcs4a0rnwia6n8s")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target @@ -572,8 +572,7 @@ end-to-end encryption support; XML console.") ("lua5.1-expat" ,lua5.1-expat) ("lua5.1-socket" ,lua5.1-socket) ("lua5.1-filesystem" ,lua5.1-filesystem) - ;; See . - ("lua5.1-sec" ,lua5.1-sec-0.5))) + ("lua5.1-sec" ,lua5.1-sec))) (home-page "https://prosody.im/") (synopsis "Jabber (XMPP) server") (description "Prosody is a modern XMPP communication server. It aims to From b191f0a6c50f2a7d47037ef8509d0351f5a2646e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 23 Feb 2017 12:08:02 -0500 Subject: [PATCH 164/436] services: guix: Support building in a directory besides '/tmp'. * gnu/services/base.scm ()[tmpdir]: New field. (guix-shepherd-service): Use 'tmpdir' in #:environment-variables. * doc/guix.texi (Base Services)[guix-configuration]: Document it. --- doc/guix.texi | 3 +++ gnu/services/base.scm | 7 ++++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 19a31c659a..be11096a43 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8615,6 +8615,9 @@ The lsof package to use. The HTTP proxy used for downloading fixed-output derivations and substitutes. +@item @code{tmpdir} (default: @code{#f}) +A directory path where the @command{guix-daemon} will perform builds. + @end table @end deftp diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 0fb7bd721c..7ae815d4b5 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -1116,6 +1116,8 @@ failed to register hydra.gnu.org public key: ~a~%" status)))))))) (lsof guix-configuration-lsof ; (default lsof)) (http-proxy guix-http-proxy ;string | #f + (default #f)) + (tmpdir guix-tmpdir ;string | #f (default #f))) (define %default-guix-configuration @@ -1127,7 +1129,7 @@ failed to register hydra.gnu.org public key: ~a~%" status)))))))) (($ guix build-group build-accounts authorize-key? keys use-substitutes? substitute-urls extra-options - log-file lsof http-proxy) + log-file lsof http-proxy tmpdir) (list (shepherd-service (documentation "Run the Guix daemon.") (provision '(guix-daemon)) @@ -1147,6 +1149,9 @@ failed to register hydra.gnu.org public key: ~a~%" status)))))))) (list (string-append "PATH=" #$lsof "/bin") #$@(if http-proxy (list (string-append "http_proxy=" http-proxy)) + '()) + #$@(if tmpdir + (list (string-append "TMPDIR=" tmpdir)) '())) #:log-file #$log-file)) From 9f05908fb1e3707cae593d94688748294717a546 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 23 Feb 2017 13:48:11 -0500 Subject: [PATCH 165/436] download: Provide a fall-back guile for older daemons. Fixes . * guix/download.scm (in-band-download): Use %bootstrap-guile as a fall-back when using older daemons that do not have a built-in downloader. Written-by: Ricardo Wurmus --- guix/download.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/guix/download.scm b/guix/download.scm index 813f51f489..86f8598812 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -418,7 +418,10 @@ GnuTLS itself and its dependencies. See ." ;; hash of the expected result. #:verify-certificate? #f))))) - (mlet %store-monad ((guile (package->derivation guile system))) + (mlet %store-monad ((guile (package->derivation + (or guile + (@@ (gnu packages bootstrap) %bootstrap-guile)) + system))) (gexp->derivation file-name builder #:guile-for-build guile #:system system From 1c851cbe0c562894bd38c0f9f39d12be306b3e59 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 23 Feb 2017 14:35:00 -0500 Subject: [PATCH 166/436] gnu: shadow: Fix CVE-2017-2616. * gnu/packages/patches/shadow-CVE-2017-2616.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/admin.scm (shadow): Use it. --- gnu/local.mk | 1 + gnu/packages/admin.scm | 3 +- .../patches/shadow-CVE-2017-2616.patch | 72 +++++++++++++++++++ 3 files changed, 75 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/shadow-CVE-2017-2616.patch diff --git a/gnu/local.mk b/gnu/local.mk index ca415ec48f..2954549759 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -901,6 +901,7 @@ dist_patch_DATA = \ %D%/packages/patches/serf-comment-style-fix.patch \ %D%/packages/patches/serf-deflate-buckets-test-fix.patch \ %D%/packages/patches/shadow-4.4-su-snprintf-fix.patch \ + %D%/packages/patches/shadow-CVE-2017-2616.patch \ %D%/packages/patches/slim-session.patch \ %D%/packages/patches/slim-config.patch \ %D%/packages/patches/slim-sigusr1.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index b2207a1205..d9c7ba3b73 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -276,7 +276,8 @@ client and server, a telnet client and server, and an rsh client and server.") (uri (string-append "https://github.com/shadow-maint/shadow/releases/" "download/" version "/shadow-" version ".tar.xz")) - (patches (search-patches "shadow-4.4-su-snprintf-fix.patch")) + (patches (search-patches "shadow-4.4-su-snprintf-fix.patch" + "shadow-CVE-2017-2616.patch")) (sha256 (base32 "0g7hf55ar2pafg5g3ldx0fwzjk36wf4xb21p4ndanbjm3c2a9ab1")))) diff --git a/gnu/packages/patches/shadow-CVE-2017-2616.patch b/gnu/packages/patches/shadow-CVE-2017-2616.patch new file mode 100644 index 0000000000..f88aac40bc --- /dev/null +++ b/gnu/packages/patches/shadow-CVE-2017-2616.patch @@ -0,0 +1,72 @@ +Fix CVE-2017-2616: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-2616 +http://seclists.org/oss-sec/2017/q1/490 +http://seclists.org/oss-sec/2017/q1/474 + +Patch copied from upstream source repository: + +https://github.com/shadow-maint/shadow/commit/08fd4b69e84364677a10e519ccb25b71710ee686 + +From 08fd4b69e84364677a10e519ccb25b71710ee686 Mon Sep 17 00:00:00 2001 +From: Tobias Stoeckmann +Date: Thu, 23 Feb 2017 09:47:29 -0600 +Subject: [PATCH] su: properly clear child PID + +If su is compiled with PAM support, it is possible for any local user +to send SIGKILL to other processes with root privileges. There are +only two conditions. First, the user must be able to perform su with +a successful login. This does NOT have to be the root user, even using +su with the same id is enough, e.g. "su $(whoami)". Second, SIGKILL +can only be sent to processes which were executed after the su process. +It is not possible to send SIGKILL to processes which were already +running. I consider this as a security vulnerability, because I was +able to write a proof of concept which unlocked a screen saver of +another user this way. +--- + src/su.c | 19 +++++++++++++++++-- + 1 file changed, 17 insertions(+), 2 deletions(-) + +diff --git a/src/su.c b/src/su.c +index f20d230..d86aa86 100644 +--- a/src/su.c ++++ b/src/su.c +@@ -379,11 +379,13 @@ static void prepare_pam_close_session (void) + /* wake child when resumed */ + kill (pid, SIGCONT); + stop = false; ++ } else { ++ pid_child = 0; + } + } while (!stop); + } + +- if (0 != caught) { ++ if (0 != caught && 0 != pid_child) { + (void) fputs ("\n", stderr); + (void) fputs (_("Session terminated, terminating shell..."), + stderr); +@@ -393,9 +395,22 @@ static void prepare_pam_close_session (void) + snprintf (wait_msg, sizeof wait_msg, _(" ...waiting for child to terminate.\n")); + + (void) signal (SIGALRM, kill_child); ++ (void) signal (SIGCHLD, catch_signals); + (void) alarm (2); + +- (void) wait (&status); ++ sigemptyset (&ourset); ++ if ((sigaddset (&ourset, SIGALRM) != 0) ++ || (sigprocmask (SIG_BLOCK, &ourset, NULL) != 0)) { ++ fprintf (stderr, _("%s: signal masking malfunction\n"), Prog); ++ kill_child (0); ++ } else { ++ while (0 == waitpid (pid_child, &status, WNOHANG)) { ++ sigsuspend (&ourset); ++ } ++ pid_child = 0; ++ (void) sigprocmask (SIG_UNBLOCK, &ourset, NULL); ++ } ++ + (void) fputs (_(" ...terminated.\n"), stderr); + } + From 1d311009fe34a7b22814cc6a3386375ff9142d51 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 23 Feb 2017 14:49:47 -0500 Subject: [PATCH 167/436] gnu: util-linux: Fix CVE-2017-2616. * gnu/packages/patches/util-linux-CVE-2017-2616.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/linux.scm (util-linux)[replacement]: New field. (util-linux/fixed): New variable. --- gnu/local.mk | 1 + gnu/packages/linux.scm | 12 ++++ .../patches/util-linux-CVE-2017-2616.patch | 65 +++++++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 gnu/packages/patches/util-linux-CVE-2017-2616.patch diff --git a/gnu/local.mk b/gnu/local.mk index 2954549759..515b154b9a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -953,6 +953,7 @@ dist_patch_DATA = \ %D%/packages/patches/unzip-overflow-long-fsize.patch \ %D%/packages/patches/unzip-remove-build-date.patch \ %D%/packages/patches/util-linux-tests.patch \ + %D%/packages/patches/util-linux-CVE-2017-2616.patch \ %D%/packages/patches/upower-builddir.patch \ %D%/packages/patches/valgrind-enable-arm.patch \ %D%/packages/patches/vdirsyncer-test-suite-slow-machines.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a6c564b275..304c9f0512 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -495,6 +495,7 @@ providing the system administrator with some help in common tasks.") (define-public util-linux (package (name "util-linux") + (replacement util-linux/fixed) (version "2.28.1") (source (origin (method url-fetch) @@ -575,6 +576,17 @@ block devices, UUIDs, TTYs, and many other tools.") (license (list license:gpl3+ license:gpl2+ license:gpl2 license:lgpl2.0+ license:bsd-4 license:public-domain)))) +(define util-linux/fixed + (package + (inherit util-linux) + (source + (origin + (inherit (package-source util-linux)) + (patches + (append + (origin-patches (package-source util-linux)) + (search-patches "util-linux-CVE-2017-2616.patch"))))))) + (define-public procps (package (name "procps") diff --git a/gnu/packages/patches/util-linux-CVE-2017-2616.patch b/gnu/packages/patches/util-linux-CVE-2017-2616.patch new file mode 100644 index 0000000000..2c82fb06d2 --- /dev/null +++ b/gnu/packages/patches/util-linux-CVE-2017-2616.patch @@ -0,0 +1,65 @@ +Fix CVE-2017-2616: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-2616 +http://seclists.org/oss-sec/2017/q1/474 + +Patch copied from upstream source repository: + +https://git.kernel.org/cgit/utils/util-linux/util-linux.git/commit/?id=dffab154d29a288aa171ff50263ecc8f2e14a891 + +From b018571132cb8c9fece3d75ed240cc74cdb5f0f7 Mon Sep 17 00:00:00 2001 +From: Karel Zak +Date: Wed, 1 Feb 2017 11:58:09 +0100 +Subject: [PATCH] su: properly clear child PID +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Reported-by: Tobias Stöckmann +Signed-off-by: Karel Zak +--- + login-utils/su-common.c | 14 ++++++++++---- + 1 file changed, 10 insertions(+), 4 deletions(-) + +diff --git a/login-utils/su-common.c b/login-utils/su-common.c +index 0ea4e40bd..b1720f037 100644 +--- a/login-utils/su-common.c ++++ b/login-utils/su-common.c +@@ -376,6 +376,9 @@ create_watching_parent (void) + } + else + status = WEXITSTATUS (status); ++ ++ /* child is gone, don't use the PID anymore */ ++ child = (pid_t) -1; + } + else if (caught_signal) + status = caught_signal + 128; +@@ -385,7 +388,7 @@ create_watching_parent (void) + else + status = 1; + +- if (caught_signal) ++ if (caught_signal && child != (pid_t)-1) + { + fprintf (stderr, _("\nSession terminated, killing shell...")); + kill (child, SIGTERM); +@@ -395,9 +398,12 @@ create_watching_parent (void) + + if (caught_signal) + { +- sleep (2); +- kill (child, SIGKILL); +- fprintf (stderr, _(" ...killed.\n")); ++ if (child != (pid_t)-1) ++ { ++ sleep (2); ++ kill (child, SIGKILL); ++ fprintf (stderr, _(" ...killed.\n")); ++ } + + /* Let's terminate itself with the received signal. + * +-- +2.11.1 + From a20b084a0437e6832e3fbee58b23a789e510654c Mon Sep 17 00:00:00 2001 From: John Darrington Date: Wed, 22 Feb 2017 20:13:15 +0100 Subject: [PATCH 168/436] gnu: Add gnushogi and xshogi * gnu/packages/games.scm (gnushogi, xshogi): New variables. --- gnu/packages/games.scm | 43 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 1d6a12a0f6..50315a6085 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -175,6 +175,49 @@ You may even apply photos to the faces instead of colors. The game is scriptable with Guile.") (license license:gpl3+))) +(define-public gnushogi + (package + (name "gnushogi") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://gnu/gnushogi/gnushogi-" + version ".tar.gz")) + (sha256 + (base32 + "0a9bsl2nbnb138lq0h14jfc5xvz7hpb2bcsj4mjn6g1hcsl4ik0y")))) + (arguments `(#:tests? #f)) ;; No check target. + (build-system gnu-build-system) + (home-page "http://www.gnu.org/software/gnushogi/") + (synopsis "The game of Shogi (Japanese chess)") + (description "GNU Shogi is a program that plays the game Shogi (Japanese +Chess). It is similar to standard chess but this variant is far more complicated.") + (license license:gpl3+))) + +(define-public xshogi + (package + (name "xshogi") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://gnu/gnushogi/xshogi-" + version ".tar.gz")) + (sha256 + (base32 + "1dns0nhymak44by18sv48m4xb2skiwbi2i3nb9hl6w9iwd2i2brf")))) + (build-system gnu-build-system) + (inputs + `(("libxaw" ,libxaw) + ("libxt" ,libxt))) + (home-page "http://www.gnu.org/software/gnushogi/") + (synopsis "User interface for @code{gnushogi}") + (description "A graphical user interface for the package @code{gnushogi}.") + ;; Contains a copy of GPLv3 but the licence notices simply + ;; state "GNU General Public Licence" without specifying a version. + (license license:gpl1+))) + (define-public abbaye (package (name "abbaye") From 533372319e4996a9d899650c9fbe703a570c35e4 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 23 Feb 2017 17:33:32 -0500 Subject: [PATCH 169/436] gnu: lightweight-desktop.tmpl: Complete i3-wm. * gnu/system/examples/lightweight-desktop.tmpl (packages): Add i3status and dmenu. (use-package-modules): Add suckless. --- gnu/system/examples/lightweight-desktop.tmpl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/system/examples/lightweight-desktop.tmpl b/gnu/system/examples/lightweight-desktop.tmpl index 131c43af77..7ecf5fde97 100644 --- a/gnu/system/examples/lightweight-desktop.tmpl +++ b/gnu/system/examples/lightweight-desktop.tmpl @@ -4,7 +4,7 @@ (use-modules (gnu) (gnu system nss)) (use-service-modules desktop) -(use-package-modules wm ratpoison certs) +(use-package-modules wm ratpoison certs suckless) (operating-system (host-name "antelope") @@ -33,8 +33,8 @@ ;; Add a bunch of window managers; we can choose one at ;; the log-in screen with F1. - (packages (cons* ratpoison i3-wm xmonad ;window managers - nss-certs ;for HTTPS access + (packages (cons* ratpoison i3-wm i3status dmenu xmonad ;window managers + nss-certs ;for HTTPS access %base-packages)) ;; Use the "desktop" services, which include the X11 From 0d7feebb622b0cf54ab435f308df347008d945b3 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 23 Feb 2017 17:42:44 -0500 Subject: [PATCH 170/436] gnu: lightweight-desktop.tmpl: Remove xmonad. * gnu/system/examples/lightweight-desktop.tmpl (packages): Remove xmonad. --- gnu/system/examples/lightweight-desktop.tmpl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/system/examples/lightweight-desktop.tmpl b/gnu/system/examples/lightweight-desktop.tmpl index 7ecf5fde97..389ec8574b 100644 --- a/gnu/system/examples/lightweight-desktop.tmpl +++ b/gnu/system/examples/lightweight-desktop.tmpl @@ -33,8 +33,8 @@ ;; Add a bunch of window managers; we can choose one at ;; the log-in screen with F1. - (packages (cons* ratpoison i3-wm i3status dmenu xmonad ;window managers - nss-certs ;for HTTPS access + (packages (cons* ratpoison i3-wm i3status dmenu ;window managers + nss-certs ;for HTTPS access %base-packages)) ;; Use the "desktop" services, which include the X11 From 398433dc96edd7d3c39a5c6d00d09838e420659f Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 24 Feb 2017 00:48:11 -0500 Subject: [PATCH 171/436] gnu: linux-libre@4.4: Update to 4.4.51. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.51. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 304c9f0512..b7be62d6e6 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -364,8 +364,8 @@ https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=5edabc "1x40slfz1qxgiaznyy13bwlh34450pkyyrkljpyjlx6c4mrzb1jj")))))) (define-public linux-libre-4.4 - (make-linux-libre "4.4.50" - "0c157kk0vgrb1fsyy4q3czqdg4npgql82n6p303afy8ylh2w6d3l" + (make-linux-libre "4.4.51" + "13iahlhpqmy880nq2zljc6j6zmr2axlayabaqp3firs6brnnmr9r" %intel-compatible-systems #:configuration-file kernel-config #:patches From 5fb34141cc8f037d3dff256f1c950903c1256b9a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 24 Feb 2017 00:49:26 -0500 Subject: [PATCH 172/436] gnu: linux-libre@4.9: Update to 4.9.12. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.12. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b7be62d6e6..bd109dbbdb 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -348,8 +348,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.11" - "1gypfg2984zr4z7hihnl3bbpxnk1mrqbynb6xd8ad2v2z04aw13q" + (make-linux-libre "4.9.12" + "0yl4khibxb2aiqm479y5ywwlzi5s3rrcqsg4zgn7wpshncb4l1ar" %intel-compatible-systems #:configuration-file kernel-config #:patches From 4fb9c83c544df07d7673495d58a941a87c632f6b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 11:16:38 +0100 Subject: [PATCH 173/436] gnu: graphicsmagick: Update to 1.3.25-2.6156b4c [security fixes]. * gnu/packages/imagemagick.scm (graphicsmagick): Update to 1.3.25-2.6156b4c. --- gnu/packages/imagemagick.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index 8918b658f2..b5a2c20655 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -162,11 +162,12 @@ script.") (license (package-license imagemagick)))) (define-public graphicsmagick - (let ((changeset "56c8cae") ; 3e01b - (revision "1")) + (let ((changeset "6156b4c2992d855ece6079653b3b93c3229fc4b8") + (revision "2")) (package (name "graphicsmagick") - (version (string-append "1.3.25-" revision "." changeset)) + (version (string-append "1.3.25-" revision "." + (string-take changeset 7))) (source (origin (method hg-fetch) (uri (hg-reference @@ -179,7 +180,7 @@ script.") ;; "/GraphicsMagick-" version ".tar.xz")) (sha256 (base32 - "1s9apvkn0kxr6i4i5wlkfw1prja02rgk689n3cf822zc0dkycxdh")))) + "08yfsn8mrqkwpax43vv1crfr55rcf004wwpzsinr5c6m0asqr08b")))) (build-system gnu-build-system) (arguments `(#:configure-flags From e1c014d7f3cc22a40917a112e9a5203a5c67a4ea Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 11:19:18 +0100 Subject: [PATCH 174/436] gnu: slop: Update to 5.3.27. * gnu/packages/xdisorg.scm (slop): Update to 5.3.27. [arguments]: Remove #:configure-flags. [inputs]: Add LIBXRENDER. --- gnu/packages/xdisorg.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 8aa4c38db4..672902e0be 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -438,7 +438,7 @@ of the screen selected by mouse.") (define-public slop (package (name "slop") - (version "5.3.21") + (version "5.3.27") (source (origin (method url-fetch) (uri (string-append @@ -447,14 +447,14 @@ of the screen selected by mouse.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0qlyksiaknd40jabra0fv71k4qc4y6dgxihjmmv9a1g4hdmmqklb")))) + "0yid1qd5l0g22cmm3mmmbg639404i7069nw5g843llb5yfc54bs0")))) (build-system cmake-build-system) (arguments - '(#:configure-flags '("-DCMAKE_CXX_FLAGS=-std=gnu++11") - #:tests? #f)) ; no "check" target + '(#:tests? #f)) ; no "check" target (inputs `(("glm" ,glm) ("libxext" ,libxext) + ("libxrender" ,libxrender) ("mesa" ,mesa))) (home-page "https://github.com/naelstrof/slop") (synopsis "Select a region and print its bounds to stdout") From 2c8b6b4f842a239c68d43f0694126bf9c3c4d24f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 11:20:22 +0100 Subject: [PATCH 175/436] gnu: maim: Update to 4.4.49. * gnu/packages/xdisorg.scm (maim): Update to 4.4.49. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 672902e0be..c34884291b 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -469,7 +469,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "4.4.47") + (version "4.4.49") (source (origin (method url-fetch) (uri (string-append @@ -478,7 +478,7 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0bfq2p158b26s913afbh6vvs4mhxs897q9zwb0hhifyx8i85863i")))) + "0cflwipjsqy1i9anviwb1zlrsyrdmhm879grc9br8wbwg4rkqnpw")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From 630bc4fc07c6bc9dbf74169eec6d05963a086d1a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 11:23:58 +0100 Subject: [PATCH 176/436] gnu: rocksdb: Update to 5.1.3. * gnu/packages/databases.scm (rocksdb): Update to 5.1.3. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index fd8baa1531..9369ec032e 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -516,7 +516,7 @@ types are supported, as is encryption.") (define-public rocksdb (package (name "rocksdb") - (version "5.1.2") + (version "5.1.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/facebook/rocksdb" @@ -524,7 +524,7 @@ types are supported, as is encryption.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1qdbs13al7g45xc2j44wzx0ywrg32q1gsdhk5j6j4952xg91rfmh")) + "0fz2ks6nxp3m9ys0ci53rg091wafbzbbynsfaq1y8v1rb3195gs8")) (modules '((guix build utils))) (snippet '(begin From 6b08982d4a07e8ed9449e2927cf014c5f419f75c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Feb 2017 13:09:45 +0100 Subject: [PATCH 177/436] gnu: gparted: Update to 0.28.1. * gnu/packages/disk.scm (gparted): Update to 0.28.1. --- gnu/packages/disk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index ec9632faca..93895278d6 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -302,14 +302,14 @@ and can dramatically shorten the lifespan of the drive if left unchecked.") (define-public gparted (package (name "gparted") - (version "0.28.0") + (version "0.28.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gparted/gparted/gparted-" version "/gparted-" version ".tar.gz")) (sha256 - (base32 "1w9xsph6fpr7l96b3bxl1bgs94cfp9iisg694h8w3fahihwldzdr")))) + (base32 "0cyk8lpimm6wani8khw0szwqkgw5wpq2mfnfxkbgfm2774a1z2bn")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; Tests require a network connection. From 588edb9c0140d907f9e0993cc1685653913f2700 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 23 Feb 2017 02:30:21 +0100 Subject: [PATCH 178/436] gnu: youtube-dl: Update to 2017.02.22. * gnu/packages/video.scm (youtube-dl): Update to 2017.02.22. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 985ff6c691..aee24b0f40 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -975,7 +975,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2017.02.16") + (version "2017.02.22") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -983,7 +983,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "1c2rx8hj960wg2sffpvg2513rl9grkwcpn4xk612ibfq4m7h3991")))) + "0abir0039igwz0830vdqknngs3hmr474j6xzh33v57p3y4imgx2i")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion From b53e4cbd2ce6a3046f51df3126818ad004d0e682 Mon Sep 17 00:00:00 2001 From: ng0 Date: Fri, 24 Feb 2017 15:14:36 +0000 Subject: [PATCH 179/436] gnu: gnurl: Update to 7.53.1. * gnu/packages/gnunet.scm (gnurl): Update to 7.53.1. (source)[uri]: Update to new upstream filename. Signed-off-by: Kei Kebreau --- gnu/packages/gnunet.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index a4514a7f41..bcd4675813 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -184,16 +184,14 @@ and support for SSL3 and TLS.") (define-public gnurl (package (name "gnurl") - (version "7.52.1") + (version "7.53.1") (source (origin (method url-fetch) - (uri (let ((version-with-underscores - (string-join (string-split version #\.) "_"))) - (string-append "https://gnunet.org/sites/default/files/" - name "-" version-with-underscores ".tar.bz2"))) + (uri (string-append "https://gnunet.org/sites/default/files/" + name "-" version ".tar.bz2")) (sha256 (base32 - "1gn6mvab2vhfj9637ykg1zjzb23fngfnyd24wlgxmjhf49pn334h")))) + "1ah2304cm6y7d201vdph170mrwxmg6r72v2zsxzjn0jk68d8kb6d")))) (build-system gnu-build-system) (outputs '("out" "doc")) ; 1.5 MiB of man3 pages From 42945fb58c4652943a036c99f9bcc59fab61909b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 18:24:06 +0100 Subject: [PATCH 180/436] gnu: python-fake-factory: Fix build on 32bit. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-fake-factory, python2-fake-factory)[source]: Use it. --- gnu/local.mk | 1 + .../python-fake-factory-fix-build-32bit.patch | 36 +++++++++++++++++++ gnu/packages/python.scm | 5 ++- 3 files changed, 41 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-fake-factory-fix-build-32bit.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0b9b5b1a1e..63eb56cc51 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -859,6 +859,7 @@ dist_patch_DATA = \ %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \ %D%/packages/patches/python-statsmodels-fix-tests.patch \ %D%/packages/patches/python-configobj-setuptools.patch \ + %D%/packages/patches/python-fake-factory-fix-build-32bit.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ %D%/packages/patches/python-pygit2-disable-network-tests.patch \ diff --git a/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch b/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch new file mode 100644 index 0000000000..cb60896fad --- /dev/null +++ b/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch @@ -0,0 +1,36 @@ +These tests fail on 32-bit due to an overflow. + +Upstream bug URL: https://github.com/joke2k/faker/issues/408 + +diff --git a/faker/tests/__init__.py b/faker/tests/__init__.py +index 6026772..58b6b83 100644 +--- a/faker/tests/__init__.py ++++ b/faker/tests/__init__.py +@@ -384,7 +384,6 @@ class FactoryTestCase(unittest.TestCase): + provider = Provider + # test century + self.assertTrue(self._datetime_to_time(provider.date_time_this_century(after_now=False)) <= self._datetime_to_time(datetime.datetime.now())) +- self.assertTrue(self._datetime_to_time(provider.date_time_this_century(before_now=False, after_now=True)) >= self._datetime_to_time(datetime.datetime.now())) + # test decade + self.assertTrue(self._datetime_to_time(provider.date_time_this_decade(after_now=False)) <= self._datetime_to_time(datetime.datetime.now())) + self.assertTrue(self._datetime_to_time(provider.date_time_this_decade(before_now=False, after_now=True)) >= self._datetime_to_time(datetime.datetime.now())) +@@ -413,8 +412,6 @@ class FactoryTestCase(unittest.TestCase): + + # ensure all methods provide timezone aware datetimes + with self.assertRaises(TypeError): +- provider.date_time_this_century(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now() +- with self.assertRaises(TypeError): + provider.date_time_this_decade(after_now=False, tzinfo=utc) <= datetime.datetime.now() + with self.assertRaises(TypeError): + provider.date_time_this_year(after_now=False, tzinfo=utc) <= datetime.datetime.now() +@@ -423,7 +420,6 @@ class FactoryTestCase(unittest.TestCase): + + # test century + self.assertTrue(provider.date_time_this_century(after_now=False, tzinfo=utc) <= datetime.datetime.now(utc)) +- self.assertTrue(provider.date_time_this_century(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now(utc)) + # test decade + self.assertTrue(provider.date_time_this_decade(after_now=False, tzinfo=utc) <= datetime.datetime.now(utc)) + self.assertTrue(provider.date_time_this_decade(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now(utc)) +-- +2.11.1 + diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8353ca178f..e26e442e58 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11228,7 +11228,10 @@ parsing UK postcodes.") (uri (pypi-uri "fake-factory" version)) (sha256 (base32 - "0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g")))) + "0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g")) + (patches + (search-patches + "python-fake-factory-fix-build-32bit.patch")))) (build-system python-build-system) (arguments '(#:phases From cf46d0715096da47535815519e2d711e631e8fd7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 14:32:37 +0100 Subject: [PATCH 181/436] gnu: fio: Update to 2.18. * gnu/packages/benchmark.scm (fio): Update to 2.18. [arguments]: Enable tests. --- gnu/packages/benchmark.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index acaeb67079..ff5715d578 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -29,7 +29,7 @@ (define-public fio (package (name "fio") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) (uri (string-append @@ -37,10 +37,10 @@ "fio-" version ".tar.bz2")) (sha256 (base32 - "1kxgad5k2m7y637g3kq8jmhwzlg3c64w9ky7066c5l09bwb6l58h")))) + "08kx2mh556xby9saayrbynwrkmh4v8wwrw759nbv025ch3xbw79n")))) (build-system gnu-build-system) (arguments - '(#:tests? #f ; No tests. + '(#:test-target "test" #:phases (modify-phases %standard-phases (add-after From 3b86a385dbf99d70c61df0b848718862eb69cac6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 19:17:26 +0100 Subject: [PATCH 182/436] gnu: python-passlib: Update to 1.7.1. * gnu/packages/python.scm (python-passlib, python2-passlib): Update to 1.7.1. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 432298472a..232f3426ac 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -458,14 +458,14 @@ pidof, tty, taskset, pmap.") (define-public python-passlib (package (name "python-passlib") - (version "1.7.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (pypi-uri "passlib" version)) (sha256 (base32 - "1vdbqsa1a31s98fxkinl052q8nnpvbxnb83qanxfpi2p6c2zdr0b")))) + "1q2khqpj9rlcgdmkypjdq1kswvhjf72bq0zk2cv669cc2dj8z51x")))) (build-system python-build-system) (native-inputs `(("python-nose" ,python-nose))) From ec867b86a0575d049922e074312b36dfb9d71868 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:27:47 +0100 Subject: [PATCH 183/436] gnu: python2-oslotest: Disable tests. * gnu/packages/openstack.scm(python2-oslotest)[arguments]: New field. (python-oslotest)[properties]: Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 381480b786..8130097c83 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -662,10 +662,16 @@ from the OpenStack project.") (description "The Oslo Test framework provides common fixtures, support for debugging, and better support for mocking results.") + (properties `((python2-variant . ,(delay python2-oslotest)))) (license asl2.0))) (define-public python2-oslotest - (package-with-python2 python-oslotest)) + (package (inherit (package-with-python2 + (strip-python2-variant python-oslotest))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-oslo.utils (package From dc6bedbacadf7d0c9871fe3b22415d12ea266f74 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:45:46 +0100 Subject: [PATCH 184/436] gnu: python2-requests-mock: Disable tests. * gnu/packages/openstack.scm (python2-requests-mock)[arguments]: New field. (python-requests-mock): Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 8130097c83..d41c9c8916 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -271,10 +271,16 @@ tested on Python version 3.2, 2.7 and 2.6.") (description "This module provides a building block to stub out the HTTP requests portions of your testing code.") + (properties `((python2-variant . ,(delay python2-requests-mock)))) (license asl2.0))) (define-public python2-requests-mock - (package-with-python2 python-requests-mock)) + (package (inherit (package-with-python2 + (strip-python2-variant python-requests-mock))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-stevedore (package From 11a8767b9482f8ff6e89b3ab782b28400e2126d5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:48:11 +0100 Subject: [PATCH 185/436] gnu: python2-stevedore: Disable tests. * gnu/packages/openstack.scm (python2-stevedore)[arguments]: New field. (python-stevedore)[properties]: New field. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index d41c9c8916..f6a399aa2f 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -317,10 +317,16 @@ mechanism by building on top of setuptools entry points. The code for managing entry points tends to be repetitive, though, so stevedore provides manager classes for implementing common patterns for using dynamically loaded extensions.") + (properties `((python2-variant . ,(delay python2-stevedore)))) (license asl2.0))) (define-public python2-stevedore - (package-with-python2 python-stevedore)) + (package (inherit (package-with-python2 + (strip-python2-variant python-stevedore))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-tempest-lib (package From 041b5932dad0944079118ec97dd0d2317ba1f802 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:51:39 +0100 Subject: [PATCH 186/436] gnu: python2-bandit: Disable tests. * gnu/packages/openstack.scm (python2-bandit)[arguments]: New field. (python-bandit)[properties]: Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index f6a399aa2f..632534fb3c 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -65,10 +65,16 @@ To do this Bandit processes each file, builds an AST from it, and runs appropriate plugins against the AST nodes. Once Bandit has finished scanning all the files it generates a report.") + (properties `((python2-variant . ,(delay python2-bandit)))) (license asl2.0))) (define-public python2-bandit - (package-with-python2 python-bandit)) + (package (inherit (package-with-python2 + (strip-python2-variant python-bandit))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-debtcollector (package From e1f2e190471ae87bc51f8e9539f4bfbe9f69caa0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:56:06 +0100 Subject: [PATCH 187/436] gnu: python2-swiftclient: Disable tests. * gnu/packages/openstack.scm (python2-swiftclient)[arguments]: New field. --- gnu/packages/openstack.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 632534fb3c..cdd37815de 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -860,6 +860,10 @@ permanence.") (define-public python2-swiftclient (let ((swiftclient (package-with-python2 python-swiftclient))) (package (inherit swiftclient) + (arguments + `(#:python ,python-2 + ;; FIXME: subunit.run discover: error: no such option: --list + #:tests? #f)) (propagated-inputs `(("python2-futures" ,python2-futures) ("python2-requests" ,python2-requests) From 154d0016b5b980c6cc0dfb1e4b80405fb6474191 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 21:25:28 +0100 Subject: [PATCH 188/436] Revert "gnu: python2-fastlmm: Update to 0.2.26." This reverts commit 594358f5b6948095dad7a638241cdb2b80a2d293. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 232f3426ac..c295c42f31 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3366,14 +3366,14 @@ objects.") (define-public python2-fastlmm (package (name "python2-fastlmm") - (version "0.2.26") + (version "0.2.21") (source (origin (method url-fetch) (uri (pypi-uri "fastlmm" version ".zip")) (sha256 (base32 - "0yxrx9xzai4fyrsi7c2p31kxvpq9czmv1p0wax5ic07m6izbszxg")))) + "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m")))) (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2.7 is supported From d6caebc4d63ac8e7ae5e82b1261557e1b6898c10 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 21:30:22 +0100 Subject: [PATCH 189/436] gnu: python2-reno: Disable tests. * gnu/packages/openstack.scm (python2-reno)[arguments]: New field. (python-reno)[properties]: Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index cdd37815de..51566b65e3 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -605,10 +605,16 @@ in transmittable and storable formats, such as JSON and MessagePack.") (synopsis "Release notes manager") (description "Reno is a tool for storing release notes in a git repository and building documentation from them.") + (properties `((python2-variant . ,(delay python2-reno)))) (license asl2.0))) (define-public python2-reno - (package-with-python2 python-reno)) + (package (inherit (package-with-python2 + (strip-python2-variant python-reno))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-oslosphinx (package From 86baa4ce8d3eef8bed0e728976ac99f513a18974 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 22:35:10 +0100 Subject: [PATCH 190/436] gnu: git: Update to 2.12.0. * gnu/packages/version-control.scm (git): Update to 2.12.0. --- gnu/packages/version-control.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 5c371b0ba0..7e2700beba 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -112,14 +112,14 @@ as well as the classic centralized workflow.") (define-public git (package (name "git") - (version "2.11.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/software/scm/git/git-" version ".tar.xz")) (sha256 (base32 - "05b4jw86w77c3pyh3nm6aw31vhxwzvhnx2x0bcfqmm15wg57k9y0")))) + "09r0lcjj5v2apj39f0ziqzjq2bi1jpnhszc9q4n0ab86g5j7c88q")))) (build-system gnu-build-system) (native-inputs `(("native-perl" ,perl) @@ -132,7 +132,7 @@ as well as the classic centralized workflow.") version ".tar.xz")) (sha256 (base32 - "0cfa3c2r7d86ksswxdl0jqdka9mai3446gg8380921gf779nwj39")))))) + "0ws7h04ijqr2l0pp9qbds65v9cd70v0qfpnhqncn9zqfspw5d0wb")))))) (inputs `(("curl" ,curl) ("expat" ,expat) From 1885bb0c08e943a2e0e37c5c0a83473c8af904d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 21 Feb 2017 18:28:21 +0100 Subject: [PATCH 191/436] gnu: python-dendropy: Fix failing tests. * gnu/packages/patches/python-dendropy-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 3 +- .../patches/python-dendropy-fix-tests.patch | 41 +++++++++++++++++++ 3 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-dendropy-fix-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 63eb56cc51..899dc06b8e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -853,6 +853,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-3-search-paths.patch \ %D%/packages/patches/python-3.4-fix-tests.patch \ %D%/packages/patches/python-3.5-fix-tests.patch \ + %D%/packages/patches/python-dendropy-fix-tests.patch \ %D%/packages/patches/python-file-double-encoding-bug.patch \ %D%/packages/patches/python-fix-tests.patch \ %D%/packages/patches/python-parse-too-many-fields.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a1738b936..de6186de27 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1981,7 +1981,8 @@ accessing bigWig files.") (uri (pypi-uri "DendroPy" version)) (sha256 (base32 - "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")))) + "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) + (patches (search-patches "python-dendropy-fix-tests.patch")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") diff --git a/gnu/packages/patches/python-dendropy-fix-tests.patch b/gnu/packages/patches/python-dendropy-fix-tests.patch new file mode 100644 index 0000000000..30ab618ff1 --- /dev/null +++ b/gnu/packages/patches/python-dendropy-fix-tests.patch @@ -0,0 +1,41 @@ +This patch fixes two test failures. It was downloaded from: +https://github.com/jeetsukumaran/DendroPy/commit/93f984bba7a6c588a28ca87f4e557ce283809453 + +From 93f984bba7a6c588a28ca87f4e557ce283809453 Mon Sep 17 00:00:00 2001 +From: jeetsukumaran +Date: Tue, 21 Feb 2017 16:41:01 -0500 +Subject: [PATCH] Update to Python 3 container and iteration semantics + +--- + dendropy/dataio/newickreader.py | 3 ++- + dendropy/datamodel/treemodel.py | 3 +++ + 2 files changed, 5 insertions(+), 1 deletion(-) + +diff --git a/dendropy/dataio/newickreader.py b/dendropy/dataio/newickreader.py +index 6dcf3c5..f978729 100644 +--- a/dendropy/dataio/newickreader.py ++++ b/dendropy/dataio/newickreader.py +@@ -303,7 +303,8 @@ def tree_iter(self, + taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol) + yield tree + if tree is None: +- raise StopIteration ++ # raise StopIteration ++ return + + def _read(self, + stream, +diff --git a/dendropy/datamodel/treemodel.py b/dendropy/datamodel/treemodel.py +index 0ecfe31..73146f0 100644 +--- a/dendropy/datamodel/treemodel.py ++++ b/dendropy/datamodel/treemodel.py +@@ -772,6 +772,9 @@ def __hash__(self): + def __eq__(self, other): + return self is other + ++ def __lt__(self, other): ++ return id(self) < id(other) ++ + ########################################################################### + ### Basic Structure + From 219369ce0f4b4dba534849507d4a16ddc0dd76d6 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 25 Feb 2017 08:03:15 +0100 Subject: [PATCH 192/436] gnu: ldc: Update to 1.1.1. * gnu/packages/ldc.scm (ldc): Update to 1.1.1. --- gnu/packages/ldc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ldc.scm b/gnu/packages/ldc.scm index b7f593712b..d1ac4cff62 100644 --- a/gnu/packages/ldc.scm +++ b/gnu/packages/ldc.scm @@ -181,7 +181,7 @@ latest DMD frontend and uses LLVM as backend.") (package (inherit ldc-bootstrap) (name "ldc") - (version "1.1.0") + (version "1.1.1") ;; Beta version needed to compile various scientific tools that require ;; the newer beta versions, and won't compile successfully with the ;; older stable version. @@ -193,7 +193,7 @@ latest DMD frontend and uses LLVM as backend.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "10zkrmx9bcmhfxvgykm3fkjamzc8js96wm032bv0fyil5c9ja2y1")))) + "0yjiwg8pnlm2286bwdkwasaqw6ys7lymrqvhh5xyb1adha1ndcav")))) (arguments `(#:phases (modify-phases %standard-phases From bcd2fddd6a8e4ddaad960d3429b4ddae826ed4d5 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 25 Feb 2017 08:33:26 +0100 Subject: [PATCH 193/436] gnu: ldc-bootstrap: Update to 0.17.3. * gnu/packages/ldc.scm (ldc-bootstrap): Update to 0.17.3. --- gnu/packages/ldc.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/ldc.scm b/gnu/packages/ldc.scm index d1ac4cff62..614e2d6d0c 100644 --- a/gnu/packages/ldc.scm +++ b/gnu/packages/ldc.scm @@ -77,7 +77,7 @@ and freshness without requiring additional information from the user.") (define-public ldc-bootstrap (package (name "ldc") - (version "0.17.2") + (version "0.17.3") (source (origin (method url-fetch) (uri (string-append @@ -86,7 +86,7 @@ and freshness without requiring additional information from the user.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0iksl6cvhsiwnlh15b7s9v8f3grxk27jn0vja9n4sad7fvfwmmlc")))) + "135rgwwk82ccqp4n3fhqz4696jmvip90fg5ql2kccq5h1r71gb82")))) (build-system cmake-build-system) (supported-systems '("x86_64-linux" "i686-linux" "armhf-linux")) (arguments @@ -140,7 +140,7 @@ and freshness without requiring additional information from the user.") version ".tar.gz")) (sha256 (base32 - "07hh3ic3r755mq9hn9gfr0wlc5y8cr91xz2ydb6gqy4zy8jgp5s9")) + "0qywnvnp019mmmr74aw90ir9f03iz0hc7cgzna609agsar0b27jl")) (patches (search-patches "ldc-disable-tests.patch")))) ("druntime-src" ,(origin @@ -150,7 +150,7 @@ and freshness without requiring additional information from the user.") version ".tar.gz")) (sha256 (base32 - "1m1dhday9dl3s04njmd29z7ism2xn2ksb9qlrwzykdgz27b3dk6x")))) + "0z418n6x2fxac07sxpi4rl69069qiym4w6r9sjppn91q58qh8hjs")))) ("dmd-testsuite-src" ,(origin (method url-fetch) @@ -159,7 +159,7 @@ and freshness without requiring additional information from the user.") version ".tar.gz")) (sha256 (base32 - "0n7gvalxwfmia4gag53r9qhcnk2cqrw3n4icj1yri0zkgc27pm60")))))) + "196mkfax5y3yqm3gz7jhqhnkjwrvr2m4a8nc9k41l0511ldzsk9x")))))) (home-page "http://wiki.dlang.org/LDC") (synopsis "LLVM compiler for the D programming language") (description From 472bf038575fce0cf83584b3433aa4b4d9a383f1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 11:56:29 +0100 Subject: [PATCH 194/436] gnu: slop: Update to 5.3.28. * gnu/packages/xdisorg.scm (slop): Update to 5.3.28. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index c34884291b..01e9f5aa13 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -438,7 +438,7 @@ of the screen selected by mouse.") (define-public slop (package (name "slop") - (version "5.3.27") + (version "5.3.28") (source (origin (method url-fetch) (uri (string-append @@ -447,7 +447,7 @@ of the screen selected by mouse.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0yid1qd5l0g22cmm3mmmbg639404i7069nw5g843llb5yfc54bs0")))) + "01k39wb1w367zbnl3ni76n3xcmcyvjf14jvk09cd409mvhwyl0p4")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From 988a5cb11eaa6fad2389e1e3ddb490b4032b1e46 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 11:57:36 +0100 Subject: [PATCH 195/436] gnu: maim: Update to 4.4.50. * gnu/packages/xdisorg.scm (maim): Update to 4.4.50. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 01e9f5aa13..b5f3dc6473 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -469,7 +469,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "4.4.49") + (version "4.4.50") (source (origin (method url-fetch) (uri (string-append @@ -478,7 +478,7 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0cflwipjsqy1i9anviwb1zlrsyrdmhm879grc9br8wbwg4rkqnpw")))) + "0lr11x77981jzx53z1zd48d8ss5swhcg3sxy8naz6945wc9i3mh8")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From b9fb6b8a24b930e0d28318a6074aee68208f7d72 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 11:58:59 +0100 Subject: [PATCH 196/436] gnu: rocksdb: Update to 5.1.4. * gnu/packages/databases.scm (rocksdb): Update to 5.1.4. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 9369ec032e..b7ce8a8bec 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -516,7 +516,7 @@ types are supported, as is encryption.") (define-public rocksdb (package (name "rocksdb") - (version "5.1.3") + (version "5.1.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/facebook/rocksdb" @@ -524,7 +524,7 @@ types are supported, as is encryption.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0fz2ks6nxp3m9ys0ci53rg091wafbzbbynsfaq1y8v1rb3195gs8")) + "0ddyj8lh5jk6vx675pdg4jhgs7c12ckw5j31rz85jlrds68ygrry")) (modules '((guix build utils))) (snippet '(begin From a343c46134531ec2a4b1ef7dfced9c4281782264 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 12:09:25 +0100 Subject: [PATCH 197/436] gnu: dlib: Update to 19.3. * gnu/packages/machine-learning.scm (dlib): Update to 19.3. [arguments]: Enable one more test. --- gnu/packages/machine-learning.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 7ed12e677a..7bad833b38 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -504,14 +504,14 @@ and a QP solver.") (define-public dlib (package (name "dlib") - (version "19.2") + (version "19.3") (source (origin (method url-fetch) (uri (string-append "http://dlib.net/files/dlib-" version ".tar.bz2")) (sha256 (base32 - "0jh840b3ynlqsvbpswzg994yk539zbhx2sk6lybd23qyd2b8zgi8")) + "0gfy83av717qymv53yv7ki6mgh6mdw4xcxxbjk8lrs72f8qvnrcw")) (modules '((guix build utils))) (snippet '(begin @@ -541,7 +541,7 @@ and a QP solver.") '("object_detector" ; timeout "data_io")) ((string-prefix? "armhf" system) - '("learning_to_track" "max_cost_assignment")) + '("learning_to_track")) ((string-prefix? "i686" system) '("optimization")) (else '())))) From 49ed5de31ebfa0a743a8fffb8dbc43092f8bf073 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 12:48:59 +0100 Subject: [PATCH 198/436] gnu: x265: Update to 2.3. * gnu/packages/video.scm (x265): Update to 2.3. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index aee24b0f40..16dc92c322 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -263,7 +263,7 @@ H.264 (MPEG-4 AVC) video streams.") (define-public x265 (package (name "x265") - (version "2.1") + (version "2.3") (source (origin (method url-fetch) @@ -271,7 +271,7 @@ H.264 (MPEG-4 AVC) video streams.") "x265_" version ".tar.gz")) (sha256 (base32 - "0hx6sr9l7586gs4qds2sj0i1m5brxkaqq3cwmibhfb559fpvkz48")) + "07z4ydxg0lk6j43h0wlh2xddb91cy4y4mny2ln71d4278b1hllj7")) (modules '((guix build utils))) (snippet '(delete-file-recursively "source/compat/getopt")))) From 61feaf3b5fce02190399795bbfef520e5018f3fc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 13:02:23 +0100 Subject: [PATCH 199/436] gnu: libx264: Update to 20170224-2245. * gnu/packages/video.scm (libx264): Update to 20170224-2245. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 16dc92c322..6494b2da5f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -215,14 +215,14 @@ television and DVD. It is also known as AC-3.") (define-public libx264 (package (name "libx264") - (version "20161205-2245") + (version "20170224-2245") (source (origin (method url-fetch) (uri (string-append "https://download.videolan.org/pub/x264/snapshots/" "x264-snapshot-" version ".tar.bz2")) (sha256 (base32 - "0jjzdwag59kqlk09bb2pykm1ss8bw3p9q7bsks2kjgdwbj121a44")))) + "0paw8vzsy2qh5jf6xg2i1risjwyvmxgfnivly4gh0bib62cp4vib")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) From 9c96d33cfd69a7eca884961a115b8735cc5f93bd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 13:05:52 +0100 Subject: [PATCH 200/436] gnu: libva: Update to 1.7.3. * gnu/packages/video.scm (libva): Update to 1.7.3. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 6494b2da5f..ba172ff87b 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -394,7 +394,7 @@ SMPTE 314M.") (define-public libva (package (name "libva") - (version "1.7.1") + (version "1.7.3") (source (origin (method url-fetch) @@ -402,7 +402,7 @@ SMPTE 314M.") "https://www.freedesktop.org/software/vaapi/releases/libva/libva-" version".tar.bz2")) (sha256 - (base32 "1j8mb3p9kafhp30r3kmndnrklvzycc2ym0w6xdqz6m7jap626028")))) + (base32 "1ndrf136rlw03xag7j1xpmf9015d1h0dpnv6v587jnh6k2a17g12")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From 5932c3d0199be6dc8e69122996081b60cf3077b0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Feb 2017 13:15:06 +0100 Subject: [PATCH 201/436] Revert "gnu: libva: Update to 1.7.3." It causes too many rebuilds for 'master'. This reverts commit 9c96d33cfd69a7eca884961a115b8735cc5f93bd. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index ba172ff87b..6494b2da5f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -394,7 +394,7 @@ SMPTE 314M.") (define-public libva (package (name "libva") - (version "1.7.3") + (version "1.7.1") (source (origin (method url-fetch) @@ -402,7 +402,7 @@ SMPTE 314M.") "https://www.freedesktop.org/software/vaapi/releases/libva/libva-" version".tar.bz2")) (sha256 - (base32 "1ndrf136rlw03xag7j1xpmf9015d1h0dpnv6v587jnh6k2a17g12")))) + (base32 "1j8mb3p9kafhp30r3kmndnrklvzycc2ym0w6xdqz6m7jap626028")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From 2f1d20a8d473d9183460d38ed34f1c3d51860c78 Mon Sep 17 00:00:00 2001 From: John Darrington Date: Sat, 25 Feb 2017 13:20:26 +0100 Subject: [PATCH 202/436] gnu: xshogi: Remove Texinfo markup from synopsis. * gnu/packages/games.scm (xshogi): Remove Texinfo markup from synopsis. --- gnu/packages/games.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 50315a6085..d26669e68f 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -212,7 +212,7 @@ Chess). It is similar to standard chess but this variant is far more complicate `(("libxaw" ,libxaw) ("libxt" ,libxt))) (home-page "http://www.gnu.org/software/gnushogi/") - (synopsis "User interface for @code{gnushogi}") + (synopsis "User interface for gnushogi") (description "A graphical user interface for the package @code{gnushogi}.") ;; Contains a copy of GPLv3 but the licence notices simply ;; state "GNU General Public Licence" without specifying a version. From ffa771d2b4c069c1fcf6d226d330ce1f514d7a49 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 11:48:20 -0500 Subject: [PATCH 203/436] gnu: vim: Use upstream fix for CVE-2017-5953. * gnu/packages/patches/vim-CVE-2017-5953.patch: Adjust to match upstream changes. --- gnu/packages/patches/vim-CVE-2017-5953.patch | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/gnu/packages/patches/vim-CVE-2017-5953.patch b/gnu/packages/patches/vim-CVE-2017-5953.patch index 7b66f1bf16..070f98c2cb 100644 --- a/gnu/packages/patches/vim-CVE-2017-5953.patch +++ b/gnu/packages/patches/vim-CVE-2017-5953.patch @@ -3,20 +3,28 @@ Fix CVE-2017-5953: https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5953 https://groups.google.com/forum/#!topic/vim_dev/t-3RSdEnrHY -Patch adapted from upstream commit, correcting the transcription error -in the bounds check: +This change is adapted from the upstream source repository: -https://github.com/vim/vim/commit/399c297aa93afe2c0a39e2a1b3f972aebba44c9d +https://github.com/vim/vim/commit/6d3c8586fc81b022e9f06c611b9926108fb878c7 diff --git a/src/spellfile.c b/src/spellfile.c -index c7d87c6..8b1a3a6 100644 +index c7d87c6..00ef019 100644 --- a/src/spellfile.c +++ b/src/spellfile.c +@@ -1585,7 +1585,7 @@ spell_read_tree( + int prefixtree, /* TRUE for the prefix tree */ + int prefixcnt) /* when "prefixtree" is TRUE: prefix count */ + { +- int len; ++ long len; + int idx; + char_u *bp; + idx_T *ip; @@ -1595,6 +1595,9 @@ spell_read_tree( len = get4c(fd); if (len < 0) return SP_TRUNCERROR; -+ if (len >= 0x3fffffff) ++ if (len >= LONG_MAX / (long)sizeof(int)) + /* Invalid length, multiply with sizeof(int) would overflow. */ + return SP_FORMERROR; if (len > 0) From 9c66b885436e6d00c846f231e1077b5bb2ee2a43 Mon Sep 17 00:00:00 2001 From: ng0 Date: Sat, 25 Feb 2017 09:16:43 +0000 Subject: [PATCH 204/436] gnu: neomutt: Update to 20170225. * gnu/packages/mail.scm (neomutt): Update to 20170225. Signed-off-by: Kei Kebreau --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index a9b2cb3ec9..f4f732ec19 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -254,7 +254,7 @@ operating systems.") (package (inherit mutt) (name "neomutt") - (version "20170113") + (version "20170225") (source (origin (method url-fetch) @@ -263,7 +263,7 @@ operating systems.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0cqr77q263b5qcmdw6g0qixdpk6gmzgzpa03v226nr55v2ips9jg")))) + "00ll35g9pcanzrxsjp09vrmq6flml249dipcznrq2z4jy2zd386p")))) (inputs `(("cyrus-sasl" ,cyrus-sasl) ("gdbm" ,gdbm) From b01a89854ba1bd22b94c2373662bc07d035be2c1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 26 Feb 2017 21:19:39 +0100 Subject: [PATCH 205/436] gnu: Remove unused patch. This is a followup to 6f9d5b2e8c861c3a1243937a26400f8394946346. * gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../patches/libssh-0.6.5-CVE-2016-0739.patch | 77 ------------------- 2 files changed, 78 deletions(-) delete mode 100644 gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch diff --git a/gnu/local.mk b/gnu/local.mk index 515b154b9a..0538601734 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -692,7 +692,6 @@ dist_patch_DATA = \ %D%/packages/patches/libmad-frame-length.patch \ %D%/packages/patches/libmad-mips-newgcc.patch \ %D%/packages/patches/libpng-CVE-2016-10087.patch \ - %D%/packages/patches/libssh-0.6.5-CVE-2016-0739.patch \ %D%/packages/patches/libtar-CVE-2013-4420.patch \ %D%/packages/patches/libtheora-config-guess.patch \ %D%/packages/patches/libtiff-CVE-2016-10092.patch \ diff --git a/gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch b/gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch deleted file mode 100644 index a5fdd7ffff..0000000000 --- a/gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch +++ /dev/null @@ -1,77 +0,0 @@ -Fix CVE-2016-0739 (Weak Diffie-Hellman secret generation in -dh_generate_x() and dh_generate_y()). - -"Due to a byte/bit confusion, the DH secret was too short. This file was -completely reworked and will be commited in a future version." -Source: -https://git.libssh.org/projects/libssh.git/commit/?id=f8d0026c65fc8a55748ae481758e2cf376c26c86 - -This patch was created by upstream for libssh-0.7.3, but applied without -modification to libssh-0.6.3 by Debian. In Guix, we apply it without -modification to libssh-0.6.5. - -References: -https://bugzilla.redhat.com/show_bug.cgi?id=CVE-2016-0739 -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-0739 -https://security-tracker.debian.org/tracker/CVE-2016-0739 - ---- - src/dh.c | 22 +++++++++++++++++----- - 1 file changed, 17 insertions(+), 5 deletions(-) - -diff --git a/src/dh.c b/src/dh.c -index e489a1d..d27b66e 100644 ---- a/src/dh.c -+++ b/src/dh.c -@@ -227,15 +227,21 @@ void ssh_crypto_finalize(void) { - } - - int dh_generate_x(ssh_session session) { -+ int keysize; -+ if (session->next_crypto->kex_type == SSH_KEX_DH_GROUP1_SHA1) { -+ keysize = 1023; -+ } else { -+ keysize = 2047; -+ } - session->next_crypto->x = bignum_new(); - if (session->next_crypto->x == NULL) { - return -1; - } - - #ifdef HAVE_LIBGCRYPT -- bignum_rand(session->next_crypto->x, 128); -+ bignum_rand(session->next_crypto->x, keysize); - #elif defined HAVE_LIBCRYPTO -- bignum_rand(session->next_crypto->x, 128, 0, -1); -+ bignum_rand(session->next_crypto->x, keysize, -1, 0); - #endif - - /* not harder than this */ -@@ -248,15 +254,21 @@ int dh_generate_x(ssh_session session) { - - /* used by server */ - int dh_generate_y(ssh_session session) { -- session->next_crypto->y = bignum_new(); -+ int keysize; -+ if (session->next_crypto->kex_type == SSH_KEX_DH_GROUP1_SHA1) { -+ keysize = 1023; -+ } else { -+ keysize = 2047; -+ } -+ session->next_crypto->y = bignum_new(); - if (session->next_crypto->y == NULL) { - return -1; - } - - #ifdef HAVE_LIBGCRYPT -- bignum_rand(session->next_crypto->y, 128); -+ bignum_rand(session->next_crypto->y, keysize); - #elif defined HAVE_LIBCRYPTO -- bignum_rand(session->next_crypto->y, 128, 0, -1); -+ bignum_rand(session->next_crypto->y, keysize, -1, 0); - #endif - - /* not harder than this */ --- -cgit v0.12 - From 5d79b1bf575139dba9b3f919c7cc7b7f0853a67c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 26 Feb 2017 21:24:41 +0100 Subject: [PATCH 206/436] gnu: libssh: Update to 0.7.4. * gnu/packages/ssh.scm (libssh): Update to 0.7.4. [home-page]: Use HTTPS. --- gnu/packages/ssh.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index 9d1d9cc0a9..be4d2a7ade 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -56,15 +56,15 @@ (define-public libssh (package (name "libssh") - (version "0.7.3") + (version "0.7.4") (source (origin (method url-fetch) (uri (string-append - "https://red.libssh.org/attachments/download/195/libssh-" + "https://red.libssh.org/attachments/download/210/libssh-" version ".tar.xz")) (sha256 (base32 - "165g49i4kmm3bfsjm0n8hm21kadv79g9yjqyq09138jxanz4dvr6")))) + "03bcp9ksqp0s1pmwfmzhcknvkxay5k0mjzzxp3rjlifbng1vxq9r")))) (build-system cmake-build-system) (arguments '(#:configure-flags '("-DWITH_GCRYPT=ON") @@ -79,7 +79,7 @@ client and server implementations. With libssh, you can remotely execute programs, transfer files, and use a secure and transparent tunnel for your remote applications.") - (home-page "http://www.libssh.org") + (home-page "https://www.libssh.org") (license license:lgpl2.1+))) (define-public libssh2 From 61f78e72843a5199fa35b28e3d5bee39c1ff22ba Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 26 Feb 2017 22:24:38 +0000 Subject: [PATCH 207/436] gnu: iproute2: Update to 4.10. * gnu/packages/linux.scm (iproute2): Update to 4.10. [arguments]: Specify HDRDIR in #:make-flags. --- gnu/packages/linux.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index bd109dbbdb..9fb74f1b89 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1063,7 +1063,7 @@ packet filter.") (define-public iproute (package (name "iproute2") - (version "4.9.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (string-append @@ -1071,7 +1071,7 @@ packet filter.") version ".tar.xz")) (sha256 (base32 - "1i0n071hiqxw1gisngw2jln3kcp9sh47n6fj5hdwqrvp7w20zwy0")))) + "1a59y1zkddvr7z0lh2y9iasbh9wpfc1n39p56xcd6jkhzk0y3c92")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no test suite @@ -1080,6 +1080,7 @@ packet filter.") (string-append "BASH_COMPDIR=" out "/etc/bash_completion.d") (string-append "LIBDIR=" out "/lib") + (string-append "HDRDIR=" out "/include") (string-append "SBINDIR=" out "/sbin") (string-append "CONFDIR=" out "/etc") (string-append "DOCDIR=" out "/share/doc/" From 3ba43a2297eae9401364568522cb847bea376f3f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 26 Feb 2017 23:41:19 +0100 Subject: [PATCH 208/436] gnu: pciutils: Update to 3.5.4. * gnu/packages/pciutils.scm (pciutils): Update to 3.5.4. --- gnu/packages/pciutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/pciutils.scm b/gnu/packages/pciutils.scm index 8422a5c574..7c9856468d 100644 --- a/gnu/packages/pciutils.scm +++ b/gnu/packages/pciutils.scm @@ -30,7 +30,7 @@ (define-public pciutils (package (name "pciutils") - (version "3.5.2") + (version "3.5.4") (source (origin (method url-fetch) (uri (string-append @@ -38,7 +38,7 @@ version ".tar.xz")) (sha256 (base32 - "1z2y4f3cyvm7a0dyan0n6jpb3p9pvh35lrim0058slj0kwd1969s")))) + "0rpy7kkb2y89wmbcbfjjjxsk2x89v5xxhxib4vpl131ip5m3qab4")))) (build-system gnu-build-system) (arguments '(#:phases From c1ed10f95e81ee1f2c6d242164fdcb6d9dfad9f3 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 19:46:19 -0500 Subject: [PATCH 209/436] gnu: gstreamer: Update to 1.10.4. * gnu/packages/gstreamer.scm (gstreamer): Update to 1.10.4. --- gnu/packages/gstreamer.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index e3e009300f..d81aad6f88 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -98,7 +98,7 @@ arrays of data.") (define-public gstreamer (package (name "gstreamer") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) @@ -107,7 +107,7 @@ arrays of data.") version ".tar.xz")) (sha256 (base32 - "0gdnxg5igbhnpjhrzp31w1ww95j805byqd6mj3x29wli54dxrfc5")))) + "062jidnw17hkpva6ddygp80gyasyigfkpm1y7w56rk56a2pzbhjh")))) (build-system gnu-build-system) (outputs '("out" "doc")) (arguments From 1d8e7273578e95f6b5e4293ac34c4f6fe5d5c579 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 19:46:48 -0500 Subject: [PATCH 210/436] gnu: gst-plugins-base: Update to 1.10.4. * gnu/packages/gstreamer.scm (gst-plugins-base): Update to 1.10.4. [source]: Remove obsolete patch 'gst-plugins-base-fix-test-on-32bit.patch' * gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/gstreamer.scm | 10 +++--- .../gst-plugins-base-fix-test-on-32bit.patch | 32 ------------------- 3 files changed, 6 insertions(+), 37 deletions(-) delete mode 100644 gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0538601734..b408cc29d9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -605,7 +605,6 @@ dist_patch_DATA = \ %D%/packages/patches/grub-gets-undeclared.patch \ %D%/packages/patches/grub-freetype.patch \ %D%/packages/patches/gsl-test-i686.patch \ - %D%/packages/patches/gst-plugins-base-fix-test-on-32bit.patch \ %D%/packages/patches/guile-1.8-cpp-4.5.patch \ %D%/packages/patches/guile-arm-fixes.patch \ %D%/packages/patches/guile-default-utf8.patch \ diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index d81aad6f88..025f665782 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -146,7 +146,7 @@ This package provides the core library and elements.") (define-public gst-plugins-base (package (name "gst-plugins-base") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) @@ -154,9 +154,11 @@ This package provides the core library and elements.") name "-" version ".tar.xz")) (sha256 (base32 - "040pifl4cgsqqz2si4s1y5khj3zwm39w21siagxwp805swbrcag6")) - (patches - (search-patches "gst-plugins-base-fix-test-on-32bit.patch")))) + "1dsyjf6rncsbg4rfj40cvf1wwpjj9h3j3c7bh4zp7jylnfv4blpn")) +; (patches +; (search-patches "gst-plugins-base-fix-test-on-32bit.patch")) + + )) (build-system gnu-build-system) (outputs '("out" "doc")) (propagated-inputs diff --git a/gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch b/gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch deleted file mode 100644 index 4c6c7ed06e..0000000000 --- a/gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch +++ /dev/null @@ -1,32 +0,0 @@ -This fixes a test failure on i686. - -Patch copied from upstream source repository: - -https://cgit.freedesktop.org/gstreamer/gst-plugins-base/commit/?id=5e2e111627871c566ffc6607eda8f4ef4699d040 - -From 5e2e111627871c566ffc6607eda8f4ef4699d040 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Sebastian=20Dr=C3=B6ge?= -Date: Thu, 2 Feb 2017 14:56:39 +0200 -Subject: [PATCH] multifdsink: Make sure to use a 64 bit integer for the - units-max property - ---- - tests/check/elements/multifdsink.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/tests/check/elements/multifdsink.c b/tests/check/elements/multifdsink.c -index af138cc92..951b1b9fa 100644 ---- a/tests/check/elements/multifdsink.c -+++ b/tests/check/elements/multifdsink.c -@@ -869,7 +869,7 @@ GST_START_TEST (test_client_kick) - gint i, initial_buffers = 3, num_buffers = 0; - - sink = setup_multifdsink (); -- g_object_set (sink, "units-max", initial_buffers, NULL); -+ g_object_set (sink, "units-max", (gint64) initial_buffers, NULL); - - fail_if (pipe (pfd1) == -1); - fail_if (pipe (pfd2) == -1); --- -2.11.0 - From 26114548310439d58c579a847c605ff700765094 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 21:34:21 -0500 Subject: [PATCH 211/436] gnu: gst-plugins-good: Update to 1.10.4. * gnu/packages/gstreamer.scm (gst-plugins-good): Update to 1.10.4. --- gnu/packages/gstreamer.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index 025f665782..f9cbd736aa 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -205,7 +205,7 @@ for the GStreamer multimedia library.") (define-public gst-plugins-good (package (name "gst-plugins-good") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) @@ -214,7 +214,7 @@ for the GStreamer multimedia library.") name "-" version ".tar.xz")) (sha256 (base32 - "0mar8ss8bvpz699ql4kgndvna8qsv7kj372py4435ffl6hzfj1sf")))) + "0zjdwxn83sp9wjp9rxjbyk8kf284g9av7l2v6rjldi586hacd1la")))) (build-system gnu-build-system) (inputs `(("aalib" ,aalib) From 869ffe8f9b6eff69e940758fbed95adb3cd91f51 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 21:34:51 -0500 Subject: [PATCH 212/436] gnu: gst-plugins-bad: Update to 1.10.4 [fixes CVE-2017-5848]. * gnu/packages/gstreamer.scm (gst-plugins-bad): Update to 1.10.4. --- gnu/packages/gstreamer.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index f9cbd736aa..82507273da 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -270,14 +270,14 @@ developers consider to have good quality code and correct functionality.") (define-public gst-plugins-bad (package (name "gst-plugins-bad") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) (uri (string-append "https://gstreamer.freedesktop.org/src/" name "/" name "-" version ".tar.xz")) (sha256 (base32 - "1rwla1p57yzygb68z2xk5l5kvqzj5w3nxq0davkwk139zd8r6294")))) + "0rk9rlzf2b0hjw5hwbadz53yh4ls7vm3w3cshsa3n8isdd8axp93")))) (outputs '("out" "doc")) (build-system gnu-build-system) (arguments From 66fff91735c3950ddabcebf174152866ea1628c4 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 21:35:21 -0500 Subject: [PATCH 213/436] gnu: gst-plugins-ugly: Update to 1.10.4 [fixes CVE-2017-5847]. * gnu/packages/gstreamer.scm (gst-plugins-ugly): Update to 1.10.4. --- gnu/packages/gstreamer.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index 82507273da..c6e9cf3b66 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -347,7 +347,7 @@ par compared to the rest.") (define-public gst-plugins-ugly (package (name "gst-plugins-ugly") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) @@ -355,7 +355,7 @@ par compared to the rest.") name "/" name "-" version ".tar.xz")) (sha256 (base32 - "1lkb8kznc9wxmhbp7k67b50y27nz8jp2x2flb91xzydz7b89f5f9")))) + "0ngsiwcsz3jd08id4mc0qiy2q1n7h2kkvdnh3r1vm725m1ycg1k3")))) (build-system gnu-build-system) (inputs `(("gst-plugins-base" ,gst-plugins-base) From b8f337c2805465b558271a361aa14e622ad936db Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 21:35:44 -0500 Subject: [PATCH 214/436] gnu: gst-libav: Update to 1.10.4. * gnu/packages/gstreamer.scm (gst-libav): Update to 1.10.4. --- gnu/packages/gstreamer.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index c6e9cf3b66..d4bab98055 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -386,7 +386,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.") (define-public gst-libav (package (name "gst-libav") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) (uri (string-append @@ -394,7 +394,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.") name "-" version ".tar.xz")) (sha256 (base32 - "1aajayv63ardkbmcg7pnh2d87r067325a5wzinwihaw6n5jw2sws")))) + "12r68ri03mgbbwsxyn6yklgfsq32rwvyq83zw0aq7m73fp5gx83c")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--with-system-libav") From 50a86ee6c9c3e4be200e2a8440a4f144bf42d769 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 26 Feb 2017 21:36:04 -0500 Subject: [PATCH 215/436] gnu: python-gst: Update to 1.10.4. * gnu/packages/gstreamer.scm (python-gst): Update to 1.10.4. --- gnu/packages/gstreamer.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index d4bab98055..5a1cf53336 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -424,7 +424,7 @@ compression formats through the use of the libav library.") (define-public python-gst (package (name "python-gst") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) (uri (string-append @@ -432,7 +432,7 @@ compression formats through the use of the libav library.") "gst-python-" version ".tar.xz")) (sha256 (base32 - "1s5437bnk0j5hfg2gwfwq4b68l6vj1lfskxh73v6ikp0vw32vymx")))) + "04l2hvvz9b0f3nyds1k3yfk5di8a91fpr6maj19c11mwp1s82l2r")))) (build-system gnu-build-system) (arguments ;; XXX: Factorize python-sitedir with python-build-system. From f11a48c0ca85dce423fdfe4fd57b08b2cfa66e17 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 27 Feb 2017 04:13:48 -0500 Subject: [PATCH 216/436] gnu: linux-libre@4.9: Update to 4.9.13. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.13. Remove patches. --- gnu/packages/linux.scm | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9fb74f1b89..f2b7a9903d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -348,20 +348,10 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.12" - "0yl4khibxb2aiqm479y5ywwlzi5s3rrcqsg4zgn7wpshncb4l1ar" + (make-linux-libre "4.9.13" + "16miggwcwfpm7kx0yz256x887rky9wgmp1grg850lf8sdkiz0a1p" %intel-compatible-systems - #:configuration-file kernel-config - #:patches - (list %boot-logo-patch - (origin - (method url-fetch) - (uri "\ -https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=5edabca9d4cff7f1f2b68f0bac55ef99d9798ba4") - (file-name "linux-libre-CVE-2017-6074.patch") - (sha256 - (base32 - "1x40slfz1qxgiaznyy13bwlh34450pkyyrkljpyjlx6c4mrzb1jj")))))) + #:configuration-file kernel-config)) (define-public linux-libre-4.4 (make-linux-libre "4.4.51" From c46d8e92decff0925b34ca1824de545dbbbf9f25 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 27 Feb 2017 04:15:18 -0500 Subject: [PATCH 217/436] gnu: linux-libre@4.4: Update to 4.4.52. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.52. Remove patches. --- gnu/packages/linux.scm | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f2b7a9903d..bc3e4d4079 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -354,20 +354,10 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.51" - "13iahlhpqmy880nq2zljc6j6zmr2axlayabaqp3firs6brnnmr9r" + (make-linux-libre "4.4.52" + "1fzcq9bbsxiij2fh6kgwrp417sy2j5gnbzs0wwlmznj7mvysl7qg" %intel-compatible-systems - #:configuration-file kernel-config - #:patches - (list %boot-logo-patch - (origin - (method url-fetch) - (uri "\ -https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=5edabca9d4cff7f1f2b68f0bac55ef99d9798ba4") - (file-name "linux-libre-CVE-2017-6074.patch") - (sha256 - (base32 - "1x40slfz1qxgiaznyy13bwlh34450pkyyrkljpyjlx6c4mrzb1jj")))))) + #:configuration-file kernel-config)) (define-public linux-libre-4.1 (make-linux-libre "4.1.38" From 31ccf5dc6cb020d4502ac54ed7342f5440ea6d83 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 12:19:46 +0100 Subject: [PATCH 218/436] gnu: slop: Update to 5.3.35. * gnu/packages/xdisorg.scm (slop): Update to 5.3.35. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index b5f3dc6473..6e38a5aa3a 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -438,7 +438,7 @@ of the screen selected by mouse.") (define-public slop (package (name "slop") - (version "5.3.28") + (version "5.3.35") (source (origin (method url-fetch) (uri (string-append @@ -447,7 +447,7 @@ of the screen selected by mouse.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "01k39wb1w367zbnl3ni76n3xcmcyvjf14jvk09cd409mvhwyl0p4")))) + "12fkwardd33xbaisjv93r49jh1dmqw323zjsd9m8kxcyv1rimsig")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From 298111a7a76fd01dd475fa27576b13751bf05de9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 12:20:31 +0100 Subject: [PATCH 219/436] gnu: maim: Update to 4.4.59. * gnu/packages/xdisorg.scm (maim): Update to 4.4.59. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 6e38a5aa3a..3d69661ba5 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -469,7 +469,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "4.4.50") + (version "4.4.59") (source (origin (method url-fetch) (uri (string-append @@ -478,7 +478,7 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0lr11x77981jzx53z1zd48d8ss5swhcg3sxy8naz6945wc9i3mh8")))) + "0h8z4wm7zgxj1vlp98n12dyiwjwphhnl6yh8aaz3krm5v2kyy6hc")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From a6d9f8837b118e2126e4b8a19bf48b524229a15c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 12:22:04 +0100 Subject: [PATCH 220/436] gnu: whois: Update to 5.2.15. * gnu/packages/networking.scm (whois): Update to 5.2.15. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index a10fbfed92..240fa517e5 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -430,7 +430,7 @@ and up to 1 Mbit/s downstream.") (define-public whois (package (name "whois") - (version "5.2.14") + (version "5.2.15") (source (origin (method url-fetch) @@ -438,7 +438,7 @@ and up to 1 Mbit/s downstream.") name "_" version ".tar.xz")) (sha256 (base32 - "1lmh7168yby1ma8r1svgvmv9hbgjyniy9c64r6lby3zdmd0sy7d4")))) + "123ingf699javzh8qm6ny10nl28zbjzasa4k5pcn0qzw1dlnnnks")))) (build-system gnu-build-system) ;; TODO: unbundle mkpasswd binary + its po files. (arguments From e9eafae289aa70a3e839902ddf48a40d3c97b05b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 12:54:19 +0100 Subject: [PATCH 221/436] gnu: khard: Disable tests. * gnu/packages/mail.scm (khard)[arguments]: Set #:tests? #f. --- gnu/packages/mail.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index f4f732ec19..8651deefb5 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1509,7 +1509,11 @@ maintained.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (doc (string-append out "/share/doc/khard"))) - (copy-recursively "misc/khard" doc))))))) + (copy-recursively "misc/khard" doc) + #t)))) + ;; FIXME: check phase fails with + ;; "Config file /tmp/.config/khard/khard.conf not available" + #:tests? #f)) (propagated-inputs `(("python-vobject" ,python-vobject) ("python-pyyaml" ,python-pyyaml) From 2982889d6826af13dd4e4983d4abd530a970662a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 13:08:41 +0100 Subject: [PATCH 222/436] gnu: potrace: Update to 1.14 [fixes CVE-2016-8685 and CVE-2016-8686]. * gnu/packages/fontutils.scm (potrace): Update to 1.14. --- gnu/packages/fontutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 60cff2e330..15109bfe13 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -393,7 +393,7 @@ and returns a sequence of positioned glyphids from the font.") (define-public potrace (package (name "potrace") - (version "1.13") + (version "1.14") (source (origin (method url-fetch) @@ -401,7 +401,7 @@ and returns a sequence of positioned glyphids from the font.") "/potrace-" version ".tar.gz")) (sha256 (base32 - "115p2vgyq7p2mf4nidk2x3aa341nvv2v8ml056vbji36df5l6lk2")))) + "0znr9i0ljb818qiwm22zw63g11a4v08gc5xkh0wbdp6g259vcwnv")))) (build-system gnu-build-system) (native-inputs `(("ghostscript" ,ghostscript))) ;for tests (inputs `(("zlib" ,zlib))) From 96eaa55ffb9877c319df09d158fca31034d8f0a2 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Fri, 17 Feb 2017 13:17:03 +0300 Subject: [PATCH 223/436] packages: Add 'search-auxiliary-file'. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Suggested-by: Ludovic Courtès at . * gnu/packages.scm (%auxiliary-files-path): New variable. (search-auxiliary-file): New procedure. --- gnu/packages.scm | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/gnu/packages.scm b/gnu/packages.scm index 0aa289d56c..10ca3bb314 100644 --- a/gnu/packages.scm +++ b/gnu/packages.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès ;;; Copyright © 2013 Mark H Weaver ;;; Copyright © 2014 Eric Bavier -;;; Copyright © 2016 Alex Kost +;;; Copyright © 2016, 2017 Alex Kost ;;; Copyright © 2016 Mathieu Lirzin ;;; ;;; This file is part of GNU Guix. @@ -40,8 +40,10 @@ #:use-module (srfi srfi-39) #:export (search-patch search-patches + search-auxiliary-file search-bootstrap-binary %patch-path + %auxiliary-files-path %bootstrap-binaries-path %package-module-path @@ -62,17 +64,27 @@ ;;; ;;; Code: -;; By default, we store patches and bootstrap binaries alongside Guile -;; modules. This is so that these extra files can be found without -;; requiring a special setup, such as a specific installation directory -;; and an extra environment variable. One advantage of this setup is -;; that everything just works in an auto-compilation setting. +;; By default, we store patches, auxiliary files and bootstrap binaries +;; alongside Guile modules. This is so that these extra files can be +;; found without requiring a special setup, such as a specific +;; installation directory and an extra environment variable. One +;; advantage of this setup is that everything just works in an +;; auto-compilation setting. (define %bootstrap-binaries-path (make-parameter (map (cut string-append <> "/gnu/packages/bootstrap") %load-path))) +(define %auxiliary-files-path + (make-parameter + (map (cut string-append <> "/gnu/packages/aux-files") + %load-path))) + +(define (search-auxiliary-file file-name) + "Search the auxiliary FILE-NAME. Return #f if not found." + (search-path (%auxiliary-files-path) file-name)) + (define (search-patch file-name) "Search the patch FILE-NAME. Raise an error if not found." (or (search-path (%patch-path) file-name) From 7994250fdb7ce786a72278554d85fccb6d152e73 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Fri, 17 Feb 2017 13:28:16 +0300 Subject: [PATCH 224/436] gnu: linux: Move configuration files to "aux-files". * gnu/packages/linux-libre-4.1-i686.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.1-i686.conf: ... this. * gnu/packages/linux-libre-4.1-x86_64.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.1-x86_64.conf: ... this. * gnu/packages/linux-libre-4.4-i686.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.4-i686.conf: ... this. * gnu/packages/linux-libre-4.4-x86_64.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.4-x86_64.conf: ... this. * gnu/packages/linux-libre-4.9-i686.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.9-i686.conf: ... this. * gnu/packages/linux-libre-4.9-x86_64.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.9-x86_64.conf: ... this. * gnu/packages/linux-libre-4.10-i686.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.10-i686.conf: ... this. * gnu/packages/linux-libre-4.10-x86_64.conf: Rename to... * gnu/packages/aux-files/linux-libre/4.10-x86_64.conf: ... this. * gnu/packages/linux.scm (kernel-config): Use 'search-auxiliary-file' to find configuration files. * Makefile.am (KCONFIGS): Rename to... (AUX_FILES): ... this. Adjust accordingly. --- Makefile.am | 24 +++++++++---------- .../linux-libre/4.1-i686.conf} | 0 .../linux-libre/4.1-x86_64.conf} | 0 .../linux-libre/4.10-i686.conf} | 0 .../linux-libre/4.10-x86_64.conf} | 0 .../linux-libre/4.4-i686.conf} | 0 .../linux-libre/4.4-x86_64.conf} | 0 .../linux-libre/4.9-i686.conf} | 0 .../linux-libre/4.9-x86_64.conf} | 0 gnu/packages/linux.scm | 9 ++++--- 10 files changed, 16 insertions(+), 17 deletions(-) rename gnu/packages/{linux-libre-4.1-i686.conf => aux-files/linux-libre/4.1-i686.conf} (100%) rename gnu/packages/{linux-libre-4.1-x86_64.conf => aux-files/linux-libre/4.1-x86_64.conf} (100%) rename gnu/packages/{linux-libre-4.10-i686.conf => aux-files/linux-libre/4.10-i686.conf} (100%) rename gnu/packages/{linux-libre-4.10-x86_64.conf => aux-files/linux-libre/4.10-x86_64.conf} (100%) rename gnu/packages/{linux-libre-4.4-i686.conf => aux-files/linux-libre/4.4-i686.conf} (100%) rename gnu/packages/{linux-libre-4.4-x86_64.conf => aux-files/linux-libre/4.4-x86_64.conf} (100%) rename gnu/packages/{linux-libre-4.9-i686.conf => aux-files/linux-libre/4.9-i686.conf} (100%) rename gnu/packages/{linux-libre-4.9-x86_64.conf => aux-files/linux-libre/4.9-x86_64.conf} (100%) diff --git a/Makefile.am b/Makefile.am index 0de2e0987c..2e048f99ae 100644 --- a/Makefile.am +++ b/Makefile.am @@ -1,7 +1,7 @@ # GNU Guix --- Functional package management for GNU # Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès # Copyright © 2013 Andreas Enge -# Copyright © 2015 Alex Kost +# Copyright © 2015, 2017 Alex Kost # Copyright © 2016 Mathieu Lirzin # Copyright © 2016, 2017 Mark H Weaver # @@ -196,16 +196,16 @@ endif BUILD_DAEMON_OFFLOAD # Internal modules with test suite support. dist_noinst_DATA = guix/tests.scm guix/tests/http.scm -# Linux-Libre configurations. -KCONFIGS = \ - gnu/packages/linux-libre-4.10-i686.conf \ - gnu/packages/linux-libre-4.10-x86_64.conf \ - gnu/packages/linux-libre-4.9-i686.conf \ - gnu/packages/linux-libre-4.9-x86_64.conf \ - gnu/packages/linux-libre-4.4-i686.conf \ - gnu/packages/linux-libre-4.4-x86_64.conf \ - gnu/packages/linux-libre-4.1-i686.conf \ - gnu/packages/linux-libre-4.1-x86_64.conf +# Auxiliary files for packages. +AUX_FILES = \ + gnu/packages/aux-files/linux-libre/4.10-i686.conf \ + gnu/packages/aux-files/linux-libre/4.10-x86_64.conf \ + gnu/packages/aux-files/linux-libre/4.9-i686.conf \ + gnu/packages/aux-files/linux-libre/4.9-x86_64.conf \ + gnu/packages/aux-files/linux-libre/4.4-i686.conf \ + gnu/packages/aux-files/linux-libre/4.4-x86_64.conf \ + gnu/packages/aux-files/linux-libre/4.1-i686.conf \ + gnu/packages/aux-files/linux-libre/4.1-x86_64.conf # Templates, examples. EXAMPLES = \ @@ -216,7 +216,7 @@ EXAMPLES = \ GOBJECTS = $(MODULES:%.scm=%.go) guix/config.go $(dist_noinst_DATA:%.scm=%.go) nobase_dist_guilemodule_DATA = \ - $(MODULES) $(KCONFIGS) $(EXAMPLES) \ + $(MODULES) $(AUX_FILES) $(EXAMPLES) \ $(MISC_DISTRO_FILES) nobase_nodist_guilemodule_DATA = $(GOBJECTS) guix/config.scm diff --git a/gnu/packages/linux-libre-4.1-i686.conf b/gnu/packages/aux-files/linux-libre/4.1-i686.conf similarity index 100% rename from gnu/packages/linux-libre-4.1-i686.conf rename to gnu/packages/aux-files/linux-libre/4.1-i686.conf diff --git a/gnu/packages/linux-libre-4.1-x86_64.conf b/gnu/packages/aux-files/linux-libre/4.1-x86_64.conf similarity index 100% rename from gnu/packages/linux-libre-4.1-x86_64.conf rename to gnu/packages/aux-files/linux-libre/4.1-x86_64.conf diff --git a/gnu/packages/linux-libre-4.10-i686.conf b/gnu/packages/aux-files/linux-libre/4.10-i686.conf similarity index 100% rename from gnu/packages/linux-libre-4.10-i686.conf rename to gnu/packages/aux-files/linux-libre/4.10-i686.conf diff --git a/gnu/packages/linux-libre-4.10-x86_64.conf b/gnu/packages/aux-files/linux-libre/4.10-x86_64.conf similarity index 100% rename from gnu/packages/linux-libre-4.10-x86_64.conf rename to gnu/packages/aux-files/linux-libre/4.10-x86_64.conf diff --git a/gnu/packages/linux-libre-4.4-i686.conf b/gnu/packages/aux-files/linux-libre/4.4-i686.conf similarity index 100% rename from gnu/packages/linux-libre-4.4-i686.conf rename to gnu/packages/aux-files/linux-libre/4.4-i686.conf diff --git a/gnu/packages/linux-libre-4.4-x86_64.conf b/gnu/packages/aux-files/linux-libre/4.4-x86_64.conf similarity index 100% rename from gnu/packages/linux-libre-4.4-x86_64.conf rename to gnu/packages/aux-files/linux-libre/4.4-x86_64.conf diff --git a/gnu/packages/linux-libre-4.9-i686.conf b/gnu/packages/aux-files/linux-libre/4.9-i686.conf similarity index 100% rename from gnu/packages/linux-libre-4.9-i686.conf rename to gnu/packages/aux-files/linux-libre/4.9-i686.conf diff --git a/gnu/packages/linux-libre-4.9-x86_64.conf b/gnu/packages/aux-files/linux-libre/4.9-x86_64.conf similarity index 100% rename from gnu/packages/linux-libre-4.9-x86_64.conf rename to gnu/packages/aux-files/linux-libre/4.9-x86_64.conf diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index bc3e4d4079..1ed6843345 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015, 2016 Efraim Flashner ;;; Copyright © 2016 Christopher Allan Webber ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice -;;; Copyright © 2016 Alex Kost +;;; Copyright © 2016, 2017 Alex Kost ;;; Copyright © 2016 Raymond Nicholson ;;; Copyright © 2016 Mathieu Lirzin ;;; Copyright © 2016 Nicolas Goaziou @@ -194,11 +194,10 @@ (define* (kernel-config arch #:key variant) "Return the absolute file name of the Linux-Libre build configuration file for ARCH and optionally VARIANT, or #f if there is no such configuration." - (let* ((name (string-append "linux-libre-" - (if variant (string-append variant "-") "") + (let* ((name (string-append (if variant (string-append variant "-") "") (if (string=? "i386" arch) "i686" arch) ".conf")) - (file (string-append "gnu/packages/" name))) - (search-path %load-path file))) + (file (string-append "linux-libre/" name))) + (search-auxiliary-file file))) (define %default-extra-linux-options `(;; https://lists.gnu.org/archive/html/guix-devel/2014-04/msg00039.html From 59d04f63dfe8b68906e4cccc60ca27cbd546db78 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sat, 18 Feb 2017 11:24:41 +0300 Subject: [PATCH 225/436] gnu: emacs: Move "guix-emacs.el" to "aux-files". * emacs/guix-emacs.el: Rename to... * gnu/packages/aux-files/emacs/guix-emacs.el: ... this. * Makefile.am (AUX_FILES): Add it. * gnu/packages/emacs.scm (emacs)[inputs]: Remove 'guix' source. [native-inputs]: Add "guix-emacs.el" auxiliary file. [arguments]: Adjust 'install-site-start' phase accordingly. --- Makefile.am | 1 + .../packages/aux-files/emacs}/guix-emacs.el | 0 gnu/packages/emacs.scm | 20 ++++++++----------- 3 files changed, 9 insertions(+), 12 deletions(-) rename {emacs => gnu/packages/aux-files/emacs}/guix-emacs.el (100%) diff --git a/Makefile.am b/Makefile.am index 2e048f99ae..ec1bd2eb8b 100644 --- a/Makefile.am +++ b/Makefile.am @@ -198,6 +198,7 @@ dist_noinst_DATA = guix/tests.scm guix/tests/http.scm # Auxiliary files for packages. AUX_FILES = \ + gnu/packages/aux-files/emacs/guix-emacs.el \ gnu/packages/aux-files/linux-libre/4.10-i686.conf \ gnu/packages/aux-files/linux-libre/4.10-x86_64.conf \ gnu/packages/aux-files/linux-libre/4.9-i686.conf \ diff --git a/emacs/guix-emacs.el b/gnu/packages/aux-files/emacs/guix-emacs.el similarity index 100% rename from emacs/guix-emacs.el rename to gnu/packages/aux-files/emacs/guix-emacs.el diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 863624fc0f..3e722c326b 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -133,19 +133,15 @@ (("/bin/pwd") "pwd")))) (add-after 'install 'install-site-start - ;; Copy guix-emacs.el from Guix and add it to site-start.el. This - ;; way, Emacs packages provided by Guix and installed in + ;; Use 'guix-emacs' in "site-start.el". This way, Emacs packages + ;; provided by Guix and installed in ;; ~/.guix-profile/share/emacs/site-lisp/guix.d/PACKAGE-VERSION are ;; automatically found. (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((guix-src (assoc-ref inputs "guix-src")) - (out (assoc-ref outputs "out")) - (lisp-dir (string-append out "/share/emacs/site-lisp")) - (unpack (assoc-ref %standard-phases 'unpack))) - (mkdir "guix") - (with-directory-excursion "guix" - (apply unpack (list #:source guix-src)) - (install-file "emacs/guix-emacs.el" lisp-dir)) + (let* ((out (assoc-ref outputs "out")) + (lisp-dir (string-append out "/share/emacs/site-lisp"))) + (copy-file (assoc-ref inputs "guix-emacs.el") + (string-append lisp-dir "/guix-emacs.el")) (with-output-to-file (string-append lisp-dir "/site-start.el") (lambda () (display "(require 'guix-emacs nil t)"))) @@ -175,13 +171,13 @@ ("libsm" ,libsm) ("alsa-lib" ,alsa-lib) ("dbus" ,dbus) - ("guix-src" ,(package-source guix)) ;; multilingualization support ("libotf" ,libotf) ("m17n-lib" ,m17n-lib))) (native-inputs - `(("pkg-config" ,pkg-config) + `(("guix-emacs.el" ,(search-auxiliary-file "emacs/guix-emacs.el")) + ("pkg-config" ,pkg-config) ("texinfo" ,texinfo))) (native-search-paths From 9bd94544be43b7d028e1aaeb4069b07bdb24610f Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sat, 18 Feb 2017 11:44:52 +0300 Subject: [PATCH 226/436] gnu: emacs: Simplify "guix-emacs.el". * gnu/packages/aux-files/emacs/guix-emacs.el: Do not try to require 'guix-profiles'. Do not call 'guix-emacs-autoload-packages' in the top level. (guix-package-enable-at-startup): Remove. This variable can't be set by a user since this file is loaded before user config. (guix-emacs-autoload-packages): Use 'guix-read-package-profile' instead of 'guix-profile-prompt' in interactive clause (it was renamed in Emacs-Guix). * gnu/packages/emacs.scm (emacs)[arguments]: Call 'guix-emacs-autoload-packages' in "site-start.el" after requiring 'guix-emacs'. --- gnu/packages/aux-files/emacs/guix-emacs.el | 21 +++++---------------- gnu/packages/emacs.scm | 4 +++- 2 files changed, 8 insertions(+), 17 deletions(-) diff --git a/gnu/packages/aux-files/emacs/guix-emacs.el b/gnu/packages/aux-files/emacs/guix-emacs.el index 099261a013..2bbd639ffd 100644 --- a/gnu/packages/aux-files/emacs/guix-emacs.el +++ b/gnu/packages/aux-files/emacs/guix-emacs.el @@ -1,6 +1,6 @@ ;;; guix-emacs.el --- Emacs packages installed with Guix -;; Copyright © 2014, 2015, 2016 Alex Kost +;; Copyright © 2014, 2015, 2016, 2017 Alex Kost ;; This file is part of GNU Guix. @@ -19,22 +19,14 @@ ;;; Commentary: -;; This file provides auxiliary code for working with Emacs packages +;; This file provides auxiliary code to autoload Emacs packages ;; installed with Guix. ;;; Code: (require 'cl-lib) -(unless (require 'guix-profiles nil t) - (defvar guix-user-profile (expand-file-name "~/.guix-profile"))) -(defcustom guix-package-enable-at-startup t - "If non-nil, activate Emacs packages installed in a user profile. -Set this variable to nil before requiring `guix-emacs' file to -avoid loading autoloads of Emacs packages installed in -`guix-user-profile'." - :type 'boolean - :group 'guix) +(defvar guix-user-profile (expand-file-name "~/.guix-profile")) (defvar guix-emacs-autoloads nil "List of the last loaded Emacs autoloads.") @@ -92,8 +84,8 @@ profiles. 'Autoload' means add directories with Emacs packages to `load-path' and load 'autoloads' files matching `guix-emacs-autoloads-regexp'." - (interactive (list (if (fboundp 'guix-profile-prompt) - (funcall 'guix-profile-prompt) + (interactive (list (if (fboundp 'guix-read-package-profile) + (funcall 'guix-read-package-profile) guix-user-profile))) (let ((profiles (or profiles (list "/run/current-system/profile" @@ -115,9 +107,6 @@ profiles. (setq guix-emacs-autoloads (append new-autoloads guix-emacs-autoloads)))))))) -(when guix-package-enable-at-startup - (guix-emacs-autoload-packages)) - (provide 'guix-emacs) ;;; guix-emacs.el ends here diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 3e722c326b..ca3b832dc0 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -144,7 +144,9 @@ (string-append lisp-dir "/guix-emacs.el")) (with-output-to-file (string-append lisp-dir "/site-start.el") (lambda () - (display "(require 'guix-emacs nil t)"))) + (display + (string-append "(when (require 'guix-emacs nil t)\n" + " (guix-emacs-autoload-packages))\n")))) #t)))))) (inputs `(("gnutls" ,gnutls) From 1162418ee88f155f6b14fd8926479c2176e40e76 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sat, 18 Feb 2017 11:27:28 +0300 Subject: [PATCH 227/436] .gitignore: Remove stale entries. This is a followup to commit deb6276dda81a69da38e842d269c5370a28fa5cf. * .gitignore: Remove "/emacs/..." lines. --- .gitignore | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.gitignore b/.gitignore index 0897c95f3e..1fc22d7e93 100644 --- a/.gitignore +++ b/.gitignore @@ -44,11 +44,6 @@ /doc/os-config-desktop.texi /doc/stamp-vti /doc/version.texi -/emacs/Makefile -/emacs/Makefile.in -/emacs/guix-autoloads.el -/emacs/guix-config.el -/emacs/guix-helper.scm /etc/guix-daemon.conf /etc/guix-daemon.service /etc/guix-publish.conf From cbfbcb2105770b616aa7a347019f5e6abfbc1196 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Mon, 27 Feb 2017 11:18:35 +0100 Subject: [PATCH 228/436] gnu: coda: Update to 2.18. * gnu/packages/python.scm (coda): Update to 2.18. Signed-off-by: Marius Bakke --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 18536c43ee..e9b6ac4020 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -142,14 +142,14 @@ interactive dialogs to guide them.") (define-public coda (package (name "coda") - (version "2.17.3") + (version "2.18") (source (origin (method url-fetch) (uri (string-append "https://github.com/stcorp/coda/releases/download/" version "/coda-" version ".tar.gz")) (sha256 - (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h")) + (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs")) (patches (search-patches "coda-use-system-libs.patch")) (modules '((guix build utils))) (snippet From d5a9783999faf6628a03495d9bae7c2b85f1d9a7 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Mon, 27 Feb 2017 11:24:39 +0100 Subject: [PATCH 229/436] gnu: python-netcdf4: Update to 1.2.7. * gnu/packages/python.scm (python-netcdf4, python2-netcdf4): Update to 1.2.7. Signed-off-by: Marius Bakke --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c295c42f31..5b8698043f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -815,14 +815,14 @@ concepts.") (define-public python-netcdf4 (package (name "python-netcdf4") - (version "1.2.6") + (version "1.2.7") (source (origin (method url-fetch) (uri (pypi-uri "netCDF4" version)) (sha256 (base32 - "1qcymsfxsdfr4sx0vl7ih5d14z66k6c9sjy4gb6rjaksk5387zvg")))) + "1fllizmnpw0zkzzm4j9pgamarlzfn3kmv9zrm0w65q1y31h9ni0c")))) (build-system python-build-system) (native-inputs `(("python-cython" ,python-cython))) From 2bb12f5a68f6547b3de295c22c2886aaa0415e47 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 15:30:03 +0100 Subject: [PATCH 230/436] gnu: ribodiff: Fix test failure. * gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK and PYTHON2-NOSE. --- gnu/packages/bioinformatics.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index de6186de27..bdcb5a4010 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -499,6 +499,9 @@ provides the Ribotaper pipeline.") ("python-matplotlib" ,python2-matplotlib) ("python-scipy" ,python2-scipy) ("python-statsmodels" ,python2-statsmodels))) + (native-inputs + `(("python-mock" ,python2-mock) + ("python-nose" ,python2-nose))) (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") (synopsis "Detect translation efficiency changes from ribosome footprints") (description "RiboDiff is a statistical tool that detects the protein From 568cd526137af8d261f60311530fae1053b8bd99 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Mon, 27 Feb 2017 18:09:53 +0300 Subject: [PATCH 231/436] gnu: guix: Update development snapshot. * gnu/packages/package-management.scm (guix-devel): Update to 1162418. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 388368e2d3..c608f397dc 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -219,9 +219,9 @@ the Nix package manager.") ;; ;; Note: use a very short commit id; with a longer one, the limit on ;; hash-bang lines would be exceeded while running the tests. - (let ((commit "d9da3a757d3081403081577c4e07763c9b809043")) + (let ((commit "1162418ee88f155f6b14fd8926479c2176e40e76")) (package (inherit guix-0.12.0) - (version (string-append "0.12.0-4." (string-take commit 4))) + (version (string-append "0.12.0-5." (string-take commit 4))) (source (origin (method git-fetch) (uri (git-reference @@ -231,7 +231,7 @@ the Nix package manager.") (commit commit))) (sha256 (base32 - "17w9jdzm3lvfbchx7qrlkczp2jsfsi6v8cpfqh290cip5gxgz9bn")) + "16pxqbywhayazdgg9l19frigncmyq20j5fvaq4zgvm0iidndhfja")) (file-name (string-append "guix-" version "-checkout")))) (arguments (substitute-keyword-arguments (package-arguments guix-0.12.0) From b4905fc1d999d8730274c08d5494a0daa237d168 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Mon, 27 Feb 2017 18:11:10 +0300 Subject: [PATCH 232/436] gnu: emacs-guix: Update to 0.3. * gnu/packages/emacs.scm (emacs-guix): Update to 0.3. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index ca3b832dc0..cc8d9c0d0c 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1324,7 +1324,7 @@ type, for example: packages, buffers, files, etc.") (define-public emacs-guix (package (name "emacs-guix") - (version "0.2.2") + (version "0.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/alezost/guix.el" @@ -1332,7 +1332,7 @@ type, for example: packages, buffers, files, etc.") "/emacs-guix-" version ".tar.gz")) (sha256 (base32 - "1i47yh24xvgmnc778765g3j9ip0xb2y85v6w83r4qmkigk9rl2ck")))) + "1327zp140c7acckk0ajl88cgwr0lk9j3mb67nsq2janxrkwmj6br")))) (build-system gnu-build-system) (arguments `(#:configure-flags From 306c4d696150802f7462919fe6d16bf4f7f99a12 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 27 Feb 2017 15:11:09 -0500 Subject: [PATCH 233/436] gnu: linux-libre: Update to 4.10.1. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.1. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 1ed6843345..1036166a27 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -337,8 +337,8 @@ It has been modified to remove all non-free binary blobs.") (define %intel-compatible-systems '("x86_64-linux" "i686-linux")) -(define %linux-libre-version "4.10") -(define %linux-libre-hash "167zzgkivpqsp07did25wjqsswddzp3gifcdkq7xk00llxlmspla") +(define %linux-libre-version "4.10.1") +(define %linux-libre-hash "0mvwrjny1bjqyjqjxff9m97j48ybfdw8qpdazr5rwk12234v4k3d") (define-public linux-libre (make-linux-libre %linux-libre-version From 48d66a9c99a9cc8e9c27c9608da7e8729be206b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 27 Feb 2017 18:43:12 +0100 Subject: [PATCH 234/436] gnu: bamtools: Update to 2.4.1. * gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a448b51c6c..1810773de4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -238,7 +238,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (define-public bamtools (package (name "bamtools") - (version "2.3.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (string-append @@ -247,7 +247,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018")))) + "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target From a995251d681b3ec36be2e38fd9c1287c50609998 Mon Sep 17 00:00:00 2001 From: Federico Beffa Date: Mon, 27 Feb 2017 18:24:16 +0100 Subject: [PATCH 235/436] gnu: wxmaxima: Downgrade to 16.04.2. * gnu/packages/maths.scm (wxmaxima): Do it. Signed-off-by: Kei Kebreau --- gnu/packages/maths.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e9b6ac4020..1f4f388c65 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2008,7 +2008,9 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "16.12.2") + ;; Versions 16.12.0 to 16.12.2 have a bug which causes output lines to + ;; overlap. See + (version "16.04.2") (source (origin (method url-fetch) @@ -2016,7 +2018,7 @@ point numbers.") version "/" name "-" version ".tar.gz")) (sha256 (base32 - "0y22zhyhyxj2cbhzvs9c4pxr44i55ryfy5xi96d39bg2nbgs9h22")))) + "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n")))) (build-system gnu-build-system) (inputs `(("wxwidgets" ,wxwidgets) From 8bb7b4f5179629f92af429bad63a48073ac29484 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:19 +0000 Subject: [PATCH 236/436] gnu: Add vim-neocomplete. * gnu/packages/vim.scm (vim-neocomplete): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 43 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 42 insertions(+), 1 deletion(-) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index cdb32ac7eb..a683537cb8 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Cyril Roelandt ;;; Copyright © 2016 Efraim Flashner -;;; Copyright © 2016 ng0 +;;; Copyright © 2016, 2017 ng0 ;;; Copyright © 2017 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. @@ -158,6 +158,47 @@ configuration files.") ("tcl" ,tcl) ,@(package-inputs vim))))) +(define-public vim-neocomplete + (package + (name "vim-neocomplete") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/Shougo/neocomplete.vim/" + "archive/ver." version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1307gbrdwam2akq9w2lpijc41740i4layk2qkd9sjkqxfch5lni2")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (autoload (string-append vimfiles "/autoload")) + (doc (string-append vimfiles "/doc")) + (plugin (string-append vimfiles "/plugin"))) + (copy-recursively "autoload" autoload) + (copy-recursively "doc" doc) + (copy-recursively "plugin" plugin) + #t)))))) + (synopsis "Next generation completion framework for Vim") + (description + "@code{neocomplete}, an abbreviation of 'neo-completion with cache', +is a plugin for Vim. +It provides keyword completion system by maintaining a cache of keywords in +the current buffer. Neocomplete can be customized easily and has many more +features than Vim's built-in completion.") + (home-page "https://github.com/Shougo/neocomplete.vim/") + (license license:expat))) + (define-public neovim (package (name "neovim") From 843b19ca883d32a257c2b8722f288f39721be480 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:20 +0000 Subject: [PATCH 237/436] gnu: Add vim-scheme. * gnu/packages/vim.scm (vim-scheme): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index a683537cb8..ee6cda04ac 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -23,6 +23,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (gnu packages) @@ -199,6 +200,46 @@ features than Vim's built-in completion.") (home-page "https://github.com/Shougo/neocomplete.vim/") (license license:expat))) +(define-public vim-scheme + (let ((commit "93827987c10f2d5dc519166a761f219204926d5f") + (revision "1")) + (package + (name "vim-scheme") + (version (string-append "0.0.0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "http://git.foldling.org/vim-scheme.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1ynjr1109dxgj0lz261gmzz3wf5ap1m6j6hnvl3lcyv66a4y8pjv")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (after (string-append vimfiles "/after")) + (syntax (string-append vimfiles "/syntax")) + (ftplugin (string-append vimfiles "/ftplugin"))) + (copy-recursively "after" after) + (copy-recursively "ftplugin" ftplugin) + (copy-recursively "syntax" syntax) + #t)))))) + (synopsis "Scheme syntax for Vim") + (description + "@code{vim-scheme} provides Scheme support for Vim (R7RS and CHICKEN).") + (home-page "http://foldling.org/git/vim-scheme.git/") + (license license:public-domain)))) + (define-public neovim (package (name "neovim") From 34af179ac73e4dd01ec3b3e311db21c6ad18c90d Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:21 +0000 Subject: [PATCH 238/436] gnu: Add vim-neosnippet-snippets. * gnu/packages/vim.scm (vim-neosnippet-snippets): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index ee6cda04ac..a2c86e5c0a 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -200,6 +200,45 @@ features than Vim's built-in completion.") (home-page "https://github.com/Shougo/neocomplete.vim/") (license license:expat))) +;; There are no release tarballs. +(define-public vim-neosnippet-snippets + (let ((commit "8e2b1c0cab9ed9a832b3743dbb65e9966a64331a") + (revision "1")) + (package + (name "vim-neosnippet-snippets") + (version (string-append "0.0.0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shougo/neosnippet-snippets") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "151wpvbj6jb9jdkbhj3b77f5sq7y328spvwfbqyj1y32rg4ifmc6")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles"))) + (copy-recursively "neosnippets" + (string-append vimfiles "/neosnippets")) + #t)))))) + (synopsis "Snippets for neosnippet") + (description + "@code{neosnippet-snippets} provides standard snippets for the Vim plugin +@code{neosnippet}. Snippets are small templates for commonly used code that +you can fill in on the fly.") + (home-page "https://github.com/Shougo/neosnippet-snippets") + (license license:expat)))) + (define-public vim-scheme (let ((commit "93827987c10f2d5dc519166a761f219204926d5f") (revision "1")) From 5890f891e7c95119ab0931fb6320850331b6a432 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:22 +0000 Subject: [PATCH 239/436] gnu: Add vim-neosnippet. * gnu/packages/vim.scm (vim-neosnippet): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 57 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index a2c86e5c0a..ca8cb5637f 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -239,6 +239,63 @@ you can fill in on the fly.") (home-page "https://github.com/Shougo/neosnippet-snippets") (license license:expat)))) +;; The released tarball is too old for our Vim. +(define-public vim-neosnippet + (let ((commit "1bd7e23c79b73da16eb0c9469b25c376d3594583") + (revision "1")) + (package + (name "vim-neosnippet") + (version (string-append "4.2-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shougo/neosnippet.vim/") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0k80syscmpnj38ks1fq02ds59g0r4jlg9ll7z4qc048mgi35alw5")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (autoload (string-append vimfiles "/autoload")) + (doc (string-append vimfiles "/doc")) + (ftdetect (string-append vimfiles "/ftdetect")) + (ftplugin (string-append vimfiles "/ftplugin")) + (indent (string-append vimfiles "/indent")) + (plugin (string-append vimfiles "/plugin")) + (rplugin (string-append vimfiles "/rplugin")) + (syntax (string-append vimfiles "/syntax"))) + (copy-recursively "autoload" autoload) + (copy-recursively "doc" doc) + (copy-recursively "ftdetect" ftdetect) + (copy-recursively "ftplugin" ftplugin) + (copy-recursively "indent" indent) + (copy-recursively "plugin" plugin) + (copy-recursively "rplugin" rplugin) + (copy-recursively "syntax" syntax) + #t)))))) + (synopsis "Snippet support for Vim") + (description + "@code{neosnippet}, is a plugin for Vim which adds snippet support to Vim. +Snippets are small templates for commonly used code that you can fill in on +the fly. To use snippets can increase your productivity in Vim a lot. +The functionality of this plug-in is quite similar to plug-ins like +@code{snipMate.vim} or @code{snippetsEmu.vim}. But since you can choose +snippets with the neocomplcache / neocomplete interface, you might have less +trouble using them, because you do not have to remember each snippet name.") + (home-page "https://github.com/Shougo/neosnippet.vim/") + (license license:expat)))) + (define-public vim-scheme (let ((commit "93827987c10f2d5dc519166a761f219204926d5f") (revision "1")) From a4c95372e28c73ec8f8a5aaba53b6de39185fc25 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:23 +0000 Subject: [PATCH 240/436] gnu: Add vim-luna. * gnu/packages/vim.scm (vim-luna): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index ca8cb5637f..b80b3f2ebf 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -336,6 +336,42 @@ trouble using them, because you do not have to remember each snippet name.") (home-page "http://foldling.org/git/vim-scheme.git/") (license license:public-domain)))) +(define-public vim-luna + (let ((commit "633619953dcf8577168e255230f96b05f28d6371") + (revision "1")) + (package + (name "vim-luna") + (version (string-append "0.0.0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/notpratheek/vim-luna") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0ka3qbhsh8lix1vyj4678j7dnchkd8khhirrnn3aylxxf8fpqyg8")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (colors (string-append vimfiles "/colors"))) + (copy-recursively "colors" colors) + #t)))))) + (synopsis "Dark color theme for Vim") + (description + "@code{vim-luna} is a dark color theme for Vim.") + (home-page "https://github.com/notpratheek/vim-luna") + (license license:expat)))) + (define-public neovim (package (name "neovim") From 25340002b6f6d54737eef6878b0569c5c1ff27bc Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:24 +0000 Subject: [PATCH 241/436] gnu: Add vim-context-filetype. * gnu/packages/vim.scm (vim-context-filetype): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index b80b3f2ebf..c702b9011b 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -372,6 +372,45 @@ trouble using them, because you do not have to remember each snippet name.") (home-page "https://github.com/notpratheek/vim-luna") (license license:expat)))) +;; There are no tarball releases. +(define-public vim-context-filetype + (let ((commit "5e85f8cae26806f391aefe2661791a6de53bcea2") + (revision "1")) + (package + (name "vim-context-filetype") + (version (string-append "0.0.0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shougo/context_filetype.vim") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0alvrfhmd91zkd9h83s8wvgyq4iakcf6rybsyjd369qbgpcqky89")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (doc (string-append vimfiles "/doc")) + (autoload (string-append vimfiles "/autoload"))) + (copy-recursively "doc" doc) + (copy-recursively "autoload" autoload) + #t)))))) + (synopsis "Context filetype library for Vim") + (description + "@code{vim-context-filetype} is context filetype library for Vim script.") + (home-page "https://github.com/Shougo/context_filetype.vim") + (license license:expat)))) ; ??? check again + (define-public neovim (package (name "neovim") From 7ffcf5c5e063ff65be1f59822f7631c497926000 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:25 +0000 Subject: [PATCH 242/436] gnu: Add vim-airline. * gnu/packages/vim.scm (vim-airline): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index c702b9011b..fbe4b2b041 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -411,6 +411,47 @@ trouble using them, because you do not have to remember each snippet name.") (home-page "https://github.com/Shougo/context_filetype.vim") (license license:expat)))) ; ??? check again +(define-public vim-airline + (package + (name "vim-airline") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/vim-airline/vim-airline/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "053sfq3jmgdc5y7zbg6jrk7r2hp0raj3y3mxa2h1c1bnkb6wvcaz")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (autoload (string-append vimfiles "/autoload")) + (doc (string-append vimfiles "/doc")) + (t (string-append vimfiles "/t")) + (plugin (string-append vimfiles "/plugin"))) + (copy-recursively "autoload" autoload) + (copy-recursively "doc" doc) + (copy-recursively "plugin" plugin) + (copy-recursively "t" t) + #t)))))) + (synopsis "Statusline for Vim") + (description + "@code{vim-airline} is an extensible statusline for Vim. +It can be extended and costumized with themes, works with unicode fonts +and powerline symbols, etc.") + (home-page "https://github.com/vim-airline/vim-airline") + (license license:expat))) + (define-public neovim (package (name "neovim") From b02a141f3e714ac70173ecbf14afe97b9a62eb2f Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 13:18:26 +0000 Subject: [PATCH 243/436] gnu: Add vim-airline-themes. * gnu/packages/vim.scm (vim-airline-themes): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/vim.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index fbe4b2b041..82403feb1d 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -452,6 +452,47 @@ and powerline symbols, etc.") (home-page "https://github.com/vim-airline/vim-airline") (license license:expat))) +;; There are no tarball releases. +(define-public vim-airline-themes + (let ((commit "6026eb78bf362cb3aa875aff8487f65728d0f7d8") + (revision "1")) + (package + (name "vim-airline-themes") + (version (string-append "0.0.0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vim-airline/vim-airline-themes") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "13ijkavh1r0935cn2rjsfbdd1q3ka8bi26kw0bdkrqlrqxwvpss8")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (doc (string-append vimfiles "/doc")) + (plugin (string-append vimfiles "/plugin")) + (autoload (string-append vimfiles "/autoload"))) + (copy-recursively "doc" doc) + (copy-recursively "autoload" autoload) + (copy-recursively "plugin" plugin) + #t)))))) + (synopsis "Collection of themes for Vim-airline") + (description + "@code{vim-airline-themes} is a collection of themes for @code{vim-airline}.") + (home-page "https://github.com/vim-airline/vim-airline-themes") + (license license:expat)))) + (define-public neovim (package (name "neovim") From a9406b2416314fa7a52fa6e9b1b14faf4567b80e Mon Sep 17 00:00:00 2001 From: John Darrington Date: Tue, 28 Feb 2017 18:50:07 +0100 Subject: [PATCH 244/436] gnu: Add ccd2cue * gnu/packages/cdrom.scm (ccd2cue): New variable. --- gnu/packages/cdrom.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index 293bf16ade..14e430646a 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2015, 2016, 2017 Efraim Flashner ;;; Copyright © 2016 Alex Kost ;;; Copyright © 2016 Marius Bakke +;;; Copyright © 2017 John Darrington ;;; ;;; This file is part of GNU Guix. ;;; @@ -496,3 +497,27 @@ session, and it can create M3U playlists.") (synopsis "Command-line program to extract audio CDs") (description "RipIT is used to extract audio from CDs.") (license gpl2))) + +(define-public ccd2cue + (package + (name "ccd2cue") + (version "0.5") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://gnu/ccd2cue/ccd2cue-" version + ".tar.gz")) + (sha256 + (base32 + "1icrkg25hwx4gsn3dski2172ia4ywjh8m1sa17zmjclnrgdwy9c7")))) + (build-system gnu-build-system) + (synopsis "CCD to CUE sheet conversion") + (description + "GNU ccd2cue is a preprocessor for CD burning software that allows +the conversion of the proprietary CCD format to the CUE format, which +is well-supported by free software. These files are commonly +distributed with CD images and are used to describe how tracks are +laid out on the image.") + (home-page "http://www.gnu.org/software/ccd2cue") + (license gpl3+))) From 05740895feebfbbedc3f20968ac172b85b90b1de Mon Sep 17 00:00:00 2001 From: Carlo Zancanaro Date: Sat, 25 Feb 2017 20:16:12 +1100 Subject: [PATCH 245/436] gnu: wine: Add 'pulseaudio' to 'inputs'. * gnu/packages/wine.scm (wine)[inputs]: Add pulseaudio. Signed-off-by: Kei Kebreau --- gnu/packages/wine.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 7b73353387..d28e2dd4e4 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages openldap) #:use-module (gnu packages perl) + #:use-module (gnu packages pulseaudio) #:use-module (gnu packages pkg-config) #:use-module (gnu packages mp3) #:use-module (gnu packages ncurses) @@ -99,6 +100,7 @@ ("libXcomposite" ,libxcomposite) ("ncurses" ,ncurses) ("openal" ,openal) + ("pulseaudio" ,pulseaudio) ("unixodbc" ,unixodbc) ("zlib" ,zlib))) (arguments From 13e4a6c8636779e26de52c796ea75832c71826a2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 28 Feb 2017 20:34:09 +0200 Subject: [PATCH 246/436] gnu: screen: Update to 4.5.1. * gnu/packages/screen.scm (screen): Update to 4.5.1. [source]: Remove patch. * gnu/packages/patches/screen-CVE-2017-5618.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../patches/screen-CVE-2017-5618.patch | 40 ------------------- gnu/packages/screen.scm | 6 +-- 3 files changed, 2 insertions(+), 45 deletions(-) delete mode 100644 gnu/packages/patches/screen-CVE-2017-5618.patch diff --git a/gnu/local.mk b/gnu/local.mk index b408cc29d9..f356a124b3 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -893,7 +893,6 @@ dist_patch_DATA = \ %D%/packages/patches/sed-hurd-path-max.patch \ %D%/packages/patches/scheme48-tests.patch \ %D%/packages/patches/scotch-test-threading.patch \ - %D%/packages/patches/screen-CVE-2017-5618.patch \ %D%/packages/patches/sdl-libx11-1.6.patch \ %D%/packages/patches/seq24-rename-mutex.patch \ %D%/packages/patches/serf-comment-style-fix.patch \ diff --git a/gnu/packages/patches/screen-CVE-2017-5618.patch b/gnu/packages/patches/screen-CVE-2017-5618.patch deleted file mode 100644 index 1b95e428c8..0000000000 --- a/gnu/packages/patches/screen-CVE-2017-5618.patch +++ /dev/null @@ -1,40 +0,0 @@ -Fixes CVE-2017-5618 (privilege escalation via opening the logfile when -screen is installed setuid root): - -https://savannah.gnu.org/bugs/?50142 -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5618 - -This patch reverts the upstream commit that introduced the bug: - -https://git.savannah.gnu.org/cgit/screen.git/commit/?id=5460f5d28c01a9a58e021eb1dffef2965e629d58 - -From f55b0cc29a0ac2a1c54e8a5e886b7393edd4a76c Mon Sep 17 00:00:00 2001 -From: Leo Famulari -Date: Sat, 11 Feb 2017 22:40:24 -0500 -Subject: [PATCH] Revert "adding permissions check for the logfile name" - -This reverts commit 5460f5d28c01a9a58e021eb1dffef2965e629d58. ---- - src/screen.c | 6 ------ - 1 file changed, 6 deletions(-) - -diff --git a/src/screen.c b/src/screen.c -index 64650e9..283c305 100644 ---- a/src/screen.c -+++ b/src/screen.c -@@ -673,12 +673,6 @@ int main(int ac, char** av) - Panic(0, "-L: logfile name can not start with \"-\" symbol"); - if (strlen(screenlogfile) > PATH_MAX) - Panic(0, "-L: logfile name too long. (max. %d char)", PATH_MAX); -- -- FILE *w_check; -- if ((w_check = fopen(screenlogfile, "w")) == NULL) -- Panic(0, "-L: logfile name access problem"); -- else -- fclose(w_check); - } - nwin_options.Lflag = 1; - break; --- -2.11.1 - diff --git a/gnu/packages/screen.scm b/gnu/packages/screen.scm index 57e6cb595e..f5c914e88a 100644 --- a/gnu/packages/screen.scm +++ b/gnu/packages/screen.scm @@ -35,15 +35,13 @@ (define-public screen (package (name "screen") - (version "4.5.0") + (version "4.5.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/screen/screen-" version ".tar.gz")) - (patches (search-patches "screen-CVE-2017-5618.patch")) - (patch-flags '("-p2")) (sha256 - (base32 "1c7grw03a9iwvqbxfd6hmjb681rp8gb55zsxm7b3apqqcb1sghq1")))) + (base32 "0bbv16gpxrh64sn4bvjy3qjy7jsxjlqlilyysin02fwnvla23nwp")))) (build-system gnu-build-system) (native-inputs `(("makeinfo" ,texinfo))) From 5f947808cd623a1b7f75da38a962b4389702463d Mon Sep 17 00:00:00 2001 From: John Darrington Date: Tue, 28 Feb 2017 21:26:37 +0100 Subject: [PATCH 247/436] gnu: Add linsmith. * gnu/packages/engineering.scm (linsmith): New variable. --- gnu/packages/engineering.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 734efcdc73..23446bafa8 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -750,3 +750,27 @@ electrical diagrams), gerbview (viewing Gerber files) and others.") (description "This package provides Kicad component, footprint and 3D render model libraries.") (license license:lgpl2.0+)))) + +(define-public linsmith + (package + (name "linsmith") + (version "0.99.30") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/linsmith/linsmith/linsmith-" + version "/linsmith-" version ".tar.gz")) + (sha256 + (base32 + "18qslhr2r45rhpj4v6bjcqx189vs0bflvsj271wr7w8kvh69qwvn")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config) + ("gtk" ,gtk+-2) + ("libgnome" ,libgnomeui))) + (home-page "http://jcoppens.com/soft/linsmith/index.en.php") + (synopsis "Smith Charting program") + (description "LinSmith is a Smith Charting program, mainly designed for +educational use. As such, there is an emphasis on capabilities that improve +the 'showing the effect of'-style of operation.") + (license license:gpl2+))) From 43fe431cce107bd311a68dea59ac0f672ac13615 Mon Sep 17 00:00:00 2001 From: David Craven Date: Tue, 14 Feb 2017 16:28:31 +0100 Subject: [PATCH 248/436] vm: Remove hard coded kernel file name. * gnu/system/vm.scm (system-qemu-image/shared-store-script, expression->derivation-in-linux-vm): Use operating-system-kernel-file and system-linux-image-file-name. * gnu/system.scm (system-linux-image-file-name): Add ARM. --- gnu/system.scm | 9 ++++++--- gnu/system/vm.scm | 5 +++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/gnu/system.scm b/gnu/system.scm index 1006c842c9..c8d4d014ed 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -97,6 +97,8 @@ operating-system-locale-directory operating-system-boot-script + system-linux-image-file-name + boot-parameters boot-parameters? boot-parameters-label @@ -255,9 +257,10 @@ from the initrd." (define* (system-linux-image-file-name #:optional (system (%current-system))) "Return the basename of the kernel image file for SYSTEM." ;; FIXME: Evaluate the conditional based on the actual current system. - (if (string-prefix? "mips" (%current-system)) - "vmlinuz" - "bzImage")) + (cond + ((string-prefix? "arm" (%current-system)) "zImage") + ((string-prefix? "mips" (%current-system)) "vmlinuz") + (else "bzImage"))) (define (operating-system-kernel-file os) "Return an object representing the absolute file name of the kernel image of diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 8a35f7fbc5..a7203d1690 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -141,7 +141,8 @@ made available under the /xchg CIFS share." (gnu build vm)) (let ((inputs '#$(list qemu coreutils)) - (linux (string-append #$linux "/bzImage")) + (linux (string-append #$linux "/" + #$(system-linux-image-file-name))) (initrd (string-append #$initrd "/initrd")) (loader #$loader) (graphs '#$(match references-graphs @@ -487,7 +488,7 @@ exec " #$qemu "/bin/" #$(qemu-command (%current-system)) #$@(if full-boot? #~() - #~(" -kernel " #$(operating-system-kernel os) "/bzImage \ + #~(" -kernel " #$(operating-system-kernel-file os) " \ -initrd " #$os-drv "/initrd \ -append \"" #$(if graphic? "" "console=ttyS0 ") "--system=" #$os-drv " --load=" #$os-drv "/boot --root=/dev/vda1 " From 26a076ed693167dd4d501a880933a75da894a57f Mon Sep 17 00:00:00 2001 From: David Craven Date: Tue, 14 Feb 2017 16:28:32 +0100 Subject: [PATCH 249/436] vm: Improve readability of run-vm.sh generation. * gnu/system/vm.scm (common-qemu-options, system-qemu-image/shared-store-script): Improve readability. --- gnu/system/vm.scm | 71 ++++++++++++++++++++++++++--------------------- 1 file changed, 39 insertions(+), 32 deletions(-) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index a7203d1690..103af37c9a 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -434,25 +434,26 @@ bootloader refers to: OS kernel, initrd, bootloader data, etc." (define* (common-qemu-options image shared-fs) "Return the a string-value gexp with the common QEMU options to boot IMAGE, with '-virtfs' options for the host file systems listed in SHARED-FS." - (define (virtfs-option fs) - #~(string-append "-virtfs local,path=\"" #$fs - "\",security_model=none,mount_tag=\"" - #$(file-system->mount-tag fs) - "\" ")) - #~(string-append - ;; Only enable kvm if we see /dev/kvm exists. + (define (virtfs-option fs) + #~(format #f "-virtfs local,path=~s,security_model=none,mount_tag=~s" + #$fs #$(file-system->mount-tag fs))) + + #~(;; Only enable kvm if we see /dev/kvm exists. ;; This allows users without hardware virtualization to still use these ;; commands. - #$(if (file-exists? "/dev/kvm") - " -enable-kvm " - "") - " -no-reboot -net nic,model=virtio \ - " #$@(map virtfs-option shared-fs) " \ - -vga std \ - -drive file=" #$image - ",if=virtio,cache=writeback,werror=report,readonly \ - -m 256")) + #$@(if (file-exists? "/dev/kvm") + '("-enable-kvm") + '()) + + "-no-reboot" + "-net nic,model=virtio" + + #$@(map virtfs-option shared-fs) + "-vga std" + (format #f "-drive file=~a,if=virtio,cache=writeback,werror=report,readonly" + #$image) + "-m 256")) (define* (system-qemu-image/shared-store-script os #:key @@ -479,25 +480,31 @@ it is mostly useful when FULL-BOOT? is true." os #:full-boot? full-boot? #:disk-image-size disk-image-size))) + (define kernel-arguments + #~(list "--root=/dev/vda1" + (string-append "--system=" #$os-drv) + (string-append "--load=" #$os-drv "/boot") + #$@(if graphic? #~() #~("console=ttyS0")) + #+@(operating-system-kernel-arguments os))) + + (define qemu-exec + #~(list (string-append #$qemu "/bin/" #$(qemu-command (%current-system))) + #$@(if full-boot? + #~() + #~("-kernel" #$(operating-system-kernel-file os) + "-initrd" #$(file-append os-drv "/initrd") + (format #f "-append ~s" + (string-join #$kernel-arguments " ")))) + #$@(common-qemu-options image + (map file-system-mapping-source + (cons %store-mapping mappings))))) + (define builder #~(call-with-output-file #$output (lambda (port) - (display - (string-append "#!" #$bash "/bin/sh -exec " #$qemu "/bin/" #$(qemu-command (%current-system)) - -#$@(if full-boot? - #~() - #~(" -kernel " #$(operating-system-kernel-file os) " \ - -initrd " #$os-drv "/initrd \ - -append \"" #$(if graphic? "" "console=ttyS0 ") - "--system=" #$os-drv " --load=" #$os-drv "/boot --root=/dev/vda1 " - (string-join (list #+@(operating-system-kernel-arguments os))) "\" ")) -#$(common-qemu-options image - (map file-system-mapping-source - (cons %store-mapping mappings))) -" \"$@\"\n") - port) + (format port "#!~a~% exec ~a \"$@\"~%" + #$(file-append bash "/bin/sh") + (string-join #$qemu-exec " ")) (chmod port #o555)))) (gexp->derivation "run-vm.sh" builder))) From 05c638984dcbd02e51a8fc47431fbce405a4c614 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 18:56:44 +0000 Subject: [PATCH 250/436] gnu: Add lush2. * gnu/packages/lisp.scm (lush2): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/lisp.scm | 76 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 75 insertions(+), 1 deletion(-) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 80161de01b..647c64dcc7 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2016 Federico Beffa -;;; Copyright © 2016 ng0 +;;; Copyright © 2016, 2017 ng0 ;;; Copyright © 2016 Andy Patterson ;;; Copyright © 2017 Ricardo Wurmus ;;; @@ -37,16 +37,27 @@ #:use-module (guix build-system asdf) #:use-module (guix build-system trivial) #:use-module (gnu packages base) + #:use-module (gnu packages compression) + #:use-module (gnu packages fontutils) + #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages bdw-gc) #:use-module (gnu packages libffi) #:use-module (gnu packages libffcall) #:use-module (gnu packages readline) + #:use-module (gnu packages sdl) #:use-module (gnu packages libsigsegv) + #:use-module (gnu packages linux) #:use-module (gnu packages admin) #:use-module (gnu packages ed) + #:use-module (gnu packages gl) + #:use-module (gnu packages gcc) + #:use-module (gnu packages glib) + #:use-module (gnu packages gettext) #:use-module (gnu packages m4) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages version-control) + #:use-module (gnu packages xorg) #:use-module (ice-9 match) #:use-module (srfi srfi-1)) @@ -530,6 +541,69 @@ The core is 12 builtin special forms and 33 builtin functions.") (home-page "https://github.com/JeffBezanson/femtolisp") (license license:bsd-3)))) +(define-public lush2 + (package + (name "lush2") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/lush/lush2/lush-" + version ".tar.gz")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "src/unix.c" + (("\\{ \"LUSH_DATE\", __DATE__ \\},") "") + (("\\{ \"LUSH_TIME\", __TIME__ \\},") "")) + (substitute* "src/main.c" + (("\" \\(built \" __DATE__ \"\\)\"") "")))) + (sha256 + (base32 + "02pkfn3nqdkm9fm44911dbcz0v3r0l53vygj8xigl6id5g3iwi4k")))) + (build-system gnu-build-system) + (arguments + `(;; We have to add these LIBS so that they are found. + #:configure-flags (list "LIBS=-lz" + "X_EXTRA_LIBS=-lfontconfig" + "--with-x") + #:tests? #f)) ; No make check. + (native-inputs `(("intltool" ,intltool))) + (inputs + `(("alsa-lib" ,alsa-lib) + ("sdl" ,sdl) + ("sdl-image" ,sdl-image) + ("sdl-mixer" ,sdl-mixer) + ("sdl-net" ,sdl-net) + ("sdl-ttf" ,sdl-ttf) + ("lapack" ,lapack) + ("libxft" ,libxft) + ("fontconfig" ,fontconfig) + ("gsl" ,gsl) + ("openblas" ,openblas) + ("glu" ,glu) + ("mesa" ,mesa) + ("mesa-utils" ,mesa-utils) + ("binutils" ,binutils) + ("libiberty" ,libiberty) + ("readline" ,readline) + ("zlib" ,zlib) + ("gettext-minimal" ,gettext-minimal))) + (synopsis "Lisp Universal Shell") + (description + "Lush is an object-oriented Lisp interpreter/compiler with features +designed to please people who want to prototype large numerical +applications. Lush includes an extensive library of +vector/matrix/tensor manipulation, numerous numerical libraries +(including GSL, LAPACK, and BLAS), a set of graphic functions, a +simple GUI toolkit, and interfaces to various graphic and multimedia +libraries such as OpenGL, SDL, Video4Linux, and ALSA (video/audio +grabbing), and others. Lush is an ideal frontend script language for +programming projects written in C or other languages. Lush also has +libraries for Machine Learning, Neural Nets and statistical estimation.") + (home-page "http://lush.sourceforge.net/") + (license license:lgpl2.1+))) + (define-public sbcl-alexandria (let ((revision "1") (commit "926a066611b7b11cb71e26c827a271e500888c30")) From e9d60ebadbea90a63138e5423b619d132410781a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 1 Mar 2017 11:31:30 +0200 Subject: [PATCH 251/436] gnu: octave: Update to 4.2.1. * gnu/packages/maths.scm (octave): Update to 4.2.1. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1f4f388c65..913a403dab 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -923,7 +923,7 @@ can solve two kinds of problems: (define-public octave (package (name "octave") - (version "4.2.0") + (version "4.2.1") (source (origin (method url-fetch) @@ -931,7 +931,7 @@ can solve two kinds of problems: version ".tar.lz")) (sha256 (base32 - "19vvliwxgip0af812vny5xy5r8kacyj7v62203mh4z2n3p14b78i")))) + "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) From f495f1bf2d34ef5dcc5c033427666be4b6beb9b8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 1 Mar 2017 11:32:30 +0200 Subject: [PATCH 252/436] gnu: enlightenment: Update to 0.21.6. * gnu/packages/enlightenment.scm (enlightenment): Update to 0.21.6. --- gnu/packages/enlightenment.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index a34578afe7..bc455c0bd4 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -197,7 +197,7 @@ Libraries with some extra bells and whistles.") (define-public enlightenment (package (name "enlightenment") - (version "0.21.5") + (version "0.21.6") (source (origin (method url-fetch) (uri @@ -205,7 +205,7 @@ Libraries with some extra bells and whistles.") name "/" name "-" version ".tar.xz")) (sha256 (base32 - "1fslq70z4s6v9ipahnk8s5fgqnqq4njv4rlqv951r1bh1xk5lx7h")))) + "0gan3c8jbvhcmvb2fpbprr3m6db0afg1dnrb87nbqb399nsi81zd")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--enable-mount-eeze"))) From bd9f8869b15891863a6c7420d1cfdae309ba8594 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 09:39:11 +0000 Subject: [PATCH 253/436] gnu: mumble: Build with 'murmur' server component. * gnu/packages/telephony.scm (mumble)[arguments]: Build 'murmur'. Remove 'no-server' and add 'no-ice' to "configure" phase. [description]: Add a sentence about mumble and murmur. Signed-off-by: Kei Kebreau --- gnu/packages/telephony.scm | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm index b0cefe4056..87261825c5 100644 --- a/gnu/packages/telephony.scm +++ b/gnu/packages/telephony.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2015, 2016 Efraim Flashner ;;; Copyright © 2016 Lukas Gradl ;;; Copyright © 2016 Francesco Frassinelli -;;; Copyright © 2016 ng0 +;;; Copyright © 2016, 2017 ng0 ;;; ;;; This file is part of GNU Guix. ;;; @@ -354,7 +354,7 @@ address of one of the participants.") (string-append "CONFIG+=" (string-join (list "no-update" - "no-server" + "no-ice" "no-embed-qt-translations" "no-bundled-speex" "pch" @@ -378,6 +378,8 @@ address of one of the participants.") (replace 'install ; install phase does not exist (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) + (etc (string-append out "/etc/murmur")) + (dbus (string-append out "/etc/dbus-1/system.d/")) (bin (string-append out "/bin")) (services (string-append out "/share/services")) (applications (string-append out "/share/applications")) @@ -391,6 +393,12 @@ address of one of the participants.") (install-file "icons/mumble.svg" icons) (install-file "man/mumble-overlay.1" man) (install-file "man/mumble.1" man) + (install-file "release/murmurd" bin) + (install-file "scripts/murmur.ini.system" etc) + (rename-file (string-append etc "/murmur.ini.system") + (string-append etc "/murmur.ini")) + (install-file "scripts/murmur.conf" dbus) + (install-file "man/murmurd.1" man) (for-each (lambda (file) (install-file file lib)) (find-files "." "\\.so\\.")) (for-each (lambda (file) (install-file file lib)) @@ -414,7 +422,9 @@ address of one of the participants.") (synopsis "Low-latency, high quality voice chat software") (description "Mumble is an low-latency, high quality voice chat -software primarily intended for use while gaming.") +software primarily intended for use while gaming. +Mumble consists of two applications for separate usage: +@code{mumble} for the client, and @code{murmur} for the server.") (home-page "https://wiki.mumble.info/wiki/Main_Page") (license (list license:bsd-3 ;; The bundled celt is bsd-2. Remove after 1.3.0. From b0377e58c30c399f9844a1607d677e525bb1d05f Mon Sep 17 00:00:00 2001 From: David Craven Date: Tue, 14 Feb 2017 16:28:26 +0100 Subject: [PATCH 254/436] file-systems: Add FAT32 support. * gnu/build/file-systems.scm (%fat32-endianness, fat32-superblock?, read-fat32-superblock, fat32-superblock-uuid, fat32-uuid->string, fat32-superblock-volume-name, check-fat32-file-system): New variables. (%partition-label-readers, %partition-uuid-readers, check-file-system): Add fat support. (latin1->string): New variable. (null-terminated-latin1->string): Use latin1->string. --- gnu/build/file-systems.scm | 66 ++++++++++++++++++++++++++++++++++---- 1 file changed, 59 insertions(+), 7 deletions(-) diff --git a/gnu/build/file-systems.scm b/gnu/build/file-systems.scm index f8ab95370c..fe98df95d5 100644 --- a/gnu/build/file-systems.scm +++ b/gnu/build/file-systems.scm @@ -106,15 +106,17 @@ takes a bytevector and returns #t when it's a valid superblock." (bytevector-copy! bv start result 0 size) result)) -(define (null-terminated-latin1->string bv) - "Return the volume name of SBLOCK as a string of at most 256 characters, or -#f if SBLOCK has no volume name." - ;; This is a Latin-1, nul-terminated string. - (let ((bytes (take-while (negate zero?) (bytevector->u8-list bv)))) +(define (latin1->string bv terminator) + "Return a string of BV, a latin1 bytevector, or #f. TERMINATOR is a predicate +that takes a number and returns #t when a termination character is found." + (let ((bytes (take-while (negate terminator) (bytevector->u8-list bv)))) (if (null? bytes) #f (list->string (map integer->char bytes))))) +(define null-terminated-latin1->string + (cut latin1->string <> zero?)) + ;;; ;;; Ext2 file systems. @@ -192,6 +194,51 @@ if DEVICE does not contain a btrfs file system." (0 'pass) (_ 'fatal-error))) + +;;; +;;; FAT32 file systems. +;;; + +;; . + +(define-syntax %fat32-endianness + ;; Endianness of fat file systems. + (identifier-syntax (endianness little))) + +(define (fat32-superblock? sblock) + "Return #t when SBLOCK is a fat32 superblock." + (bytevector=? (sub-bytevector sblock 82 8) + (string->utf8 "FAT32 "))) + +(define (read-fat32-superblock device) + "Return the raw contents of DEVICE's fat32 superblock as a bytevector, or +#f if DEVICE does not contain a fat32 file system." + (read-superblock device 0 90 fat32-superblock?)) + +(define (fat32-superblock-uuid sblock) + "Return the Volume ID of a fat superblock SBLOCK as a 4-byte bytevector." + (sub-bytevector sblock 67 4)) + +(define (fat32-uuid->string uuid) + "Convert fat32 UUID, a 4-byte bytevector, to its string representation." + (let ((high (bytevector-uint-ref uuid 0 %fat32-endianness 2)) + (low (bytevector-uint-ref uuid 2 %fat32-endianness 2))) + (format #f "~:@(~x-~x~)" low high))) + +(define (fat32-superblock-volume-name sblock) + "Return the volume name of SBLOCK as a string of at most 11 characters, or +#f if SBLOCK has no volume name. The volume name is a latin1 string. +Trailing spaces are trimmed." + (string-trim-right (latin1->string (sub-bytevector sblock 71 11) (lambda (c) #f)) #\space)) + +(define (check-fat32-file-system device) + "Return the health of a fat file system on DEVICE." + (match (status:exit-val + (system* "fsck.vfat" "-v" "-a" device)) + (0 'pass) + (1 'errors-corrected) + (_ 'fatal-error))) + ;;; ;;; LUKS encrypted devices. @@ -307,13 +354,17 @@ partition field reader that returned a value." (list (partition-field-reader read-ext2-superblock ext2-superblock-volume-name) (partition-field-reader read-btrfs-superblock - btrfs-superblock-volume-name))) + btrfs-superblock-volume-name) + (partition-field-reader read-fat32-superblock + fat32-superblock-volume-name))) (define %partition-uuid-readers (list (partition-field-reader read-ext2-superblock ext2-superblock-uuid) (partition-field-reader read-btrfs-superblock - btrfs-superblock-uuid))) + btrfs-superblock-uuid) + (partition-field-reader read-fat32-superblock + fat32-superblock-uuid))) (define read-partition-label (cut read-partition-field <> %partition-label-readers)) @@ -481,6 +532,7 @@ the following: (cond ((string-prefix? "ext" type) check-ext2-file-system) ((string-prefix? "btrfs" type) check-btrfs-file-system) + ((string-suffix? "fat" type) check-fat32-file-system) (else #f))) (if check-procedure From 0da8313c679f101c3f99970c50d6f0fef995f633 Mon Sep 17 00:00:00 2001 From: John Darrington Date: Wed, 1 Mar 2017 07:00:05 +0100 Subject: [PATCH 255/436] gnu: Add unrar. * gnu/packages/compression.scm (unrar): New variable. --- gnu/packages/compression.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 9897883184..73b2b846ea 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1128,3 +1128,21 @@ or junctions, and always follows hard links.") ;; libzpaq.cpp contains a mix of public-domain and ;; expat-licenced (or ‘MIT’) code. license:expat)))) + +(define-public unrar + (package + (name "unrar") + (version "0.0.1") + (source (origin + (method url-fetch) + (uri (string-append + "http://download.gna.org/unrar/unrar-" version ".tar.gz")) + (sha256 + (base32 + "1fgmjaxffj3shyxgy765jhxwz1cq88hk0fih1bsdzyvymyyz6mz7")))) + (build-system gnu-build-system) + (home-page "http://download.gna.org/unrar") + (synopsis "RAR archive extraction tool") + (description "Unrar is a simple command-line program to list and extract +RAR archives.") + (license license:gpl2+))) From 3a263368dd658ca5dc81e171ef041712c9e9b7a4 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 18:26:41 +0000 Subject: [PATCH 256/436] gnu: Add blists. * gnu/packages/mail.scm (blists): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/mail.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index f4f732ec19..a6cef7ab8d 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1951,3 +1951,38 @@ installation on systems where resources are limited. Its features include: @item Rich and customisable texts for automated operations. @end enumerate\n") (license license:expat))) + +(define-public blists + (package + (name "blists") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (string-append "http://download.openwall.net/pub/projects/" + "blists/blists-" version ".tar.gz")) + (sha256 + (base32 + "1gp51kmb8yv8d693wcpdslmwlbw5w2kgz4kxhrcaf7y89w8wy4qd")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; No tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (install-file "bindex" bin) + (install-file "bit" bin) + #t)))))) + (home-page "http://www.openwall.com/blists/") + (synopsis "Web interface to mailing list archives") + (description + "Blists is a web interface to mailing list archives that works off +indexed mbox files. There are two programs: @code{bindex} and @code{bit}. +@code{bindex} generates or updates the index file (incremental updates +are supported). @code{bit} is a CGI/SSI program that generates web pages +on the fly. Both programs are written in C and are very fast.") + (license license:expat))) From d2839defeca0b134d4238a1fbc7849bcecc8ce4f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 1 Mar 2017 05:33:03 +0100 Subject: [PATCH 257/436] gnu: jemalloc: Update to 4.5.0. * gnu/packages/jemalloc.scm (jemalloc): Update to 4.5.0. --- gnu/packages/jemalloc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm index 52b9216827..fcc9cc8082 100644 --- a/gnu/packages/jemalloc.scm +++ b/gnu/packages/jemalloc.scm @@ -27,7 +27,7 @@ (define-public jemalloc (package (name "jemalloc") - (version "4.4.0") + (version "4.5.0") (source (origin (method url-fetch) (uri (string-append @@ -35,7 +35,7 @@ version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "0cxhhybcbi02szavlxzwhvmqvddi7kgy71qxz2nz3lhqjwzadbm7")))) + "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl")))) (build-system gnu-build-system) (home-page "http://jemalloc.net/") (synopsis "General-purpose scalable concurrent malloc implementation") From ef23ed9e258718caf0d379bf7129b9f694d465d9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 1 Mar 2017 15:47:21 +0100 Subject: [PATCH 258/436] gnu: sessreg: Update to 1.1.1. * gnu/packages/xorg.scm (sessreg): Update to 1.1.1. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 911621a93c..7075d72043 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -1719,7 +1719,7 @@ features and to query screensaver info on specific windows.") (define-public sessreg (package (name "sessreg") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) @@ -1729,7 +1729,7 @@ features and to query screensaver info on specific windows.") ".tar.bz2")) (sha256 (base32 - "0z013rskwmdadd8cdlxvh4asmgim61qijyzfbqmr1q1mg1jpf4am")))) + "1qd66mg2bnppqz4xgdjzif2488zl82vx2c26ld3nb8pnyginm9vq")))) (build-system gnu-build-system) (inputs `(("xproto" ,xproto))) From 8c58c53beba33beefd657f466d2ba758f2096a08 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 1 Mar 2017 15:49:19 +0100 Subject: [PATCH 259/436] gnu: re2: Update to 2017-03-01. * gnu/packages/regex.scm (re2): Update to 2017-03-01. --- gnu/packages/regex.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm index f04cba706d..11f4716033 100644 --- a/gnu/packages/regex.scm +++ b/gnu/packages/regex.scm @@ -27,7 +27,7 @@ (define-public re2 (package (name "re2") - (version "2017-01-01") + (version "2017-03-01") (source (origin (method url-fetch) (uri @@ -37,7 +37,7 @@ (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0yij1ajh66h3pj3kfz7y0ldrsww8rlpjzaavyr5lchl98as1jq74")))) + "1s3kdcrz2mwi30k6pz9jkv5vk8b704bz65xgcr67wbn2pn3hpnqr")))) (build-system gnu-build-system) (arguments `(#:test-target "test" From ad839aeaee59f624f95edef529b95206522d0d41 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 1 Mar 2017 15:54:21 +0100 Subject: [PATCH 260/436] gnu: slop: Update to 5.3.37. * gnu/packages/xdisorg.scm (slop): Update to 5.3.37. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 3d69661ba5..548b278764 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -438,7 +438,7 @@ of the screen selected by mouse.") (define-public slop (package (name "slop") - (version "5.3.35") + (version "5.3.37") (source (origin (method url-fetch) (uri (string-append @@ -447,7 +447,7 @@ of the screen selected by mouse.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "12fkwardd33xbaisjv93r49jh1dmqw323zjsd9m8kxcyv1rimsig")))) + "1p2ih123zkj8rxz8acsxpaim1kq57f4rbq7zqsibafn5rkw5c5is")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From 7166221c624ae9b7663ca9743612a13c1576095a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 1 Mar 2017 15:55:03 +0100 Subject: [PATCH 261/436] gnu: maim: Update to 4.4.60. * gnu/packages/xdisorg.scm (maim): Update to 4.4.60. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 548b278764..a9c2e06b44 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -469,7 +469,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "4.4.59") + (version "4.4.60") (source (origin (method url-fetch) (uri (string-append @@ -478,7 +478,7 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0h8z4wm7zgxj1vlp98n12dyiwjwphhnl6yh8aaz3krm5v2kyy6hc")))) + "1j8czhbgilmv9c9hlind1w847yk856dzvxx1sj17fx89xkg8nixk")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From 07feb580315d6d1a4474634a272cfd5a3b90f652 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 1 Mar 2017 20:41:00 +0100 Subject: [PATCH 262/436] gnu: notmuch: Update to 0.23.7. * gnu/packages/mail.scm (notmuch, python2-notmuch): Update to 0.23.7. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index a6cef7ab8d..ffa088d49b 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -659,14 +659,14 @@ invoking @command{notifymuch} from the post-new hook.") (define-public notmuch (package (name "notmuch") - (version "0.23.5") + (version "0.23.7") (source (origin (method url-fetch) (uri (string-append "https://notmuchmail.org/releases/notmuch-" version ".tar.gz")) (sha256 (base32 - "0ry2k9sdwd1vw8cf6svch8wk98523s07mwxvsf7b8kghqnrr89n6")))) + "04w90c43zk23pys6prkqb14al408qypifcfj2qznqpwlf46v26zi")))) (build-system gnu-build-system) (arguments '(#:make-flags (list "V=1") ; Verbose test output. From 428af2c68391f9648bb6fe7423cccf38e7852f98 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 1 Mar 2017 12:27:35 -0500 Subject: [PATCH 263/436] gnu: graphicsmagick: Add comment about CVE-2017-6335. * gnu/packages/imagemagick.scm (graphicsmagick): Add comment. --- gnu/packages/imagemagick.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index b5a2c20655..74483965dd 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -162,7 +162,7 @@ script.") (license (package-license imagemagick)))) (define-public graphicsmagick - (let ((changeset "6156b4c2992d855ece6079653b3b93c3229fc4b8") + (let ((changeset "6156b4c2992d855ece6079653b3b93c3229fc4b8") ; fix CVE-2017-6335 (revision "2")) (package (name "graphicsmagick") From ea9e58ef66f0fc0235eb1b36690ad4e41bf8771d Mon Sep 17 00:00:00 2001 From: Carlo Zancanaro Date: Sun, 26 Feb 2017 11:34:44 +1100 Subject: [PATCH 264/436] gnu: icedtea-6: Modify certificate import to not fail for icedtea-8. Co-authored-by: Roel Janssen * gnu/packages/java.scm (icedtea-6)[arguments]: Do not fail install-keystore phase when attempting to import unsupported certificate types. Also ensure that the keystore is able to be written to before copying it. (icedtea-8)[arguments]: Restore "install-keystore" phase. --- gnu/packages/java.scm | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index e7479e1b08..1abdf607f5 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1,7 +1,8 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016 Ricardo Wurmus ;;; Copyright © 2016 Leo Famulari -;;; Copyright © 2016 Roel Janssen +;;; Copyright © 2016, 2017 Roel Janssen +;;; Copyright © 2017 Carlo Zancanaro ;;; ;;; This file is part of GNU Guix. ;;; @@ -706,7 +707,7 @@ build process and its dependencies, whereas Make uses Makefile format.") "-file" temp))) (display "yes\n" port) (when (not (zero? (status:exit-val (close-pipe port)))) - (error "failed to import" cert))) + (format #t "failed to import ~a\n" cert))) (delete-file temp))) ;; This is necessary because the certificate directory contains @@ -719,6 +720,15 @@ build process and its dependencies, whereas Make uses Makefile format.") "/lib/security")) (mkdir-p (string-append (assoc-ref outputs "jdk") "/jre/lib/security")) + + ;; The cacerts files we are going to overwrite are chmod'ed as + ;; read-only (444) in icedtea-8 (which derives from this + ;; package). We have to change this so we can overwrite them. + (chmod (string-append (assoc-ref outputs "out") + "/lib/security/" keystore) #o644) + (chmod (string-append (assoc-ref outputs "jdk") + "/jre/lib/security/" keystore) #o644) + (install-file keystore (string-append (assoc-ref outputs "out") "/lib/security")) @@ -1023,9 +1033,6 @@ build process and its dependencies, whereas Make uses Makefile format.") (find-files "openjdk.src/jdk/src/solaris/native" "\\.c|\\.h")) #t))) - ;; FIXME: This phase is needed but fails with this version of - ;; IcedTea. - (delete 'install-keystore) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((doc (string-append (assoc-ref outputs "doc") From d8bcf080883ac72457bf099a936dc7b87b1ed421 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 1 Mar 2017 22:32:02 -0500 Subject: [PATCH 265/436] gnu: vdirsyncer: Update to 0.15.0. * gnu/packages/dav.scm (vdirsyncer): Update to 0.15.0. [source]: Remove obsolete patch 'vdirsyncer-test-suite-slow-machines.patch'. * gnu/packages/patches/vdirsyncer-test-suite-slow-machines.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/dav.scm | 6 +-- .../vdirsyncer-test-suite-slow-machines.patch | 42 ------------------- 3 files changed, 2 insertions(+), 47 deletions(-) delete mode 100644 gnu/packages/patches/vdirsyncer-test-suite-slow-machines.patch diff --git a/gnu/local.mk b/gnu/local.mk index f356a124b3..406e0dc963 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -953,7 +953,6 @@ dist_patch_DATA = \ %D%/packages/patches/util-linux-CVE-2017-2616.patch \ %D%/packages/patches/upower-builddir.patch \ %D%/packages/patches/valgrind-enable-arm.patch \ - %D%/packages/patches/vdirsyncer-test-suite-slow-machines.patch \ %D%/packages/patches/vim-CVE-2017-5953.patch \ %D%/packages/patches/vorbis-tools-CVE-2014-9638+CVE-2014-9639.patch \ %D%/packages/patches/vorbis-tools-CVE-2014-9640.patch \ diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm index 546597c617..7901e1c1d8 100644 --- a/gnu/packages/dav.scm +++ b/gnu/packages/dav.scm @@ -55,15 +55,13 @@ clients.") (define-public vdirsyncer (package (name "vdirsyncer") - (version "0.14.1") + (version "0.15.0") (source (origin (method url-fetch) (uri (pypi-uri name version)) - (patches - (search-patches "vdirsyncer-test-suite-slow-machines.patch")) (sha256 (base32 - "044f01fjd8dpz4y9dm3qcc1a8cihcxxbr1sz6y6fkvglpb6k85y5")))) + "08aa5yxcj7ziz2r0hz4p554q8hgpfl2bh8r6r85f4g24mg6arxsj")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/patches/vdirsyncer-test-suite-slow-machines.patch b/gnu/packages/patches/vdirsyncer-test-suite-slow-machines.patch deleted file mode 100644 index 03093e8330..0000000000 --- a/gnu/packages/patches/vdirsyncer-test-suite-slow-machines.patch +++ /dev/null @@ -1,42 +0,0 @@ -Fix test failures caused by some build machines running more slowly than -expected, which manifest like this: - ------- -> raise FailedHealthCheck(message) -E hypothesis.errors.FailedHealthCheck: Data generation is extremely slow: Only produced 4 valid examples in 1.08 seconds (1 invalid ones and 0 exceeded maximum size). Try decreasing size of the data you're generating (with e.g.average_size or max_leaves parameters). -E See http://hypothesis.readthedocs.org/en/latest/healthchecks.html for more information about this. If you want to disable just this health check, add HealthCheck.too_slowto the suppress_health_check settings for this test. - -/gnu/store/b8d1r8bilvm3jkncgrpvmg3dni9cgcr1-python-hypothesis-3.1.0/lib/python3.5/site-packages/hypothesis/core.py:296: FailedHealthCheck ------- - -Patch copied from upstream source repository: - -https://github.com/pimutils/vdirsyncer/commit/10490a12f13f03495e0945eb9d45d7aed9ab0a6c - -From 10490a12f13f03495e0945eb9d45d7aed9ab0a6c Mon Sep 17 00:00:00 2001 -From: Markus Unterwaditzer -Date: Sat, 18 Feb 2017 15:45:06 +0100 -Subject: [PATCH] Unconditionally disable HealthCheck.too_slow - ---- - tests/conftest.py | 4 +++- - 1 file changed, 3 insertions(+), 1 deletion(-) - -diff --git a/tests/conftest.py b/tests/conftest.py -index e0a07d5..3afd7cd 100644 ---- a/tests/conftest.py -+++ b/tests/conftest.py -@@ -26,10 +26,12 @@ def benchmark(): - else: - del pytest_benchmark - -+ -+settings.suppress_health_check = [HealthCheck.too_slow] -+ - settings.register_profile("ci", settings( - max_examples=1000, - verbosity=Verbosity.verbose, -- suppress_health_check=[HealthCheck.too_slow] - )) - settings.register_profile("deterministic", settings( - derandomize=True, From 0204187296366af3ba89ad4319d94ab4125fc2b4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 28 Feb 2017 22:18:59 +0100 Subject: [PATCH 266/436] gnu: iproute2: Use @command in description. * gnu/packages/linux.scm (iproute2)[description]: Use @command mark-up when referring to the separate tools. --- gnu/packages/linux.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 1036166a27..6ff6d0b64e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1096,10 +1096,10 @@ allows a system administrator to make use of all iproute2 features, including traffic control. iproute2 is usually shipped in a package called iproute or iproute2 and -consists of several tools, of which the most important are ip and tc. ip -controls IPv4 and IPv6 configuration and tc stands for traffic control. Both -tools print detailed usage messages and are accompanied by a set of -manpages.") +consists of several tools, of which the most important are @command{ip} and +@command{tc}. @command{ip} controls IPv4 and IPv6 configuration and +@command{tc} stands for traffic control. Both tools print detailed usage +messages and are accompanied by a set of manpages.") (license license:gpl2+))) (define-public net-tools From 02de2f7bb2ff5e288a6f262a594570137d7779a4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 28 Feb 2017 22:47:34 +0100 Subject: [PATCH 267/436] gnu: youtube-dl: Update to 2017.02.28. * gnu/packages/video.scm (youtube-dl): Update to 2017.02.28. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 6494b2da5f..c609eadeec 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -975,7 +975,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2017.02.22") + (version "2017.02.28") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -983,7 +983,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "0abir0039igwz0830vdqknngs3hmr474j6xzh33v57p3y4imgx2i")))) + "194np8s2khzkdlpn6bmif5w9rzlwvdfapi1jnpg0wyq6mscasnj9")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion From 53c36279c20ac27c465c8314bfbd6f3dda8e4f92 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 1 Mar 2017 07:05:03 +0100 Subject: [PATCH 268/436] gnu: txt2man: Update to 1.6.0. * gnu/packages/man.scm (txt2man): Update to 1.6.0. --- gnu/packages/man.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm index 69c560c1b0..3763292fe4 100644 --- a/gnu/packages/man.scm +++ b/gnu/packages/man.scm @@ -202,7 +202,7 @@ automatically.") (define-public txt2man (package (name "txt2man") - (version "1.5.6") + (version "1.6.0") (source (origin (method url-fetch) @@ -211,7 +211,7 @@ automatically.") version ".tar.gz")) (sha256 (base32 - "0sjq687jknq65wbnjh2siq8hc09ydpnlmrkrnwl66mrhd4n9g7fz")))) + "168cj96974n2z0igin6j1ic1m45zyic7nm5ark7frq8j78rrx4zn")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target From 5f643dbe08bfda7817866a7911e352f268e16539 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 1 Mar 2017 20:36:50 +0100 Subject: [PATCH 269/436] gnu: tidy-html: Update to 5.4.0. * gnu/packages/web.scm (tidy-html): Update to 5.4.0. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 116ccf231b..f63a3eb9da 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4365,7 +4365,7 @@ used to start services with both privileged and non-privileged port numbers.") (define-public tidy-html (package (name "tidy-html") - (version "5.2.0") + (version "5.4.0") (source (origin (method url-fetch) @@ -4374,7 +4374,7 @@ used to start services with both privileged and non-privileged port numbers.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0kbwzh15dlapp3s3vff2qgz0yfcf8hwsnx5q4igwa6pimhak8lw0")))) + "0yhbgbjl45b4sjxwc394cjra6iy02q1pi66p28zy70lr6jvm9mx2")))) (build-system cmake-build-system) (outputs '("out" "static")) ; 1.0MiB of .a files From 63f5d53cf148b1d506fb55d64d69059ddd307c71 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 00:30:00 +0100 Subject: [PATCH 270/436] gnu: di: Update to 4.43. * gnu/packages/admin.scm (di): Update to 4.43. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index d9c7ba3b73..6bded60c11 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1718,13 +1718,13 @@ a new command using the matched rule, and runs it.") (define-public di (package (name "di") - (version "4.42") + (version "4.43") (source (origin (method url-fetch) (uri (string-append "https://gentoo.com/di/di-" version ".tar.gz")) (sha256 - (base32 "1i6m9zdnidn8268q1lz9fd8payk7s4pgwh5zlam9rr4dy6h6a67n")))) + (base32 "1q25jy51qfzsym9b2w0cqzscq2j492gn60dy6gbp88m8nwm4sdy8")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; Obscure test failures. From 1a01551a9b35830a9980abec76ca7cd0c5663aa4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 05:46:42 +0100 Subject: [PATCH 271/436] gnu: cbatticon: Update to 1.6.5. * gnu/packages/admin.scm (cbatticon): Update to 1.6.5. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 6bded60c11..17d726b7ac 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1749,14 +1749,14 @@ highly portable. Great for heterogenous networks.") (define-public cbatticon (package (name "cbatticon") - (version "1.6.4") + (version "1.6.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/valr/" name "/archive/" version ".tar.gz")) (sha256 (base32 - "023fvsa4q7rl98rqgwrb1shyzaybdkkbyz5sywd0s5p7ixkksxqx")) + "0xzz1faqgm57bwlkw6sjdfbckf5hck81879zbfk18p7xn9vhvixv")) (file-name (string-append name "-" version ".tar.gz")))) (build-system gnu-build-system) (arguments From 0558e9684f3c2558bbce4e8aaeb9ab0a317e55d0 Mon Sep 17 00:00:00 2001 From: John Darrington Date: Thu, 2 Mar 2017 06:58:34 +0100 Subject: [PATCH 272/436] gnu: Add stellarium. * gnu/packages/astronomy.scm (stellarium): New variable. --- gnu/packages/astronomy.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index f390ce4486..799b5fe031 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -21,7 +21,13 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) #:use-module (gnu packages image) + #:use-module (gnu packages compression) + #:use-module (gnu packages gettext) + #:use-module (gnu packages perl) + #:use-module (gnu packages gl) + #:use-module (gnu packages qt) #:use-module (gnu packages maths) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu)) (define-public cfitsio @@ -107,3 +113,29 @@ systems in a FITS image header.") (description "The GNU Astronomy Utilities (Gnuastro) is a suite of programs for the manipulation and analysis of astronomical data.") (license license:gpl3+))) + +(define-public stellarium + (package + (name "stellarium") + (version "0.15.1") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/stellarium/Stellarium-sources/" + version "/stellarium-" version ".tar.gz")) + (sha256 + (base32 + "04avigz8i8mi2x6x71bqr9np85n1p9qnvbj2hxr947f1jv22zr8g")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f)) ; There are no tests. + (home-page "https://www.gnu.org/software/stellarium") + (inputs `(("qt" ,qt) + ("zlib" ,zlib))) + (native-inputs `(("gettext" ,gettext-minimal) + ("perl" ,perl))) + (synopsis "Nocturnal sky renderering program") + (description "Stellarium renders a realistic image of the sky in real time. +With Stellarium, you really see what you can see with your eyes, binoculars or a +small telescope.") + (license license:gpl2+))) From 47ddf3e5f07351c738d6199a0df540d193d14e31 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Thu, 2 Mar 2017 11:46:06 +0300 Subject: [PATCH 273/436] services: ssh: Remove 'openssh-service' exported symbol. This is a followup to commit d8f3128119d32bcc186c8a1fe15b037bba25b4b8. Reported by thomasd on #guix. * gnu/services/ssh.scm: Do not export 'openssh-service' as it does not exist. --- gnu/services/ssh.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/services/ssh.scm b/gnu/services/ssh.scm index 58c35c9f5e..7b2d4a8f06 100644 --- a/gnu/services/ssh.scm +++ b/gnu/services/ssh.scm @@ -38,7 +38,6 @@ openssh-configuration openssh-configuration? openssh-service-type - openssh-service dropbear-configuration dropbear-configuration? From 1a10cefc91cc954ef62ca069c02a35031deb4944 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 2 Mar 2017 12:39:26 +0200 Subject: [PATCH 274/436] gnu: nano: Update to 2.7.5. * gnu/packages/nano.scm (nano): Update to 2.7.5. [description]: Updated with help from 'guix lint'. --- gnu/packages/nano.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm index 5fafe78e2e..571770b459 100644 --- a/gnu/packages/nano.scm +++ b/gnu/packages/nano.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2012 Nikita Karetnikov -;;; Copyright © 2015, 2016 Efraim Flashner +;;; Copyright © 2015, 2016, 2017 Efraim Flashner ;;; Copyright © 2016 Rene Saavedra ;;; ;;; This file is part of GNU Guix. @@ -29,7 +29,7 @@ (define-public nano (package (name "nano") - (version "2.7.4") + (version "2.7.5") (source (origin (method url-fetch) @@ -37,7 +37,7 @@ version ".tar.gz")) (sha256 (base32 - "135wzlv77p9za8679j2jpfkpvainvyagrhkdxngp71ynabgc5zr3")))) + "01yrh66rph0vn9q9r2d2jji5yzaakxrj75j9fsm0g41m8qpy4sr2")))) (build-system gnu-build-system) (inputs `(("gettext" ,gettext-minimal) @@ -45,7 +45,8 @@ (home-page "https://www.nano-editor.org/") (synopsis "Small, user-friendly console text editor") (description - "GNU Nano is a small and simple text editor. In addition to basic -editing, it supports interactive search and replace, go to line and column -number, auto-indentation and more.") + "GNU nano is a small and simple text editor for use in a terminal. Besides +basic editing, it supports: undo/redo, syntax highlighting, spell checking, +justifying, auto-indentation, bracket matching, interactive search-and-replace +(with regular expressions), and the editing of multiple files.") (license gpl3+))) ; some files are under GPLv2+ From a047122c6a263417f18ab69ba3d24a9fca1aa223 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 2 Mar 2017 12:45:50 +0200 Subject: [PATCH 275/436] gnu: mutt: Update to 1.8.0. * gnu/packages/mail.scm (mutt): Update to 1.8.0. --- gnu/packages/mail.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index ffa088d49b..90ebbb99bd 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015 Paul van der Walt ;;; Copyright © 2015, 2016 Eric Bavier ;;; Copyright © 2015 Andreas Enge -;;; Copyright © 2015, 2016 Efraim Flashner +;;; Copyright © 2015, 2016, 2017 Efraim Flashner ;;; Copyright © 2016 Christopher Allan Webber ;;; Copyright © 2016 Al McElrath ;;; Copyright © 2016 Leo Famulari @@ -214,14 +214,14 @@ aliasing facilities to work just as they would on normal mail.") (define-public mutt (package (name "mutt") - (version "1.7.2") + (version "1.8.0") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.mutt.org/pub/mutt/mutt-" version ".tar.gz")) (sha256 (base32 - "1yazrl82s9fxmamnlvwmsxhwrxnwv6kwakgfmawda8ndhwb50lqm")) + "1axdcylyv0p194y6lj1jx127g5yc74zqzzxdc014cjw02bd1x125")) (patches (search-patches "mutt-store-references.patch")))) (build-system gnu-build-system) (inputs From a9f754d73320703c257a29f926aae77a23ef66db Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 2 Mar 2017 21:13:39 +1000 Subject: [PATCH 276/436] gnu: diamond: Update to 0.8.36. * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1810773de4..0fc8c0483e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus -;;; Copyright © 2015, 2016 Ben Woodcroft +;;; Copyright © 2015, 2016, 2017 Ben Woodcroft ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016 Roel Janssen @@ -2047,7 +2047,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.34") + (version "0.8.36") (source (origin (method url-fetch) (uri (string-append @@ -2056,7 +2056,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jvr34g346gbz7z1zb9bs0vplivm9p4cxk0lbzklvdpa7g236p39")))) + "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target From ec4102f57f724c3abafe9840f118160abfdbf292 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 2 Mar 2017 21:16:09 +1000 Subject: [PATCH 277/436] gnu: bundler: Update to 1.14.5. * gnu/packages/ruby.scm (bundler): Update to 1.14.5. --- gnu/packages/ruby.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 59370447b2..972bd230d2 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -426,13 +426,13 @@ expectations and mocks frameworks.") (define-public bundler (package (name "bundler") - (version "1.14.4") + (version "1.14.5") (source (origin (method url-fetch) (uri (rubygems-uri "bundler" version)) (sha256 (base32 - "1hafmb7p41pm40a2z7f4x5zpgrb72xvgwlvkxnflmzqkvq2prkfv")))) + "0635s6naz9hn4iqbvkhnm1by4j4spvv13mb7nzwwimnpbqgx663i")))) (build-system ruby-build-system) (arguments '(#:tests? #f)) ; avoid dependency cycles From f1021afb41613f5eba3ea4f5225b9a4cd1c15ecb Mon Sep 17 00:00:00 2001 From: John Darrington Date: Thu, 2 Mar 2017 17:57:25 +0100 Subject: [PATCH 278/436] gnu: Merge the two stellaria into one. * gnu/packages/astronomy.scm (stellaruim): Merge details from stellarium-0.14. * gnu/packages/education.scm (stellarium): Remove variable. --- gnu/packages/astronomy.scm | 41 ++++++++++++++++++++++---------------- gnu/packages/education.scm | 38 ----------------------------------- 2 files changed, 24 insertions(+), 55 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 799b5fe031..73fbb09d10 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -118,24 +118,31 @@ programs for the manipulation and analysis of astronomical data.") (package (name "stellarium") (version "0.15.1") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/stellarium/Stellarium-sources/" - version "/stellarium-" version ".tar.gz")) - (sha256 - (base32 - "04avigz8i8mi2x6x71bqr9np85n1p9qnvbj2hxr947f1jv22zr8g")))) + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/stellarium/" + "Stellarium-sources/" + version "/stellarium-" version ".tar.gz")) + (sha256 + (base32 + "04avigz8i8mi2x6x71bqr9np85n1p9qnvbj2hxr947f1jv22zr8g")))) (build-system cmake-build-system) - (arguments - `(#:tests? #f)) ; There are no tests. - (home-page "https://www.gnu.org/software/stellarium") (inputs `(("qt" ,qt) ("zlib" ,zlib))) - (native-inputs `(("gettext" ,gettext-minimal) - ("perl" ,perl))) - (synopsis "Nocturnal sky renderering program") - (description "Stellarium renders a realistic image of the sky in real time. -With Stellarium, you really see what you can see with your eyes, binoculars or a -small telescope.") + (native-inputs `(("gettext" ,gettext-minimal) ; xgettext is used at compile time + ("perl" ,perl))) ; For pod2man + (arguments + `(#:test-target "tests" + #:phases (modify-phases %standard-phases + (add-before 'check 'set-offscreen-display + (lambda _ + (setenv "QT_QPA_PLATFORM" "offscreen") + (setenv "HOME" "/tmp") + #t))))) + (home-page "http://www.stellarium.org/") + (synopsis "3D sky viewer") + (description "Stellarium is a planetarium. It shows a realistic sky in +3D, just like what you see with the naked eye, binoculars, or a telescope. It +can be used to control telescopes over a serial port for tracking celestial +objects.") (license license:gpl2+))) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 5444579059..808be203c2 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -43,44 +43,6 @@ #:use-module (guix build-system cmake) #:use-module (srfi srfi-1)) -(define-public stellarium - (package - (name "stellarium") - (version "0.14.2") - (source (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/stellarium/" - "Stellarium-sources/" - version "/stellarium-" version ".tar.gz")) - (sha256 (base32 - "1xxil0rv61zc08znfv83cpsc47y1gjl2f3njhz0pn5zd8jpaa15a")))) - (build-system cmake-build-system) - (inputs - `(("qtbase" ,qtbase) - ("zlib" ,zlib) - ("qtserialport" ,qtserialport) - ("qtscript" ,qtscript) - ("gettext" ,gettext-minimal))) - (native-inputs - `(("qtbase" ,qtbase) ;Qt MOC is needed at compile time - ("qttools" ,qttools) - ("perl" ,perl))) ;for 'pod2man' - (arguments - `(#:test-target "tests" - #:phases (modify-phases %standard-phases - (add-before 'check 'set-offscreen-display - (lambda _ - (setenv "QT_QPA_PLATFORM" "offscreen") - (setenv "HOME" "/tmp") - #t))))) - (home-page "http://www.stellarium.org/") - (synopsis "3D sky viewer") - (description "Stellarium is a planetarium. It shows a realistic sky in -3D, just like what you see with the naked eye, binoculars, or a telescope. It -can be used to control telescopes over a serial port for tracking celestial -objects.") - (license license:gpl2+))) - (define-public gcompris (package (name "gcompris") From 07ef08a73685b910c663395e98ae88f97d3b3a7f Mon Sep 17 00:00:00 2001 From: John Darrington Date: Sun, 26 Feb 2017 20:18:26 +0100 Subject: [PATCH 279/436] gnu: Add slib. * gnu/packages/scheme.scm (slib): New variable. --- gnu/packages/scheme.scm | 42 +++++++++++++++++++++++++++++++++++++++-- 1 file changed, 40 insertions(+), 2 deletions(-) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index af416c502a..9e7c749f4f 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; Copyright © 2016, 2017 ng0 +;;; Copyright © 2017 John Darrington ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,8 +26,8 @@ (define-module (gnu packages scheme) #:use-module (gnu packages) #:use-module ((guix licenses) - #:select (gpl2+ lgpl2.0+ lgpl2.1+ asl2.0 bsd-3 - cc-by-sa4.0)) + #:select (gpl2+ lgpl2.0+ lgpl2.1+ lgpl3+ asl2.0 bsd-3 + cc-by-sa4.0 non-copyleft)) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -57,6 +58,7 @@ #:use-module (gnu packages xorg) #:use-module (gnu packages tls) #:use-module (gnu packages gl) + #:use-module (gnu packages zip) #:use-module (ice-9 match)) (define (mit-scheme-source-directory system version) @@ -844,3 +846,39 @@ metalinguistic abstraction, recursion, interpreters, and modular programming.") "String pattern-matching library for scheme48 based on the SRE regular-expression notation.") (license bsd-3)))) + +(define-public slib + (package + (name "slib") + (version "3b5") + (source (origin + (method url-fetch) + (uri (string-append "http://groups.csail.mit.edu/mac/ftpdir/scm/slib-" + version ".zip")) + (sha256 + (base32 + "0q0p2d53p8qw2592yknzgy2y1p5a9k7ppjx0cfrbvk6242c4mdpq")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There is no check target. + #:phases + (modify-phases %standard-phases + (add-after 'install 'remove-bin-share + (lambda* (#:key inputs outputs #:allow-other-keys) + (delete-file-recursively + (string-append (assoc-ref outputs "out") "/bin")))) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (zero? (system* "./configure" + (string-append "--prefix=" + (assoc-ref outputs "out"))))))))) + (native-inputs `(("unzip" ,unzip) + ("texinfo" ,texinfo))) + (home-page "http://people.csail.mit.edu/jaffer/SLIB/") + (synopsis "Compatibility and utility library for Scheme") + (description "SLIB is a portable Scheme library providing compatibility and +utility functions for all standard Scheme implementations.") + (license (non-copyleft + "http://people.csail.mit.edu/jaffer/SLIB_COPYING.txt" + "Or see COPYING in the distribution.")))) + From 8c48d0eb339f38522570a4032a75f77e9c91cca8 Mon Sep 17 00:00:00 2001 From: John Darrington Date: Sun, 26 Feb 2017 20:22:11 +0100 Subject: [PATCH 280/436] gnu: Add scm. * gnu/packages/scheme.scm (scm): New variable. --- gnu/packages/scheme.scm | 61 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index 9e7c749f4f..e1dba9bed7 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -882,3 +882,64 @@ utility functions for all standard Scheme implementations.") "http://people.csail.mit.edu/jaffer/SLIB_COPYING.txt" "Or see COPYING in the distribution.")))) +(define-public scm + (package + (name "scm") + (version "5f2") + (source (origin + (method url-fetch) + (uri (string-append + "http://groups.csail.mit.edu/mac/ftpdir/scm/scm-" + version ".zip")) + (sha256 + (base32 + "050ijb51jm1cij9g3r89zl9rawsrikhbb5y8zb7lspb7bsxq5w99")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (zero? (system* "./configure" + (string-append "--prefix=" + (assoc-ref outputs "out")))))) + (add-before 'build 'pre-build + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile" + (("ginstall-info") "install-info")))) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "SCHEME_LIBRARY_PATH" + (string-append (assoc-ref inputs "slib") + "/lib/slib/")) + (and + (zero? (system* "make" "scmlit" "CC=gcc")) + (zero? (system* "make" "all"))))) + (add-after 'install 'post-install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((req + (string-append (assoc-ref outputs "out") + "/lib/scm/require.scm"))) + (and + (delete-file req) + (format (open req (logior O_WRONLY O_CREAT)) + "(define (library-vicinity) ~s)\n" + (string-append (assoc-ref inputs "slib") + "/lib/slib/")) + + ;; We must generate the slibcat file + (zero? (system* + (string-append + (assoc-ref outputs "out") + "/bin/scm") + "-br" "new-catalog"))))))))) + (inputs `(("slib" ,slib))) + (native-inputs `(("unzip" ,unzip) + ("texinfo" ,texinfo))) + (home-page "http://people.csail.mit.edu/jaffer/SCM") + (synopsis "Scheme implementation conforming to R5RS and IEEE P1178") + (description "GNU SCM is an implementation of Scheme. This +implementation includes Hobbit, a Scheme-to-C compiler, which can +generate C files whose binaries can be dynamically or statically +linked with a SCM executable.") + (license lgpl3+))) From 479c4273e6ae899f16da2ebcb36e11baca1af9c8 Mon Sep 17 00:00:00 2001 From: John Darrington Date: Sun, 26 Feb 2017 20:28:48 +0100 Subject: [PATCH 281/436] gnu: Add jacal. * gnu/packages/maths.scm (jacal): New variable. * gnu/packages/patches/jacal-fix-texinfo.patch: New file. --- gnu/packages/maths.scm | 52 +++++++++++ gnu/packages/patches/jacal-fix-texinfo.patch | 92 ++++++++++++++++++++ 2 files changed, 144 insertions(+) create mode 100644 gnu/packages/patches/jacal-fix-texinfo.patch diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 913a403dab..9533f5f0a8 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -83,6 +83,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages tbb) + #:use-module (gnu packages scheme) #:use-module (gnu packages shells) #:use-module (gnu packages tcl) #:use-module (gnu packages texinfo) @@ -2958,3 +2959,54 @@ algorithm for LCS. It is a fast program to compute the approximate Longest Commons Subsequence of a set of strings.") (home-page "https://github.com/gdv/Reduce-Expand-for-LCS") (license license:gpl3+)))) + +(define-public jacal + (package + (name "jacal") + (version "1c4") + (source (origin + (method url-fetch) + (uri (string-append + "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-" + version ".zip")) + (sha256 (base32 + "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q")) + (patches (search-patches "jacal-fix-texinfo.patch")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'pre-build + ;; Don't use upstream's script - it really doesn't fit into + ;; Guix's functional paradigm. + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "Makefile" + (("^install: install-script") "install: ")))) + (add-after 'install 'post-install + ;; Instead, we provide our own simplified script. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((wrapper (string-append (assoc-ref outputs "out") + "/bin/jacal"))) + (format (open wrapper (logior O_WRONLY O_CREAT)) + (string-append "#!~a\nexec ~a/bin/scm -ip1 " + "-e '(slib:load \"~a/lib/jacal/math\") " + "(math)' \"$@\"\n") + (which "bash") + (assoc-ref inputs "scm") + (assoc-ref outputs "out")) + (chmod wrapper #o555)))) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (zero? (system* "./configure" + (string-append "--prefix=" + (assoc-ref outputs "out"))))))))) + (inputs `(("scm" ,scm))) + (native-inputs `(("unzip" ,unzip) + ("texinfo" ,texinfo))) + (synopsis "Symbolic mathematics system") + (description "GNU JACAL is an interactive symbolic mathematics program based on +Scheme. It manipulate and simplify a range of mathematical expressions such +as equations, scalars, vectors, and matrices.") + (home-page "http://www.gnu.org/software/jacal") + (license license:gpl3+))) + diff --git a/gnu/packages/patches/jacal-fix-texinfo.patch b/gnu/packages/patches/jacal-fix-texinfo.patch new file mode 100644 index 0000000000..83e44a3164 --- /dev/null +++ b/gnu/packages/patches/jacal-fix-texinfo.patch @@ -0,0 +1,92 @@ +Fix the broken Texinfo in the Jacal package documentation + +--- jacal/jacal.texi,orig 2017-02-23 20:35:55.303980444 +0100 ++++ jacal/jacal.texi 2017-02-23 20:53:14.539024674 +0100 +@@ -343,7 +343,7 @@ + + With the standard input grammar, the precedence of @samp{-} as a prefix + behaves strangely. @code{a^-b*c} becomes @code{a^(-b*c)} while +-@code{@result{a^b*c} (a^b)*c}. ++@code{a^b*c @result{} (a^b)*c}. + + Using @code{divide} to divide a polynomial by an integer does not work. + +@@ -675,8 +675,9 @@ + e1: --------- + a + @end example ++@end deffn + +-@deffnx Command suchthat var exp ++@deffn Command suchthat var exp + + If an expression rather than an equation is given to @code{suchthat}, it + is as though the equation @code{@var{exp}=0} was given. +@@ -688,8 +689,9 @@ + e2: --------- + a + @end example ++@end deffn + +-@deffnx Operator | var exp_or_eqn ++@deffn Operator | var exp_or_eqn + + An alternative infix notation is also available for @code{suchthat}. + +@@ -857,8 +859,9 @@ + + Returns the degree of polynomial or equation @var{poly} in variable + @var{var}. ++@end deffn + +-@deffnx Operator degree poly ++@deffn Operator degree poly + + Returns the total-degree, the degree of its highest degree monomial, + of polynomial or equation @var{poly}. +@@ -1016,10 +1019,12 @@ + Returns @var{poly1} reduced with respect to @var{poly2} (or @var{eqn}) + and @var{var}. If @var{poly2} is univariate, the third argument is not + needed. ++@end deffn + +-@deffnx Command mod poly1 n ++@deffn Command mod poly1 n + Returns @var{poly1} with all the coefficients taken modulo @var{n}. +-@deffnx Command mod poly1 ++@end deffn ++@deffn Command mod poly1 + Returns @var{poly1} with all the coefficients taken modulo the + current modulus. + +@@ -1220,8 +1225,9 @@ + e1: -1 2 3 5 + @end group + @end example ++@end deffn + +-@deffnx Command factor polyratio ++@deffn Command factor polyratio + Given a univariate ratio of polynomials @var{polyratio}, returns a + matrix of factors and exponents. + +@@ -2028,7 +2034,7 @@ + formed from the pair-wise products of components of the inputs. For + example, for the input tensors @code{x[a,b]} and @code{y[c]} + @example +-@result{z:tmult(x,y);} z[a,b,c] = x[a,b]*y[c] ++z:tmult(x,y); @result{} z[a,b,c] = x[a,b]*y[c] + @end example + + With an additional argument, @code{tmult} will produce the inner product +@@ -2464,8 +2470,9 @@ + If you do not wish to return to Jacal but really want to terminate the + session and return to the operating system, then after typing + @code{qed();}, type @code{(slib:exit)} or use @code{quit}. ++@end deffn + +-@deffnx Command quit ++@deffn Command quit + Exit directly from Jacal to the operating system. You will not be able + to continue your Jacal session. + From 04c88363da76878fb91b008f6c82b05ebf8f47fe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 2 Mar 2017 17:36:08 +0100 Subject: [PATCH 282/436] gnu: leveldb: Update to 1.20. * gnu/packages/databases.scm (leveldb): Update to 1.20. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index b7ce8a8bec..f502a8586b 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -215,7 +215,7 @@ SQL, Key/Value, XML/XQuery or Java Object storage for their data model.") (define-public leveldb (package (name "leveldb") - (version "1.19") + (version "1.20") (source (origin (method url-fetch) (uri (string-append "https://github.com/google/leveldb" @@ -223,7 +223,7 @@ SQL, Key/Value, XML/XQuery or Java Object storage for their data model.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "00jjgs9xlwycfkg0xd7n1rj6v9zrx7xc7hann6zalrjyhap18ykx")))) + "0r36bcrj6b2afsp4aw1gjai3jbs1c7734pxpc1jz7hh9nasyiazm")))) (build-system gnu-build-system) (arguments '(#:make-flags (list "CC=gcc") From 811f4f5b4c0e5a58d2aef06f871e1bbd59e2156b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 17:32:38 +0100 Subject: [PATCH 283/436] gnu: Add perl-async-interrupt. * gnu/packages/perl.scm (perl-async-interrupt): New variable. --- gnu/packages/perl.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index eee688354a..f80a95f3e0 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; Copyright © 2017 Raoul J.P. Bonnal +;;; Copyright © 2017 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -268,6 +269,39 @@ manipulate, read, and write Zip archive files.") list manipulation routines.") (license (package-license perl)))) +(define-public perl-async-interrupt + (package + (name "perl-async-interrupt") + (version "1.21") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/M/ML/MLEHMANN/" + "Async-Interrupt-" version ".tar.gz")) + (sha256 + (base32 + "092zs7b72f8q109c3z829nqfgwqghp3nhw44c0gcyhacbb4wgpk3")))) + (build-system perl-build-system) + (propagated-inputs + `(("perl-common-sense" ,perl-common-sense))) + (home-page "http://search.cpan.org/dist/Async-Interrupt") + (synopsis "Allow C/XS libraries to interrupt perl asynchronously") + (description + "@code{Async::Interrupt} implements a single feature only of interest +to advanced perl modules, namely asynchronous interruptions (think \"UNIX +signals\", which are very similar). + +Sometimes, modules wish to run code asynchronously (in another thread, +or from a signal handler), and then signal the perl interpreter on +certain events. One common way is to write some data to a pipe and use +an event handling toolkit to watch for I/O events. Another way is to +send a signal. Those methods are slow, and in the case of a pipe, also +not asynchronous - it won't interrupt a running perl interpreter. + +This module implements asynchronous notifications that enable you to +signal running perl code from another thread, asynchronously, and +sometimes even without using a single syscall.") + (license (package-license perl)))) + (define-public perl-autovivification (package (name "perl-autovivification") From 647b6d3847a56c9b95e505cdb6e18a261329f998 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 18:00:55 +0100 Subject: [PATCH 284/436] gnu: Add perl-canary-stability. * gnu/packages/perl.scm (perl-canary-stability): New variable. --- gnu/packages/perl.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index f80a95f3e0..4c51681bab 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -596,6 +596,25 @@ code or from an external program. Optionally, output can be teed so that it is captured while being passed through to the original file handles.") (license asl2.0))) +(define-public perl-canary-stability + (package + (name "perl-canary-stability") + (version "2012") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/M/ML/MLEHMANN/" + "Canary-Stability-" version ".tar.gz")) + (sha256 + (base32 + "01vih43hvpqy67m6a6fwmlswli91mqpv8n8ccglvlkc33l8hn97x")))) + (build-system perl-build-system) + (home-page "http://search.cpan.org/dist/Canary-Stability") + (synopsis "Check compatibility with the installed perl version") + (description + "This module is used by Schmorp's modules during configuration stage +to test the installed perl for compatibility with his modules.") + (license (package-license perl)))) + (define-public perl-carp-assert (package (name "perl-carp-assert") From ad8f8e759575b77b5f589654246b786356b9bb0a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 18:13:58 +0100 Subject: [PATCH 285/436] gnu: Add perl-ev. * gnu/packages/libevent.scm (perl-ev): New variable. --- gnu/packages/libevent.scm | 43 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index e552a4ee38..8aca5daf87 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -26,9 +26,11 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) + #:use-module (guix build-system perl) #:use-module (gnu packages base) #:use-module (gnu packages python) #:use-module (gnu packages autotools) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config)) (define-public libevent @@ -149,3 +151,44 @@ resolution, asynchronous file system operations, and threading primitives.") ;; A few files fall under other non-copyleft licenses; see 'LICENSE' for ;; details. (license x11))) + +(define-public perl-ev + (package + (name "perl-ev") + (version "4.22") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/M/ML/MLEHMANN/EV-" + version ".tar.gz")) + (sha256 + (base32 + "14d9115q8f2ca2q3vbcalm55zqsbx8xjq5aj098laj9f9rrzirra")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Drop bundled libev. + (delete-file-recursively "libev") + #t)))) + (build-system perl-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-libev + ;; This package requires the libev *sources* in order + ;; to build. Unpack system libev here... + (lambda* (#:key inputs #:allow-other-keys) + (mkdir "./libev") + (zero? (system* "tar" "-xf" (assoc-ref inputs "libev-source") + "-C" "./libev" "--strip-components=1"))))))) + (native-inputs + `(("libev-source" ,(package-source libev)) + ("perl-canary-stability" ,perl-canary-stability))) + (propagated-inputs + `(("perl-common-sense" ,perl-common-sense))) + (home-page "http://search.cpan.org/dist/EV") + (synopsis "Perl interface to libev") + (description + "This module provides an interface to @code{libev}, a high performance +full-featured event loop. It can be used through the @code{AnyEvent} module +and still be faster than other event loops currently supported in Perl.") + (license (package-license perl)))) From c1adb4ebd6d702712c6d4ccd353b09bbcc15707c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 20:39:40 +0100 Subject: [PATCH 286/436] gnu: Add perl-devel-checkcompiler. * gnu/packages/perl.scm (perl-devel-checkcompiler): New variable. --- gnu/packages/perl.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 4c51681bab..b097c4c630 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -2150,6 +2150,27 @@ the appropriate objects.") particular command is available.") (license (package-license perl)))) +(define-public perl-devel-checkcompiler + (package + (name "perl-devel-checkcompiler") + (version "0.07") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/S/SY/SYOHEX/" + "Devel-CheckCompiler-" version ".tar.gz")) + (sha256 + (base32 + "1db973a4dbyknjxq608hywil5ai6vplnayshqxrd7m5qnjbpd2vn")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build-tiny" ,perl-module-build-tiny))) + (home-page "http://search.cpan.org/dist/Devel-CheckCompiler") + (synopsis "Check compiler availability") + (description "@code{Devel::CheckCompiler} is a tiny module to check +whether a compiler is available. It can test for a C99 compiler, or +you can tell it to compile a C source file with optional linker flags.") + (license (package-license perl)))) + (define-public perl-devel-globaldestruction (package (name "perl-devel-globaldestruction") From 3ce3ecd3d7706d04ef25ef41b7a44ed540ca2ae4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 20:46:10 +0100 Subject: [PATCH 287/436] gnu: Add perl-cwd-guard. * gnu/packages/perl.scm (perl-cwd-guard): New variable. --- gnu/packages/perl.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index b097c4c630..834e38ce09 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -1343,6 +1343,28 @@ contained in Appendix A of FIPS Publication 181, \"Standard for Automated Password Generator\".") (license (package-license perl)))) +(define-public perl-cwd-guard + (package + (name "perl-cwd-guard") + (version "0.05") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/K/KA/KAZEBURO/" + "Cwd-Guard-" version ".tar.gz")) + (sha256 + (base32 + "0xwf4rmii55k3lp19mpbh00mbgby7rxdk2lk84148bjhp6i7rz3s")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build" ,perl-module-build) + ("perl-test-requires" ,perl-test-requires))) + (home-page "http://search.cpan.org/dist/Cwd-Guard") + (synopsis "Temporarily change working directory") + (description + "@code{Cwd::Guard} changes the current directory using a limited scope. +It returns to the previous working directory when the object is destroyed.") + (license (package-license perl)))) + (define-public perl-czplib (package (name "perl-czplib") From 00aa3ae79bc88e40f9f6a4c4e55a3c6f01b2e3dc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 20:48:56 +0100 Subject: [PATCH 288/436] gnu: Add perl-module-build-xsutil. * gnu/packages/perl.scm (perl-module-build-xsutil): New variable. --- gnu/packages/perl.scm | 44 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 834e38ce09..b86cb96bd1 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -4049,6 +4049,50 @@ replacement. Whereas Module::Build has over 6,700 lines of code; this module has less than 120, yet supports the features needed by most distributions.") (license (package-license perl)))) +(define-public perl-module-build-xsutil + (package + (name "perl-module-build-xsutil") + (version "0.16") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/H/HI/HIDEAKIO/" + "Module-Build-XSUtil-" version ".tar.gz")) + (sha256 + (base32 + "1nrs0b6hmwl3sw3g50b9857qgp5cbbbpl716zwn30h9vwjj2yxhm")))) + (build-system perl-build-system) + (native-inputs + `(("perl-capture-tiny" ,perl-capture-tiny) + ("perl-cwd-guard" ,perl-cwd-guard) + ("perl-file-copy-recursive" ,perl-file-copy-recursive) + ("perl-module-build" ,perl-module-build))) + (propagated-inputs + `(("perl-devel-checkcompiler" ,perl-devel-checkcompiler))) + (home-page "http://search.cpan.org/dist/Module-Build-XSUtil") + (synopsis "Module::Build class for building XS modules") + (description + "@code{Module::Build::XSUtil} is subclass of @code{Module::Build} +for support building XS modules. + +This is a list of a new parameters in the @code{Module::Build::new} method: + +@enumerate +@item @code{needs_compiler_c99}: This option checks C99 compiler availability. +@item @code{needs_compiler_cpp}: This option checks C++ compiler availability. +Can also pass @code{extra_compiler_flags} and @code{extra_linker_flags} for C++. +@item @code{generate_ppport_h}: Generate @file{ppport.h} by @code{Devel::PPPort}. +@item @code{generate_xshelper_h}: Generate @file{xshelper.h} which is a helper +header file to include @file{EXTERN.h}, @file{perl.h}, @file{XSUB.h} and +@file{ppport.h}, and defines some portability stuff which are not supported by +@file{ppport.h}. + +It is ported from @code{Module::Install::XSUtil}. +@item @code{cc_warnings}: Toggle compiler warnings. Enabled by default. +@item @code{-g options}: Invoke @file{Build.PL} with @code{-g} to enable +debug options. +@end enumerate") + (license (package-license perl)))) + (define-public perl-module-find (package (name "perl-module-find") From 456f14f0fec907391e1a729107cec894c52bdda6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 20:49:39 +0100 Subject: [PATCH 289/436] gnu: Add perl-mouse. * gnu/packages/perl.scm (perl-mouse): New variable. --- gnu/packages/perl.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index b86cb96bd1..2321a0536e 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -4872,6 +4872,36 @@ own set of Moose-like types. These custom types can then be used to describe fields in Moo-based classes.") (license (package-license perl)))) +(define-public perl-mouse + (package + (name "perl-mouse") + (version "2.4.9") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/S/SY/SYOHEX/Mouse-v" + version + ".tar.gz")) + (sha256 + (base32 + "1y20sl97x1h4y1iid47hj0w1hb2887dchh4nfffgmqpyggkslh4n")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build" ,perl-module-build) + ("perl-module-build-xsutil" ,perl-module-build-xsutil) + ("perl-test-exception" ,perl-test-exception) + ("perl-test-fatal" ,perl-test-fatal) + ("perl-test-leaktrace" ,perl-test-leaktrace) + ("perl-test-output" ,perl-test-output) + ("perl-test-requires" ,perl-test-requires) + ("perl-try-tiny" ,perl-try-tiny))) + (home-page "https://github.com/gfx/p5-Mouse") + (synopsis "Fast Moose-compatible object system for perl5") + (description + "Mouse is a @code{Moose} compatible object system that implements a +subset of the functionality for reduced startup time.") + (license (package-license perl)))) + (define-public perl-mozilla-ca (package (name "perl-mozilla-ca") From 62b28f192b87797ca3d0c7c7c90bd29bb55ae4a3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:16:18 +0100 Subject: [PATCH 290/436] gnu: Add perl-xml-tokeparser. * gnu/packages/xml.scm (perl-xml-parser): New variable. --- gnu/packages/xml.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index b91471690f..f66b8a65b7 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -269,6 +269,29 @@ as extra arguments to the parse methods, in which case they override options given at XML::Parser creation time.") (home-page "http://search.cpan.org/dist/XML-Parser"))) +(define-public perl-xml-tokeparser + (package + (name "perl-xml-tokeparser") + (version "0.05") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/P/PO/PODMASTER/" + "XML-TokeParser-" version ".tar.gz")) + (sha256 + (base32 + "1hnpwb3lh6cbgwvjjgqzcp6jm4mp612qn6ili38adc9nhkwv8fc5")))) + (build-system perl-build-system) + (propagated-inputs `(("perl-xml-parser" ,perl-xml-parser))) + (home-page "http://search.cpan.org/dist/XML-TokeParser") + (synopsis "Simplified interface to XML::Parser") + (description + "@code{XML::TokeParser} provides a procedural (\"pull mode\") interface +to @code{XML::Parser} in much the same way that Gisle Aas' +@code{HTML::TokeParser} provides a procedural interface to @code{HTML::Parser}. +@code{XML::TokeParser} splits its XML input up into \"tokens\", each +corresponding to an @code{XML::Parser} event.") + (license (package-license perl)))) + (define-public perl-libxml (package (name "perl-libxml") From d66fa69618d476362d39b893facf90bc81c8f241 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:17:02 +0100 Subject: [PATCH 291/436] gnu: Add perl-xml-descent. * gnu/packages/xml.scm (perl-xml-descent): New variable. --- gnu/packages/xml.scm | 30 +++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index f66b8a65b7..9a22535c28 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -13,7 +13,7 @@ ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; Copyright © 2016 ng0 ;;; Copyright © 2016 Tobias Geerinckx-Rice -;;; Copyright © 2016 Marius Bakke +;;; Copyright © 2016, 2017 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -238,6 +238,34 @@ the @code{Graph} class and write it out in a specific file format.") @code{XML::Atom} implements the feed format as well as a client for the API.") (license (package-license perl)))) +(define-public perl-xml-descent + (package + (name "perl-xml-descent") + (version "1.04") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/A/AN/ANDYA/" + "XML-Descent-" version ".tar.gz")) + (sha256 + (base32 + "0l5xmw2hd95ypppz3lyvp4sn02ccsikzjwacli3ydxfdz1bbh4d7")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build" ,perl-module-build))) + (propagated-inputs + `(("perl-test-differences" ,perl-test-differences) + ("perl-xml-tokeparser" ,perl-xml-tokeparser))) + (home-page "http://search.cpan.org/dist/XML-Descent") + (synopsis "Recursive descent XML parsing") + (description + "The conventional models for parsing XML are either @dfn{DOM} +(a data structure representing the entire document tree is created) or +@dfn{SAX} (callbacks are issued for each element in the XML). + +XML grammar is recursive - so it's nice to be able to write recursive +parsers for it. @code{XML::Descent} allows such parsers to be created.") + (license (package-license perl)))) + (define-public perl-xml-parser (package (name "perl-xml-parser") From 25c3cf3edb42eddc7fd8071fceba36cbf3656756 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:28:46 +0100 Subject: [PATCH 292/436] gnu: Add perl-test-number-delta. * gnu/packages/perl.scm (perl-test-number-delta): New variable. --- gnu/packages/perl.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 2321a0536e..29c6b07b95 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -6615,6 +6615,29 @@ including a stack trace of what was going on when it occurred.") "Test-NoWarnings-" version)) (license lgpl2.1))) +(define-public perl-test-number-delta + (package + (name "perl-test-number-delta") + (version "1.06") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/D/DA/DAGOLDEN/" + "Test-Number-Delta-" version ".tar.gz")) + (sha256 + (base32 + "0jfhzhpzkc23mkrlbnv085ykpfncmy99hvppbzjnrpvgks8k0m2k")))) + (build-system perl-build-system) + (home-page "http://search.cpan.org/dist/Test-Number-Delta") + (synopsis + "Compare the difference between numbers against a given tolerance") + (description + "At some point or another, most programmers find they need to compare +floating-point numbers for equality. The typical idiom is to test if the +absolute value of the difference of the numbers is within a desired tolerance, +usually called epsilon. This module provides such a function for use with +@code{Test::More}.") + (license asl2.0))) + (define-public perl-test-output (package (name "perl-test-output") From 84e8b19fe150ae843d63ca7343aa7172f35153f3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:29:48 +0100 Subject: [PATCH 293/436] gnu: Add perl-extutils-depends. * gnu/packages/perl.scm (perl-extutils-depends): New variable. --- gnu/packages/perl.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 29c6b07b95..3470fc3cbe 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -2699,6 +2699,29 @@ By itself it is not a particularly interesting module by any measure, however it ties together a family of modern toolchain modules.") (license (package-license perl)))) +(define-public perl-extutils-depends + (package + (name "perl-extutils-depends") + (version "0.405") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/X/XA/XAOC/" + "ExtUtils-Depends-" version ".tar.gz")) + (sha256 + (base32 + "0b4ab9qmcihsfs2ajhn5qzg7nhazr68v3r0zvb7076smswd41mla")))) + (build-system perl-build-system) + (native-inputs + `(("perl-test-number-delta" ,perl-test-number-delta))) + (home-page "http://search.cpan.org/dist/ExtUtils-Depends") + (synopsis "Easily build XS extensions that depend on XS extensions") + (description + "This module tries to make it easy to build Perl extensions that use +functions and typemaps provided by other perl extensions. This means that a +perl extension is treated like a shared library that provides also a C and an +XS interface besides the perl one.") + (license (package-license perl)))) + (define-public perl-extutils-helpers (package (name "perl-extutils-helpers") From 38e29d03bfb89bba837799d182fbaeafb7bf095a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:40:31 +0100 Subject: [PATCH 294/436] gnu: Add perl-extutils-pkgconfig. * gnu/packages/perl.scm (perl-extutils-pkgconfig): New variable. --- gnu/packages/perl.scm | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 3470fc3cbe..38466b9953 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -37,7 +37,8 @@ #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system perl) - #:use-module (gnu packages perl-web)) + #:use-module (gnu packages perl-web) + #:use-module (gnu packages pkg-config)) ;;; ;;; Please: Try to add new module packages in alphabetic order. @@ -2764,6 +2765,29 @@ C code in your Perl programs, there isn't a clear method to compile standard, self-contained C libraries. This module main goal is to help in that task.") (license (package-license perl)))) +(define-public perl-extutils-pkgconfig + (package + (name "perl-extutils-pkgconfig") + (version "1.15") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/X/XA/XAOC/" + "ExtUtils-PkgConfig-" version ".tar.gz")) + (sha256 + (base32 + "1cxh6w8vmyqmhl6afys2q6z6jkp1m6zvacpk70196zmk48p1kcv9")))) + (build-system perl-build-system) + (propagated-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://search.cpan.org/dist/ExtUtils-PkgConfig") + (synopsis "Simplistic interface to pkg-config") + (description + "@code{ExtUtils::PkgConfig} is a very simplistic interface to the +@command{pkg-config} utility, intended for use in the @file{Makefile.PL} +of perl extensions which bind libraries that @command{pkg-config} knows. +It is really just boilerplate code that you would have written yourself.") + (license lgpl2.1+))) + (define-public perl-file-changenotify (package (name "perl-file-changenotify") From 6578c56728323a498c5c7cd85b5352a4b74dd4a5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:47:46 +0100 Subject: [PATCH 295/436] gnu: Add perl-xs-object-magic. * gnu/packages/perl.scm (perl-xs-object-magic): New variable. --- gnu/packages/perl.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 38466b9953..cbd92a9701 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -7732,6 +7732,30 @@ attribute names.") ;; modification, are permitted under any circumstances. No warranty. (license public-domain))) +(define-public perl-xs-object-magic + (package + (name "perl-xs-object-magic") + (version "0.04") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/F/FL/FLORA/" + "XS-Object-Magic-" version ".tar.gz")) + (sha256 + (base32 + "03fghj7hq0fiicmfdxhmzfm4mzv7s097pgkd32ji7jnljvhm9six")))) + (build-system perl-build-system) + (native-inputs + `(("perl-extutils-depends" ,perl-extutils-depends) + ("perl-test-fatal" ,perl-test-fatal))) + (home-page "http://search.cpan.org/dist/XS-Object-Magic") + (synopsis "Opaque, extensible XS pointer backed objects using sv_magic") + (description + "This way of associating structs with Perl space objects is designed to +supersede Perl's builtin @code{T_PTROBJ} with something that is extensible +(structs can be associated with any data type) and opaque (the C pointer is +neither visible nor modifiable from Perl space).") + (license (package-license perl)))) + (define-public perl-yaml (package (name "perl-yaml") From 68e31f81c1b14523275f48ba7e353ebf026268ea Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:56:25 +0100 Subject: [PATCH 296/436] gnu: Add perl-any-moose. * gnu/packages/perl.scm (perl-any-moose): New variable. --- gnu/packages/perl.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index cbd92a9701..05ad95b5cc 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -208,6 +208,31 @@ explicitly alias the class to another name or, if you prefer, you can do so implicitly.") (license (package-license perl)))) +(define-public perl-any-moose + (package + (name "perl-any-moose") + (version "0.27") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/" + "Any-Moose-" version ".tar.gz")) + (sha256 + (base32 + "0dc55mpayrixwx8dwql0vj0jalg4rlb3k64rprc84bl0z8vkx9m8")))) + (build-system perl-build-system) + (native-inputs + `(("perl-mouse" ,perl-mouse) + ("perl-moose" ,perl-moose))) + (home-page "http://search.cpan.org/dist/Any-Moose") + (synopsis "Transparently use Moose or Mouse modules") + (description + "This module facilitates using @code{Moose} or @code{Mouse} modules +without changing the code. By default, Mouse will be provided to libraries, +unless Moose is already loaded, or explicitly requested by the end-user. End +users can force the decision of which backend to use by setting the environment +variable ANY_MOOSE to be Moose or Mouse.") + (license (package-license perl)))) + (define-public perl-appconfig (package (name "perl-appconfig") From 418852f903b71fa91a257073fb3ad04a06542737 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 21:03:44 +0100 Subject: [PATCH 297/436] gnu: Add perl-mousex-nativetraits. * gnu/packages/perl.scm (perl-mousex-nativetraits): New variable. --- gnu/packages/perl.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 05ad95b5cc..840e0b763e 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -4974,6 +4974,32 @@ fields in Moo-based classes.") subset of the functionality for reduced startup time.") (license (package-license perl)))) +(define-public perl-mousex-nativetraits + (package + (name "perl-mousex-nativetraits") + (version "1.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/G/GF/GFUJI/" + "MouseX-NativeTraits-" version ".tar.gz")) + (sha256 + (base32 + "0pnbchkxfz9fwa8sniyjqp0mz75b3k2fafq9r09znbbh51dbz9gq")))) + (build-system perl-build-system) + (native-inputs + `(("perl-any-moose" ,perl-any-moose) + ("perl-test-fatal" ,perl-test-fatal))) + (propagated-inputs + `(("perl-mouse" ,perl-mouse))) + (home-page "http://search.cpan.org/dist/MouseX-NativeTraits") + (synopsis "Extend attribute interfaces for Mouse") + (description + "While @code{Mouse} attributes provide a way to name your accessors, +readers, writers, clearers and predicates, @code{MouseX::NativeTraits} +provides commonly used attribute helper methods for more specific types +of data.") + (license (package-license perl)))) + (define-public perl-mozilla-ca (package (name "perl-mozilla-ca") From e17dc7397e94a11f4906376cd8b444fabe1a81b1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 20:52:05 +0100 Subject: [PATCH 298/436] gnu: Add perl-x11-xcb. * gnu/packages/xorg.scm (perl-x11-xcb): New variable. --- gnu/packages/xorg.scm | 56 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 7075d72043..d300f232d4 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2016 Alex Kost ;;; Copyright © 2016 David Craven ;;; Copyright © 2016, 2017 John Darrington +;;; Copyright © 2017 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -5623,6 +5624,61 @@ provides DEC VT102/VT220 (VTxxx) and Tektronix 4014 compatible terminals for programs that cannot use the window system directly.") (license license:x11))) +(define-public perl-x11-xcb + (package + (name "perl-x11-xcb") + (version "0.16") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/M/MS/MSTPLBG/" + "X11-XCB-" version ".tar.gz")) + (sha256 + (base32 + "14mnvr1001py2z1n43l18yaw0plwvjg5pcsyc7k81sa0amw8ahzw")))) + (build-system perl-build-system) + (arguments + '(;; Disable parallel build to prevent a race condition. + #:parallel-build? #f + #:phases + (modify-phases %standard-phases + (add-before 'build 'patch-Makefile + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile" + ;; XXX: Without this hack, attempts at using XCB.so fails with + ;; an error such as "XCB.so: undefined symbol: xcb_xinerama_id" + (("^LDDLFLAGS = ") + (string-append "LDDLFLAGS = " + "-lxcb -lxcb-util -lxcb-xinerama -lxcb-icccm "))) + #t))) + ;; Tests require a running X11 server. + #:tests? #f)) + (native-inputs + `(("perl-extutils-depends" ,perl-extutils-depends) + ("perl-extutils-pkgconfig" ,perl-extutils-pkgconfig) + ("perl-test-deep" ,perl-test-deep) + ("perl-test-exception" ,perl-test-exception))) + (propagated-inputs + `(("perl-data-dump" ,perl-data-dump) + ("perl-mouse" ,perl-mouse) + ("perl-mousex-nativetraits" ,perl-mousex-nativetraits) + ("perl-try-tiny" ,perl-try-tiny) + ("perl-xml-descent" ,perl-xml-descent) + ("perl-xml-simple" ,perl-xml-simple) + ("perl-xs-object-magic" ,perl-xs-object-magic))) + (inputs + `(("libxcb" ,libxcb) + ("xcb-proto" ,xcb-proto) + ("xcb-util" ,xcb-util) + ("xcb-util-wm" ,xcb-util-wm))) + (home-page "http://search.cpan.org/dist/X11-XCB") + (synopsis "Perl bindings for libxcb") + (description + "These bindings wrap @code{libxcb} (a C library to speak with X11, +in many cases better than @code{Xlib}), and provides an object oriented +interface to its methods (using @code{Mouse}).") + (license (package-license perl)))) + (define-public perl-x11-protocol (package (name "perl-x11-protocol") From 0a030a9c678620a4061b8cc402670153de21a954 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 17:26:00 +0100 Subject: [PATCH 299/436] gnu: Add perl-anyevent. * gnu/packages/libevent.scm (perl-anyevent): New variable. --- gnu/packages/libevent.scm | 41 ++++++++++++++++++++++++++++++++++++--- 1 file changed, 38 insertions(+), 3 deletions(-) diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index 8aca5daf87..dd5f7c4067 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -27,11 +27,12 @@ #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system perl) - #:use-module (gnu packages base) - #:use-module (gnu packages python) #:use-module (gnu packages autotools) + #:use-module (gnu packages base) #:use-module (gnu packages perl) - #:use-module (gnu packages pkg-config)) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages tls)) (define-public libevent (package @@ -152,6 +153,40 @@ resolution, asynchronous file system operations, and threading primitives.") ;; details. (license x11))) +(define-public perl-anyevent + (package + (name "perl-anyevent") + (version "7.13") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/M/ML/MLEHMANN/" + "AnyEvent-" version ".tar.gz")) + (sha256 + (base32 + "1b84ilkbrfbzqapv25x8z6gva92skbrf2srybdabb1wnxx6ky454")))) + (build-system perl-build-system) + (native-inputs + `(("perl-canary-stability" ,perl-canary-stability))) + (propagated-inputs + `(("perl-async-interrupt" ,perl-async-interrupt) + ("perl-ev" ,perl-ev) + ("perl-guard" ,perl-guard) + ("perl-json" ,perl-json) + ("perl-json-xs" ,perl-json-xs) + ("perl-net-ssleay" ,perl-net-ssleay) + ("perl-task-weaken" ,perl-task-weaken))) + (home-page "http://search.cpan.org/dist/AnyEvent") + (synopsis + "API for I/O, timer, signal, child process and completion events") + (description + "This module allows using a variety of events without forcing module +authors to pick a specific event loop, and without noticable overhead. +Currently supported event loops are EV, Event, Glib/Gtk2, Tk, Qt, +@code{Event::Lib}, Irssi, @code{IO::Async} and POE (and thus also WxWidgets +and Prima). It also comes with a very fast Pure Perl event loop that does +not rely on XS.") + (license (package-license perl)))) + (define-public perl-ev (package (name "perl-ev") From 3e7cb70a2a845ed672f816176565e0b8da661bdb Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 9 Dec 2016 20:50:52 +0100 Subject: [PATCH 300/436] gnu: Add perl-anyevent-i3. * gnu/packages/wm.scm (perl-anyevent-i3): New variable. --- gnu/packages/wm.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 7ae8e4b7f8..7d76a2d202 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2016 doncatnip ;;; Copyright © 2016 Ivan Vilata i Balaguer ;;; Copyright © 2017 Mekeor Melire +;;; Copyright © 2017 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -37,6 +38,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system haskell) + #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (gnu packages haskell) #:use-module (gnu packages base) @@ -232,6 +234,31 @@ from scratch. i3 is primarily targeted at advanced users and developers.") (license license:bsd-3))) +(define-public perl-anyevent-i3 + (package + (name "perl-anyevent-i3") + (version "0.16") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/M/MS/MSTPLBG/" + "AnyEvent-I3-" version ".tar.gz")) + (sha256 + (base32 + "1qwva5vmmn929l6k9wzhp4h80ad4qm4m1g2dyv4nlas624003hig")))) + (build-system perl-build-system) + (propagated-inputs + `(("perl-anyevent" ,perl-anyevent) + ("perl-json-xs" ,perl-json-xs))) + (home-page "http://search.cpan.org/dist/AnyEvent-I3") + (synopsis + "Communicate with the i3 window manager through perl") + (description + "This module connects to the i3 window manager using the UNIX socket +based IPC interface it provides (if enabled in the configuration file). +You can then subscribe to events or send messages and receive their replies.") + ;; Can be used with either license. + (license (list license:gpl3+ (package-license perl))))) + (define-public python-i3-py (package (name "python-i3-py") From 38510546d9bfdd3d3c72b9039e6a048b1cb66199 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 26 Feb 2017 10:52:21 +0000 Subject: [PATCH 301/436] gnu: Add speedtest-cli. * gnu/packages/networking.scm (speedtest-cli): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/networking.scm | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 240fa517e5..eb3047c81b 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2016, 2017 ng0 ;;; Copyright © 2016 Arun Isaac ;;; Copyright © 2016 Benz Schenk +;;; Copyright © 2016, 2017 Pjotr Prins ;;; ;;; This file is part of GNU Guix. ;;; @@ -80,7 +81,7 @@ (description "GNU MAC Changer is a utility for viewing and changing MAC addresses of networking devices. New addresses may be set explicitly or randomly. They can include MAC addresses of the same or other hardware vendors -or, more generally, MAC addresses of the same category of hardware.") +or, more generally, MAC addresses of the same category of hardware.") (license license:gpl2+))) (define-public miredo @@ -1119,3 +1120,24 @@ IPFIX, RSPAN, CLI, LACP, 802.1ag).") license:gpl2 ; datapath license:bsd-2 license:bsd-3 license:asl2.0)))) ; all other + +(define-public speedtest-cli + (package + (name "speedtest-cli") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/sivel/speedtest-cli/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ir9fqwr7cl9kfq7dgh9vkydkwf59wsx0cwbzbffw8i313xhzxa1")))) + (build-system python-build-system) + (home-page "https://github.com/sivel/speedtest-cli") + (synopsis "Internet bandwidth tester") + (description + "Command line interface for testing internet bandwidth using +speedtest.net.") + (license license:asl2.0))) From 0b181ff901f7470068088fc8ce40f93b698e1459 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 2 Mar 2017 13:30:48 -0500 Subject: [PATCH 302/436] gnu: podofo: Update to 0.9.5. * gnu/packages/pdf.scm (podofo): Update to 0.9.5. --- gnu/packages/pdf.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 2ea48e5999..a229d689dd 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -438,14 +438,14 @@ interaction.") (define-public podofo (package (name "podofo") - (version "0.9.3") + (version "0.9.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/podofo/podofo/" version "/podofo-" version ".tar.gz")) (sha256 (base32 - "1n12lbq9x15vqn7dc0hsccp56l5jdff1xrhvlfqlbklxx0qiw9pc")))) + "012kgfx5j5n6w4zkc1d290d2cwjk60jhzsjlr2x19g3yi75q2jc5")))) (build-system cmake-build-system) (inputs ; TODO: Add cppunit for tests `(("lua" ,lua-5.1) From bdc11dc4c0d326205f811a10b29a0385db9e4721 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 19:21:27 +0000 Subject: [PATCH 303/436] gnu: Add tokyocabinet. * gnu/packages/databases.scm (tokyocabinet): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/databases.scm | 33 ++++++++++++++++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index f502a8586b..5199d0c4f1 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2015 Leo Famulari ;;; Copyright © 2016 Efraim Flashner -;;; Copyright © 2016 ng0 +;;; Copyright © 2016, 2017 ng0 ;;; Copyright © 2016 Roel Janssen ;;; Copyright © 2016 David Craven ;;; Copyright © 2016 Jan Nieuwenhuizen @@ -1201,6 +1201,37 @@ and B+ Tree data storage models. It is a fast key-value lightweight database and supports many programming languages. It is a NoSQL database.") (license license:gpl3+))) +(define-public tokyocabinet + (package + (name "tokyocabinet") + (version "1.4.48") + (source + (origin + (method url-fetch) + (uri (string-append "http://fallabs.com/tokyocabinet/" + name "-" version ".tar.gz")) + (sha256 + (base32 + "140zvr0n8kvsl0fbn2qn3f2kh3yynfwnizn4dgbj47m975yg80x0")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list "--enable-pthread" "--enable-off64" "--enable-fastest" + (string-append "LDFLAGS=-Wl,-rpath=" + (assoc-ref %outputs "out") "/lib")))) + (inputs + `(("zlib" ,zlib))) + (home-page "http://fallabs.com/tokyocabinet/") + (synopsis "Tokyo Cabinet is a modern implementation of the DBM database") + (description + "Tokyo Cabinet is a library of routines for managing a database. +The database is a simple data file containing records, each is a pair of a +key and a value. Every key and value is serial bytes with variable length. +Both binary data and character string can be used as a key and a value. +There is neither concept of data tables nor data types. Records are +organized in hash table, B+ tree, or fixed-length array.") + (license license:lgpl2.1+))) + (define-public wiredtiger (package (name "wiredtiger") From ef91e2b964ec0952698dd1bf7daf76624fed2145 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 19:21:28 +0000 Subject: [PATCH 304/436] gnu: neomutt: Configure with 'lmdb' and 'tokyocabinet'. * gnu/packages/mail.scm (neomutt)[configure]: Add '--with-tokyocabinet' and '--with-lmdb'. [inputs]: Add 'lmdb' and 'tokyocabinet'. Signed-off-by: Kei Kebreau --- gnu/packages/mail.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 90ebbb99bd..ee82a1b8bb 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -267,6 +267,8 @@ operating systems.") (inputs `(("cyrus-sasl" ,cyrus-sasl) ("gdbm" ,gdbm) + ("lmdb" ,lmdb) + ("tokyocabinet" ,tokyocabinet) ("gpgme" ,gpgme) ("ncurses" ,ncurses) ("gnutls" ,gnutls) @@ -289,10 +291,11 @@ operating systems.") "--enable-gpgme" ;; database, implies header caching - "--without-tokyocabinet" + ;; neomutt supports building multiple backends + "--with-tokyocabinet" "--without-qdbm" "--without-bdb" - "--without-lmdb" + "--with-lmdb" "--with-gdbm" "--with-gnutls" From de959250411830584366a0397367032f10c3c352 Mon Sep 17 00:00:00 2001 From: ng0 Date: Sun, 19 Feb 2017 12:03:31 +0000 Subject: [PATCH 305/436] gnu: Add python-eventlet. * gnu/packages/python.scm (python-eventlet): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/python.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5b8698043f..a2f0db74fa 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1006,6 +1006,40 @@ etc.). The package is structured to make adding new modules easy.") "python" (package-inputs pycrypto))))))) +(define-public python-eventlet + (package + (name "python-eventlet") + (version "0.20.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "eventlet" version)) + (sha256 + (base32 + "0f3q55mq4n021wb7qa53pz3ix6i2py64sap66vsaqm2scjw83m9s")))) + (build-system python-build-system) + (propagated-inputs + `(("python-greenlet" ,python-greenlet))) + (home-page "http://eventlet.net") + (synopsis "Concurrent networking library for Python") + (description + "Eventlet is a concurrent networking library for Python that +allows you to change how you run your code, not how you write it. +It uses @code{epoll} or @code{libevent} for highly scalable non-blocking I/O. +Coroutines ensure that the developer uses a blocking style of programming +that is similar to threading, but provide the benefits of non-blocking I/O. +The event dispatch is implicit, which means you can easily use @code{Eventlet} +from the Python interpreter, or as a small part of a larger application.") + (license license:expat))) + +(define-public python2-eventlet + (let ((base (package-with-python2 + (strip-python2-variant python-eventlet)))) + (package (inherit base) + (propagated-inputs + `(("python2-enum34" ,python2-enum34) + ,@(package-propagated-inputs base)))))) + (define-public python-keyring (package (name "python-keyring") From a80488c20481e2a86a1808b85530342cf119b424 Mon Sep 17 00:00:00 2001 From: ng0 Date: Mon, 17 Oct 2016 10:30:58 +0000 Subject: [PATCH 306/436] gnu: Add python-pykka. * gnu/packages/python.scm (python-pykka): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/python.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a2f0db74fa..0bfc8598ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2648,6 +2648,35 @@ somewhat intelligeble.") (define-public python2-pyjwt (package-with-python2 python-pyjwt)) +(define-public python-pykka + (package + (name "python-pykka") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "Pykka" version)) + (sha256 + (base32 + "049w3r0mdnnw7xv19jiq7rvls9k7xs73x05b4qs5d6z4vvmgyiz8")))) + (build-system python-build-system) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose) + ("python-gevent" ,python-gevent) + ("python-eventlet" ,python-eventlet))) + (home-page "https://www.pykka.org/") + (synopsis "Pykka is a Python implementation of the actor model") + (description + "Pykka is a Python implementation of the actor model. +The actor model introduces some simple rules to control the sharing +of state and cooperation between execution units, which makes it +easier to build concurrent applications.") + (license license:asl2.0))) + +(define-public python2-pykka + (package-with-python2 python-pykka)) + (define-public python-oauthlib (package (name "python-oauthlib") From 71053e1477b9f207072e64e831c6f55211cf6022 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 2 Mar 2017 09:11:54 +0100 Subject: [PATCH 307/436] gnu: Remove icedtea-6. * gnu/packages/java.scm (icedtea-6): Remove variable. (icedtea-7): Do not inherit from icedtea-6. --- gnu/packages/java.scm | 1000 ++++++++++++++++++----------------------- 1 file changed, 436 insertions(+), 564 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 1abdf607f5..cf4ba69d6a 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -335,463 +335,6 @@ and is best suited to building Java projects. Ant uses XML to describe the build process and its dependencies, whereas Make uses Makefile format.") (license license:asl2.0))) -(define-public icedtea-6 - (package - (name "icedtea") - (version "1.13.13") - (source (origin - (method url-fetch) - (uri (string-append - "http://icedtea.wildebeest.org/download/source/icedtea6-" - version ".tar.xz")) - (sha256 - (base32 - "0bg9sb4f7qbq77c0zf9m17p47ga0kf0r9622g9p12ysg26jd1ksg")) - (modules '((guix build utils))) - (snippet - '(substitute* "Makefile.in" - ;; link against libgcj to avoid linker error - (("-o native-ecj") - "-lgcj -o native-ecj") - ;; do not leak information about the build host - (("DISTRIBUTION_ID=\"\\$\\(DIST_ID\\)\"") - "DISTRIBUTION_ID=\"\\\"guix\\\"\""))))) - (build-system gnu-build-system) - (outputs '("out" ; Java Runtime Environment - "jdk" ; Java Development Kit - "doc")) ; all documentation - (arguments - `(;; There are many failing tests and many are known to fail upstream. - ;; - ;; * Hotspot VM tests: - ;; FAILED: compiler/7082949/Test7082949.java - ;; FAILED: compiler/7088020/Test7088020.java - ;; FAILED: runtime/6929067/Test6929067.sh - ;; FAILED: serviceability/sa/jmap-hashcode/Test8028623.java - ;; => Test results: passed: 161; failed: 4 - ;; - ;; * langtools tests: - ;; FAILED: com/sun/javadoc/testHtmlDefinitionListTag/TestHtmlDefinitionListTag.java - ;; FAILED: tools/javac/6627362/T6627362.java - ;; FAILED: tools/javac/7003595/T7003595.java - ;; FAILED: tools/javac/7024568/T7024568.java - ;; FAILED: tools/javap/4111861/T4111861.java - ;; FAILED: tools/javap/ListTest.java - ;; FAILED: tools/javap/OptionTest.java - ;; FAILED: tools/javap/T4884240.java - ;; FAILED: tools/javap/T4975569.java - ;; --> fails because of insignificant whitespace differences - ;; in output of javap - ;; FAILED: tools/javap/T6868539.java - ;; => Test results: passed: 1,445; failed: 10 - ;; - ;; * JDK tests: - ;; Tests are incomplete because of a segfault after this test: - ;; javax/crypto/spec/RC5ParameterSpec/RC5ParameterSpecEquals.java - ;; A bug report has already been filed upstream: - ;; http://icedtea.classpath.org/bugzilla/show_bug.cgi?id=2188 - ;; - ;; The tests require xvfb-run, a wrapper script around Xvfb, which - ;; has not been packaged yet. Without it many AWT tests fail, so I - ;; made no attempts to make a list of failing JDK tests. At least - ;; 222 tests are failing of which at least 132 are AWT tests. - #:tests? #f - - ;; The DSOs use $ORIGIN to refer to each other, but (guix build - ;; gremlin) doesn't support it yet, so skip this phase. - #:validate-runpath? #f - - #:modules ((guix build utils) - (guix build gnu-build-system) - (ice-9 popen) - (ice-9 rdelim) - (srfi srfi-19)) - - #:configure-flags - (let* ((gcjdir (assoc-ref %build-inputs "gcj")) - (ecj (string-append gcjdir "/share/java/ecj.jar")) - (jdk (string-append gcjdir "/lib/jvm/")) - (gcj (string-append gcjdir "/bin/gcj"))) - `("--enable-bootstrap" - "--enable-nss" - "--without-rhino" - "--disable-downloading" - "--disable-tests" ;they are run in the check phase instead - "--with-openjdk-src-dir=./openjdk.src" - ,(string-append "--with-javac=" jdk "/bin/javac") - ,(string-append "--with-ecj-jar=" ecj) - ,(string-append "--with-gcj=" gcj) - ,(string-append "--with-jdk-home=" jdk) - ,(string-append "--with-java=" jdk "/bin/java"))) - #:phases - (modify-phases %standard-phases - (replace 'unpack - (lambda* (#:key source inputs #:allow-other-keys) - (and (zero? (system* "tar" "xvf" source)) - (begin - (chdir (string-append "icedtea6-" ,version)) - (mkdir "openjdk.src") - (with-directory-excursion "openjdk.src" - (copy-file (assoc-ref inputs "openjdk6-src") - "openjdk6-src.tar.xz") - (zero? (system* "tar" "xvf" "openjdk6-src.tar.xz"))))))) - (add-after 'unpack 'patch-patches - (lambda _ - ;; shebang in patches so that they apply cleanly - (substitute* '("patches/jtreg-jrunscript.patch" - "patches/hotspot/hs23/drop_unlicensed_test.patch") - (("#!/bin/sh") (string-append "#!" (which "sh")))) - #t)) - (add-after 'unpack 'patch-paths - (lambda _ - ;; buildtree.make generates shell scripts, so we need to replace - ;; the generated shebang - (substitute* '("openjdk.src/hotspot/make/linux/makefiles/buildtree.make") - (("/bin/sh") (which "bash"))) - - (let ((corebin (string-append - (assoc-ref %build-inputs "coreutils") "/bin/")) - (binbin (string-append - (assoc-ref %build-inputs "binutils") "/bin/")) - (grepbin (string-append - (assoc-ref %build-inputs "grep") "/bin/"))) - (substitute* '("openjdk.src/jdk/make/common/shared/Defs-linux.gmk" - "openjdk.src/corba/make/common/shared/Defs-linux.gmk") - (("UNIXCOMMAND_PATH = /bin/") - (string-append "UNIXCOMMAND_PATH = " corebin)) - (("USRBIN_PATH = /usr/bin/") - (string-append "USRBIN_PATH = " corebin)) - (("DEVTOOLS_PATH *= */usr/bin/") - (string-append "DEVTOOLS_PATH = " corebin)) - (("COMPILER_PATH *= */usr/bin/") - (string-append "COMPILER_PATH = " - (assoc-ref %build-inputs "gcc") "/bin/")) - (("DEF_OBJCOPY *=.*objcopy") - (string-append "DEF_OBJCOPY = " (which "objcopy")))) - - ;; fix path to alsa header - (substitute* "openjdk.src/jdk/make/common/shared/Sanity.gmk" - (("ALSA_INCLUDE=/usr/include/alsa/version.h") - (string-append "ALSA_INCLUDE=" - (assoc-ref %build-inputs "alsa-lib") - "/include/alsa/version.h"))) - - ;; fix hard-coded utility paths - (substitute* '("openjdk.src/jdk/make/common/shared/Defs-utils.gmk" - "openjdk.src/corba/make/common/shared/Defs-utils.gmk") - (("ECHO *=.*echo") - (string-append "ECHO = " (which "echo"))) - (("^GREP *=.*grep") - (string-append "GREP = " (which "grep"))) - (("EGREP *=.*egrep") - (string-append "EGREP = " (which "egrep"))) - (("CPIO *=.*cpio") - (string-append "CPIO = " (which "cpio"))) - (("READELF *=.*readelf") - (string-append "READELF = " (which "readelf"))) - (("^ *AR *=.*ar") - (string-append "AR = " (which "ar"))) - (("^ *TAR *=.*tar") - (string-append "TAR = " (which "tar"))) - (("AS *=.*as") - (string-append "AS = " (which "as"))) - (("LD *=.*ld") - (string-append "LD = " (which "ld"))) - (("STRIP *=.*strip") - (string-append "STRIP = " (which "strip"))) - (("NM *=.*nm") - (string-append "NM = " (which "nm"))) - (("^SH *=.*sh") - (string-append "SH = " (which "bash"))) - (("^FIND *=.*find") - (string-append "FIND = " (which "find"))) - (("LDD *=.*ldd") - (string-append "LDD = " (which "ldd"))) - (("NAWK *=.*(n|g)awk") - (string-append "NAWK = " (which "gawk"))) - (("XARGS *=.*xargs") - (string-append "XARGS = " (which "xargs"))) - (("UNZIP *=.*unzip") - (string-append "UNZIP = " (which "unzip"))) - (("ZIPEXE *=.*zip") - (string-append "ZIPEXE = " (which "zip"))) - (("SED *=.*sed") - (string-append "SED = " (which "sed")))) - - ;; Some of these timestamps cause problems as they are more than - ;; 10 years ago, failing the build process. - (substitute* - "openjdk.src/jdk/src/share/classes/java/util/CurrencyData.properties" - (("AZ=AZM;2005-12-31-20-00-00;AZN") "AZ=AZN") - (("MZ=MZM;2006-06-30-22-00-00;MZN") "MZ=MZN") - (("RO=ROL;2005-06-30-21-00-00;RON") "RO=RON") - (("TR=TRL;2004-12-31-22-00-00;TRY") "TR=TRY"))))) - (add-before 'configure 'set-additional-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ((gcjdir (assoc-ref %build-inputs "gcj")) - (gcjlib (string-append gcjdir "/lib")) - ;; Get target-specific include directory so that - ;; libgcj-config.h is found when compiling hotspot. - (gcjinclude (let* ((port (open-input-pipe "gcj -print-file-name=include")) - (str (read-line port))) - (close-pipe port) - str))) - (setenv "CPATH" - (string-append gcjinclude ":" - (assoc-ref %build-inputs "libxrender") - "/include/X11/extensions" ":" - (assoc-ref %build-inputs "libxtst") - "/include/X11/extensions" ":" - (assoc-ref %build-inputs "libxinerama") - "/include/X11/extensions" ":" - (or (getenv "CPATH") ""))) - (setenv "ALT_CUPS_HEADERS_PATH" - (string-append (assoc-ref %build-inputs "cups") - "/include")) - (setenv "ALT_FREETYPE_HEADERS_PATH" - (string-append (assoc-ref %build-inputs "freetype") - "/include")) - (setenv "ALT_FREETYPE_LIB_PATH" - (string-append (assoc-ref %build-inputs "freetype") - "/lib"))))) - (add-before 'check 'fix-test-framework - (lambda _ - ;; Fix PATH in test environment - (substitute* "src/jtreg/com/sun/javatest/regtest/Main.java" - (("PATH=/bin:/usr/bin") - (string-append "PATH=" (getenv "PATH")))) - (substitute* "src/jtreg/com/sun/javatest/util/SysEnv.java" - (("/usr/bin/env") (which "env"))) - #t)) - (add-before 'check 'fix-hotspot-tests - (lambda _ - (with-directory-excursion "openjdk.src/hotspot/test/" - (substitute* "jprt.config" - (("PATH=\"\\$\\{path4sdk\\}\"") - (string-append "PATH=" (getenv "PATH"))) - (("make=/usr/bin/make") - (string-append "make=" (which "make")))) - (substitute* '("runtime/6626217/Test6626217.sh" - "runtime/7110720/Test7110720.sh") - (("/bin/rm") (which "rm")) - (("/bin/cp") (which "cp")) - (("/bin/mv") (which "mv")))) - #t)) - (add-before 'check 'fix-jdk-tests - (lambda _ - (with-directory-excursion "openjdk.src/jdk/test/" - (substitute* "com/sun/jdi/JdbReadTwiceTest.sh" - (("/bin/pwd") (which "pwd"))) - (substitute* "com/sun/jdi/ShellScaffold.sh" - (("/bin/kill") (which "kill"))) - (substitute* "start-Xvfb.sh" - ;;(("/usr/bin/X11/Xvfb") (which "Xvfb")) - (("/usr/bin/nohup") (which "nohup"))) - (substitute* "javax/security/auth/Subject/doAs/Test.sh" - (("/bin/rm") (which "rm"))) - (substitute* "tools/launcher/MultipleJRE.sh" - (("echo \"#!/bin/sh\"") - (string-append "echo \"#!" (which "rm") "\"")) - (("/usr/bin/zip") (which "zip"))) - (substitute* "com/sun/jdi/OnThrowTest.java" - (("#!/bin/sh") (string-append "#!" (which "sh")))) - (substitute* "java/lang/management/OperatingSystemMXBean/GetSystemLoadAverage.java" - (("/usr/bin/uptime") (which "uptime"))) - (substitute* "java/lang/ProcessBuilder/Basic.java" - (("/usr/bin/env") (which "env")) - (("/bin/false") (which "false")) - (("/bin/true") (which "true")) - (("/bin/cp") (which "cp")) - (("/bin/sh") (which "sh"))) - (substitute* "java/lang/ProcessBuilder/FeelingLucky.java" - (("/bin/sh") (which "sh"))) - (substitute* "java/lang/ProcessBuilder/Zombies.java" - (("/usr/bin/perl") (which "perl")) - (("/bin/ps") (which "ps")) - (("/bin/true") (which "true"))) - (substitute* "java/lang/Runtime/exec/ConcurrentRead.java" - (("/usr/bin/tee") (which "tee"))) - (substitute* "java/lang/Runtime/exec/ExecWithDir.java" - (("/bin/true") (which "true"))) - (substitute* "java/lang/Runtime/exec/ExecWithInput.java" - (("/bin/cat") (which "cat"))) - (substitute* "java/lang/Runtime/exec/ExitValue.java" - (("/bin/sh") (which "sh")) - (("/bin/true") (which "true")) - (("/bin/kill") (which "kill"))) - (substitute* "java/lang/Runtime/exec/LotsOfDestroys.java" - (("/usr/bin/echo") (which "echo"))) - (substitute* "java/lang/Runtime/exec/LotsOfOutput.java" - (("/usr/bin/cat") (which "cat"))) - (substitute* "java/lang/Runtime/exec/SleepyCat.java" - (("/bin/cat") (which "cat")) - (("/bin/sleep") (which "sleep")) - (("/bin/sh") (which "sh"))) - (substitute* "java/lang/Runtime/exec/StreamsSurviveDestroy.java" - (("/bin/cat") (which "cat"))) - (substitute* "java/rmi/activation/CommandEnvironment/SetChildEnv.java" - (("/bin/chmod") (which "chmod"))) - (substitute* "java/util/zip/ZipFile/Assortment.java" - (("/bin/sh") (which "sh")))) - #t)) - (replace 'check - (lambda _ - ;; The "make check-*" targets always return zero, so we need to - ;; check for errors in the associated log files to determine - ;; whether any tests have failed. - (use-modules (ice-9 rdelim)) - (let* ((error-pattern (make-regexp "^(Error|FAILED):.*")) - (checker (lambda (port) - (let loop () - (let ((line (read-line port))) - (cond - ((eof-object? line) #t) - ((regexp-exec error-pattern line) #f) - (else (loop))))))) - (run-test (lambda (test) - (system* "make" test) - (call-with-input-file - (string-append "test/" test ".log") - checker)))) - (or #t ; skip tests - (and (run-test "check-hotspot") - (run-test "check-langtools") - (run-test "check-jdk")))))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((doc (string-append (assoc-ref outputs "doc") - "/share/doc/icedtea")) - (jre (assoc-ref outputs "out")) - (jdk (assoc-ref outputs "jdk"))) - (copy-recursively "openjdk.build/docs" doc) - (copy-recursively "openjdk.build/j2re-image" jre) - (copy-recursively "openjdk.build/j2sdk-image" jdk)))) - ;; By default IcedTea only generates an empty keystore. In order to - ;; be able to use certificates in Java programs we need to generate a - ;; keystore from a set of certificates. For convenience we use the - ;; certificates from the nss-certs package. - (add-after 'install 'install-keystore - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((keystore "cacerts") - (certs-dir (string-append (assoc-ref inputs "nss-certs") - "/etc/ssl/certs")) - (keytool (string-append (assoc-ref outputs "jdk") - "/bin/keytool"))) - (define (extract-cert file target) - (call-with-input-file file - (lambda (in) - (call-with-output-file target - (lambda (out) - (let loop ((line (read-line in 'concat)) - (copying? #f)) - (cond - ((eof-object? line) #t) - ((string-prefix? "-----BEGIN" line) - (display line out) - (loop (read-line in 'concat) #t)) - ((string-prefix? "-----END" line) - (display line out) - #t) - (else - (when copying? (display line out)) - (loop (read-line in 'concat) copying?))))))))) - (define (import-cert cert) - (format #t "Importing certificate ~a\n" (basename cert)) - (let ((temp "tmpcert")) - (extract-cert cert temp) - (let ((port (open-pipe* OPEN_WRITE keytool - "-import" - "-alias" (basename cert) - "-keystore" keystore - "-storepass" "changeit" - "-file" temp))) - (display "yes\n" port) - (when (not (zero? (status:exit-val (close-pipe port)))) - (format #t "failed to import ~a\n" cert))) - (delete-file temp))) - - ;; This is necessary because the certificate directory contains - ;; files with non-ASCII characters in their names. - (setlocale LC_ALL "en_US.utf8") - (setenv "LC_ALL" "en_US.utf8") - - (for-each import-cert (find-files certs-dir "\\.pem$")) - (mkdir-p (string-append (assoc-ref outputs "out") - "/lib/security")) - (mkdir-p (string-append (assoc-ref outputs "jdk") - "/jre/lib/security")) - - ;; The cacerts files we are going to overwrite are chmod'ed as - ;; read-only (444) in icedtea-8 (which derives from this - ;; package). We have to change this so we can overwrite them. - (chmod (string-append (assoc-ref outputs "out") - "/lib/security/" keystore) #o644) - (chmod (string-append (assoc-ref outputs "jdk") - "/jre/lib/security/" keystore) #o644) - - (install-file keystore - (string-append (assoc-ref outputs "out") - "/lib/security")) - (install-file keystore - (string-append (assoc-ref outputs "jdk") - "/jre/lib/security")) - #t)))))) - (native-inputs - `(("ant" ,ant) - ("alsa-lib" ,alsa-lib) - ("attr" ,attr) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("coreutils" ,coreutils) - ("diffutils" ,diffutils) ;for tests - ("gawk" ,gawk) - ("grep" ,grep) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("cups" ,cups) - ("wget" ,wget) - ("which" ,which) - ("cpio" ,cpio) - ("zip" ,zip) - ("unzip" ,unzip) - ("fastjar" ,fastjar) - ("libxslt" ,libxslt) ;for xsltproc - ("mit-krb5" ,mit-krb5) - ("nss" ,nss) - ("nss-certs" ,nss-certs) - ("libx11" ,libx11) - ("libxcomposite" ,libxcomposite) - ("libxt" ,libxt) - ("libxtst" ,libxtst) - ("libxi" ,libxi) - ("libxinerama" ,libxinerama) - ("libxrender" ,libxrender) - ("libjpeg" ,libjpeg) - ("libpng" ,libpng) - ("giflib" ,giflib) - ("perl" ,perl) - ("procps" ,procps) ;for "free", even though I'm not sure we should use it - ("openjdk6-src" - ,(origin - (method url-fetch) - (uri "https://java.net/downloads/openjdk6/openjdk-6-src-b41-04_jan_2017.tar.xz") - (sha256 - (base32 - "058szix0j280g14jzajvsixx1j2dxmc10r848f5swpy6rr8x8d4f")))) - ("lcms" ,lcms) - ("zlib" ,zlib) - ("gtk" ,gtk+-2) - ("fontconfig" ,fontconfig) - ("freetype" ,freetype) - ("gcj" ,gcj))) - (home-page "http://icedtea.classpath.org") - (synopsis "Java development kit") - (description - "The OpenJDK built with the IcedTea build harness.") - ;; IcedTea is released under the GPL2 + Classpath exception, which is the - ;; same license as both GNU Classpath and OpenJDK. - (license license:gpl2+))) - (define-public icedtea-7 (let* ((version "2.6.9") (drop (lambda (name hash) @@ -801,7 +344,8 @@ build process and its dependencies, whereas Make uses Makefile format.") "http://icedtea.classpath.org/download/drops/" "/icedtea7/" version "/" name ".tar.bz2")) (sha256 (base32 hash)))))) - (package (inherit icedtea-6) + (package + (name "icedtea") (version version) (source (origin (method url-fetch) @@ -820,6 +364,10 @@ build process and its dependencies, whereas Make uses Makefile format.") ;; do not leak information about the build host (("DISTRIBUTION_ID=\"\\$\\(DIST_ID\\)\"") "DISTRIBUTION_ID=\"\\\"guix\\\"\""))))) + (build-system gnu-build-system) + (outputs '("out" ; Java Runtime Environment + "jdk" ; Java Development Kit + "doc")) ; all documentation (arguments `(;; There are many test failures. Some are known to ;; fail upstream, others relate to not having an X @@ -830,110 +378,390 @@ build process and its dependencies, whereas Make uses Makefile format.") ;; langtools: passed: 1,934; failed: 26 ;; jdk: unknown #:tests? #f + + ;; The DSOs use $ORIGIN to refer to each other, but (guix build + ;; gremlin) doesn't support it yet, so skip this phase. + #:validate-runpath? #f + ;; Apparently, the C locale is needed for some of the tests. #:locale "C" - ,@(substitute-keyword-arguments (package-arguments icedtea-6) - ((#:modules modules) - `((ice-9 match) - (srfi srfi-26) - ,@modules)) - ((#:configure-flags flags) - ;; TODO: package pcsc and sctp, and add to inputs - `(append '("--disable-system-pcsc" - "--disable-system-sctp") - ,flags)) - ((#:phases phases) - `(modify-phases ,phases - (replace 'unpack - (lambda* (#:key source inputs #:allow-other-keys) - (let ((target (string-append "icedtea-" ,version)) - (unpack (lambda* (name #:optional dir) - (let ((dir (or dir - (string-drop-right name 5)))) - (mkdir dir) - (zero? (system* "tar" "xvf" - (assoc-ref inputs name) - "-C" dir - "--strip-components=1")))))) - (mkdir target) - (and - (zero? (system* "tar" "xvf" source - "-C" target "--strip-components=1")) - (chdir target) - (unpack "openjdk-src" "openjdk.src") - (with-directory-excursion "openjdk.src" - (for-each unpack - (filter (cut string-suffix? "-drop" <>) - (map (match-lambda - ((name . _) name)) - inputs)))) - #t)))) - (replace - 'set-additional-paths - (lambda* (#:key inputs #:allow-other-keys) - (let (;; Get target-specific include directory so that - ;; libgcj-config.h is found when compiling hotspot. - (gcjinclude (let* ((port (open-input-pipe "gcj -print-file-name=include")) - (str (read-line port))) - (close-pipe port) - str))) - (substitute* "openjdk.src/jdk/make/common/shared/Sanity.gmk" - (("ALSA_INCLUDE=/usr/include/alsa/version.h") - (string-append "ALSA_INCLUDE=" - (assoc-ref inputs "alsa-lib") - "/include/alsa/version.h"))) - (setenv "CC" "gcc") - (setenv "CPATH" - (string-append gcjinclude ":" - (assoc-ref inputs "libxcomposite") - "/include/X11/extensions" ":" - (assoc-ref inputs "libxrender") - "/include/X11/extensions" ":" - (assoc-ref inputs "libxtst") - "/include/X11/extensions" ":" - (assoc-ref inputs "libxinerama") - "/include/X11/extensions" ":" - (or (getenv "CPATH") ""))) - (setenv "ALT_OBJCOPY" (which "objcopy")) - (setenv "ALT_CUPS_HEADERS_PATH" - (string-append (assoc-ref inputs "cups") - "/include")) - (setenv "ALT_FREETYPE_HEADERS_PATH" - (string-append (assoc-ref inputs "freetype") - "/include")) - (setenv "ALT_FREETYPE_LIB_PATH" - (string-append (assoc-ref inputs "freetype") - "/lib"))))) - (add-after - 'unpack 'fix-x11-extension-include-path - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "openjdk.src/jdk/make/sun/awt/mawt.gmk" - (((string-append "\\$\\(firstword \\$\\(wildcard " - "\\$\\(OPENWIN_HOME\\)" - "/include/X11/extensions\\).*$")) - (string-append (assoc-ref inputs "libxrender") - "/include/X11/extensions" - " -I" (assoc-ref inputs "libxtst") - "/include/X11/extensions" - " -I" (assoc-ref inputs "libxinerama") - "/include/X11/extensions")) - (("\\$\\(wildcard /usr/include/X11/extensions\\)\\)") "")) - #t)) - (replace - 'fix-test-framework - (lambda _ - ;; Fix PATH in test environment - (substitute* "test/jtreg/com/sun/javatest/regtest/Main.java" - (("PATH=/bin:/usr/bin") - (string-append "PATH=" (getenv "PATH")))) - (substitute* "test/jtreg/com/sun/javatest/util/SysEnv.java" - (("/usr/bin/env") (which "env"))) - (substitute* "openjdk.src/hotspot/test/test_env.sh" - (("/bin/rm") (which "rm")) - (("/bin/cp") (which "cp")) - (("/bin/mv") (which "mv"))) - #t)) - (delete 'patch-patches)))))) + + #:modules ((guix build utils) + (guix build gnu-build-system) + (ice-9 match) + (ice-9 popen) + (ice-9 rdelim) + (srfi srfi-19) + (srfi srfi-26)) + + #:configure-flags + (let* ((gcjdir (assoc-ref %build-inputs "gcj")) + (ecj (string-append gcjdir "/share/java/ecj.jar")) + (jdk (string-append gcjdir "/lib/jvm/")) + (gcj (string-append gcjdir "/bin/gcj"))) + ;; TODO: package pcsc and sctp, and add to inputs + `("--disable-system-pcsc" + "--disable-system-sctp" + "--enable-bootstrap" + "--enable-nss" + "--without-rhino" + "--disable-downloading" + "--disable-tests" ;they are run in the check phase instead + "--with-openjdk-src-dir=./openjdk.src" + ,(string-append "--with-javac=" jdk "/bin/javac") + ,(string-append "--with-ecj-jar=" ecj) + ,(string-append "--with-gcj=" gcj) + ,(string-append "--with-jdk-home=" jdk) + ,(string-append "--with-java=" jdk "/bin/java"))) + + #:phases + (modify-phases %standard-phases + (replace 'unpack + (lambda* (#:key source inputs #:allow-other-keys) + (let ((target (string-append "icedtea-" ,version)) + (unpack (lambda* (name #:optional dir) + (let ((dir (or dir + (string-drop-right name 5)))) + (mkdir dir) + (zero? (system* "tar" "xvf" + (assoc-ref inputs name) + "-C" dir + "--strip-components=1")))))) + (mkdir target) + (and + (zero? (system* "tar" "xvf" source + "-C" target "--strip-components=1")) + (chdir target) + (unpack "openjdk-src" "openjdk.src") + (with-directory-excursion "openjdk.src" + (for-each unpack + (filter (cut string-suffix? "-drop" <>) + (map (match-lambda + ((name . _) name)) + inputs)))) + #t)))) + (add-after 'unpack 'fix-x11-extension-include-path + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "openjdk.src/jdk/make/sun/awt/mawt.gmk" + (((string-append "\\$\\(firstword \\$\\(wildcard " + "\\$\\(OPENWIN_HOME\\)" + "/include/X11/extensions\\).*$")) + (string-append (assoc-ref inputs "libxrender") + "/include/X11/extensions" + " -I" (assoc-ref inputs "libxtst") + "/include/X11/extensions" + " -I" (assoc-ref inputs "libxinerama") + "/include/X11/extensions")) + (("\\$\\(wildcard /usr/include/X11/extensions\\)\\)") "")) + #t)) + (add-after 'unpack 'patch-paths + (lambda _ + ;; buildtree.make generates shell scripts, so we need to replace + ;; the generated shebang + (substitute* '("openjdk.src/hotspot/make/linux/makefiles/buildtree.make") + (("/bin/sh") (which "bash"))) + + (let ((corebin (string-append + (assoc-ref %build-inputs "coreutils") "/bin/")) + (binbin (string-append + (assoc-ref %build-inputs "binutils") "/bin/")) + (grepbin (string-append + (assoc-ref %build-inputs "grep") "/bin/"))) + (substitute* '("openjdk.src/jdk/make/common/shared/Defs-linux.gmk" + "openjdk.src/corba/make/common/shared/Defs-linux.gmk") + (("UNIXCOMMAND_PATH = /bin/") + (string-append "UNIXCOMMAND_PATH = " corebin)) + (("USRBIN_PATH = /usr/bin/") + (string-append "USRBIN_PATH = " corebin)) + (("DEVTOOLS_PATH *= */usr/bin/") + (string-append "DEVTOOLS_PATH = " corebin)) + (("COMPILER_PATH *= */usr/bin/") + (string-append "COMPILER_PATH = " + (assoc-ref %build-inputs "gcc") "/bin/")) + (("DEF_OBJCOPY *=.*objcopy") + (string-append "DEF_OBJCOPY = " (which "objcopy")))) + + ;; fix path to alsa header + (substitute* "openjdk.src/jdk/make/common/shared/Sanity.gmk" + (("ALSA_INCLUDE=/usr/include/alsa/version.h") + (string-append "ALSA_INCLUDE=" + (assoc-ref %build-inputs "alsa-lib") + "/include/alsa/version.h"))) + + ;; fix hard-coded utility paths + (substitute* '("openjdk.src/jdk/make/common/shared/Defs-utils.gmk" + "openjdk.src/corba/make/common/shared/Defs-utils.gmk") + (("ECHO *=.*echo") + (string-append "ECHO = " (which "echo"))) + (("^GREP *=.*grep") + (string-append "GREP = " (which "grep"))) + (("EGREP *=.*egrep") + (string-append "EGREP = " (which "egrep"))) + (("CPIO *=.*cpio") + (string-append "CPIO = " (which "cpio"))) + (("READELF *=.*readelf") + (string-append "READELF = " (which "readelf"))) + (("^ *AR *=.*ar") + (string-append "AR = " (which "ar"))) + (("^ *TAR *=.*tar") + (string-append "TAR = " (which "tar"))) + (("AS *=.*as") + (string-append "AS = " (which "as"))) + (("LD *=.*ld") + (string-append "LD = " (which "ld"))) + (("STRIP *=.*strip") + (string-append "STRIP = " (which "strip"))) + (("NM *=.*nm") + (string-append "NM = " (which "nm"))) + (("^SH *=.*sh") + (string-append "SH = " (which "bash"))) + (("^FIND *=.*find") + (string-append "FIND = " (which "find"))) + (("LDD *=.*ldd") + (string-append "LDD = " (which "ldd"))) + (("NAWK *=.*(n|g)awk") + (string-append "NAWK = " (which "gawk"))) + (("XARGS *=.*xargs") + (string-append "XARGS = " (which "xargs"))) + (("UNZIP *=.*unzip") + (string-append "UNZIP = " (which "unzip"))) + (("ZIPEXE *=.*zip") + (string-append "ZIPEXE = " (which "zip"))) + (("SED *=.*sed") + (string-append "SED = " (which "sed")))) + + ;; Some of these timestamps cause problems as they are more than + ;; 10 years ago, failing the build process. + (substitute* + "openjdk.src/jdk/src/share/classes/java/util/CurrencyData.properties" + (("AZ=AZM;2005-12-31-20-00-00;AZN") "AZ=AZN") + (("MZ=MZM;2006-06-30-22-00-00;MZN") "MZ=MZN") + (("RO=ROL;2005-06-30-21-00-00;RON") "RO=RON") + (("TR=TRL;2004-12-31-22-00-00;TRY") "TR=TRY"))) + #t)) + (add-before 'configure 'set-additional-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ( ;; Get target-specific include directory so that + ;; libgcj-config.h is found when compiling hotspot. + (gcjinclude (let* ((port (open-input-pipe "gcj -print-file-name=include")) + (str (read-line port))) + (close-pipe port) + str))) + (substitute* "openjdk.src/jdk/make/common/shared/Sanity.gmk" + (("ALSA_INCLUDE=/usr/include/alsa/version.h") + (string-append "ALSA_INCLUDE=" + (assoc-ref inputs "alsa-lib") + "/include/alsa/version.h"))) + (setenv "CC" "gcc") + (setenv "CPATH" + (string-append gcjinclude ":" + (assoc-ref inputs "libxcomposite") + "/include/X11/extensions" ":" + (assoc-ref inputs "libxrender") + "/include/X11/extensions" ":" + (assoc-ref inputs "libxtst") + "/include/X11/extensions" ":" + (assoc-ref inputs "libxinerama") + "/include/X11/extensions" ":" + (or (getenv "CPATH") ""))) + (setenv "ALT_OBJCOPY" (which "objcopy")) + (setenv "ALT_CUPS_HEADERS_PATH" + (string-append (assoc-ref inputs "cups") + "/include")) + (setenv "ALT_FREETYPE_HEADERS_PATH" + (string-append (assoc-ref inputs "freetype") + "/include")) + (setenv "ALT_FREETYPE_LIB_PATH" + (string-append (assoc-ref inputs "freetype") + "/lib"))) + #t)) + (add-before 'check 'fix-test-framework + (lambda _ + ;; Fix PATH in test environment + (substitute* "test/jtreg/com/sun/javatest/regtest/Main.java" + (("PATH=/bin:/usr/bin") + (string-append "PATH=" (getenv "PATH")))) + (substitute* "test/jtreg/com/sun/javatest/util/SysEnv.java" + (("/usr/bin/env") (which "env"))) + (substitute* "openjdk.src/hotspot/test/test_env.sh" + (("/bin/rm") (which "rm")) + (("/bin/cp") (which "cp")) + (("/bin/mv") (which "mv"))) + #t)) + (add-before 'check 'fix-hotspot-tests + (lambda _ + (with-directory-excursion "openjdk.src/hotspot/test/" + (substitute* "jprt.config" + (("PATH=\"\\$\\{path4sdk\\}\"") + (string-append "PATH=" (getenv "PATH"))) + (("make=/usr/bin/make") + (string-append "make=" (which "make")))) + (substitute* '("runtime/6626217/Test6626217.sh" + "runtime/7110720/Test7110720.sh") + (("/bin/rm") (which "rm")) + (("/bin/cp") (which "cp")) + (("/bin/mv") (which "mv")))) + #t)) + (add-before 'check 'fix-jdk-tests + (lambda _ + (with-directory-excursion "openjdk.src/jdk/test/" + (substitute* "com/sun/jdi/JdbReadTwiceTest.sh" + (("/bin/pwd") (which "pwd"))) + (substitute* "com/sun/jdi/ShellScaffold.sh" + (("/bin/kill") (which "kill"))) + (substitute* "start-Xvfb.sh" + ;;(("/usr/bin/X11/Xvfb") (which "Xvfb")) + (("/usr/bin/nohup") (which "nohup"))) + (substitute* "javax/security/auth/Subject/doAs/Test.sh" + (("/bin/rm") (which "rm"))) + (substitute* "tools/launcher/MultipleJRE.sh" + (("echo \"#!/bin/sh\"") + (string-append "echo \"#!" (which "rm") "\"")) + (("/usr/bin/zip") (which "zip"))) + (substitute* "com/sun/jdi/OnThrowTest.java" + (("#!/bin/sh") (string-append "#!" (which "sh")))) + (substitute* "java/lang/management/OperatingSystemMXBean/GetSystemLoadAverage.java" + (("/usr/bin/uptime") (which "uptime"))) + (substitute* "java/lang/ProcessBuilder/Basic.java" + (("/usr/bin/env") (which "env")) + (("/bin/false") (which "false")) + (("/bin/true") (which "true")) + (("/bin/cp") (which "cp")) + (("/bin/sh") (which "sh"))) + (substitute* "java/lang/ProcessBuilder/FeelingLucky.java" + (("/bin/sh") (which "sh"))) + (substitute* "java/lang/ProcessBuilder/Zombies.java" + (("/usr/bin/perl") (which "perl")) + (("/bin/ps") (which "ps")) + (("/bin/true") (which "true"))) + (substitute* "java/lang/Runtime/exec/ConcurrentRead.java" + (("/usr/bin/tee") (which "tee"))) + (substitute* "java/lang/Runtime/exec/ExecWithDir.java" + (("/bin/true") (which "true"))) + (substitute* "java/lang/Runtime/exec/ExecWithInput.java" + (("/bin/cat") (which "cat"))) + (substitute* "java/lang/Runtime/exec/ExitValue.java" + (("/bin/sh") (which "sh")) + (("/bin/true") (which "true")) + (("/bin/kill") (which "kill"))) + (substitute* "java/lang/Runtime/exec/LotsOfDestroys.java" + (("/usr/bin/echo") (which "echo"))) + (substitute* "java/lang/Runtime/exec/LotsOfOutput.java" + (("/usr/bin/cat") (which "cat"))) + (substitute* "java/lang/Runtime/exec/SleepyCat.java" + (("/bin/cat") (which "cat")) + (("/bin/sleep") (which "sleep")) + (("/bin/sh") (which "sh"))) + (substitute* "java/lang/Runtime/exec/StreamsSurviveDestroy.java" + (("/bin/cat") (which "cat"))) + (substitute* "java/rmi/activation/CommandEnvironment/SetChildEnv.java" + (("/bin/chmod") (which "chmod"))) + (substitute* "java/util/zip/ZipFile/Assortment.java" + (("/bin/sh") (which "sh")))) + #t)) + (replace 'check + (lambda _ + ;; The "make check-*" targets always return zero, so we need to + ;; check for errors in the associated log files to determine + ;; whether any tests have failed. + (use-modules (ice-9 rdelim)) + (let* ((error-pattern (make-regexp "^(Error|FAILED):.*")) + (checker (lambda (port) + (let loop () + (let ((line (read-line port))) + (cond + ((eof-object? line) #t) + ((regexp-exec error-pattern line) #f) + (else (loop))))))) + (run-test (lambda (test) + (system* "make" test) + (call-with-input-file + (string-append "test/" test ".log") + checker)))) + (or #t ; skip tests + (and (run-test "check-hotspot") + (run-test "check-langtools") + (run-test "check-jdk")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((doc (string-append (assoc-ref outputs "doc") + "/share/doc/icedtea")) + (jre (assoc-ref outputs "out")) + (jdk (assoc-ref outputs "jdk"))) + (copy-recursively "openjdk.build/docs" doc) + (copy-recursively "openjdk.build/j2re-image" jre) + (copy-recursively "openjdk.build/j2sdk-image" jdk)) + #t)) + ;; By default IcedTea only generates an empty keystore. In order to + ;; be able to use certificates in Java programs we need to generate a + ;; keystore from a set of certificates. For convenience we use the + ;; certificates from the nss-certs package. + (add-after 'install 'install-keystore + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((keystore "cacerts") + (certs-dir (string-append (assoc-ref inputs "nss-certs") + "/etc/ssl/certs")) + (keytool (string-append (assoc-ref outputs "jdk") + "/bin/keytool"))) + (define (extract-cert file target) + (call-with-input-file file + (lambda (in) + (call-with-output-file target + (lambda (out) + (let loop ((line (read-line in 'concat)) + (copying? #f)) + (cond + ((eof-object? line) #t) + ((string-prefix? "-----BEGIN" line) + (display line out) + (loop (read-line in 'concat) #t)) + ((string-prefix? "-----END" line) + (display line out) + #t) + (else + (when copying? (display line out)) + (loop (read-line in 'concat) copying?))))))))) + (define (import-cert cert) + (format #t "Importing certificate ~a\n" (basename cert)) + (let ((temp "tmpcert")) + (extract-cert cert temp) + (let ((port (open-pipe* OPEN_WRITE keytool + "-import" + "-alias" (basename cert) + "-keystore" keystore + "-storepass" "changeit" + "-file" temp))) + (display "yes\n" port) + (when (not (zero? (status:exit-val (close-pipe port)))) + (format #t "failed to import ~a\n" cert))) + (delete-file temp))) + + ;; This is necessary because the certificate directory contains + ;; files with non-ASCII characters in their names. + (setlocale LC_ALL "en_US.utf8") + (setenv "LC_ALL" "en_US.utf8") + + (for-each import-cert (find-files certs-dir "\\.pem$")) + (mkdir-p (string-append (assoc-ref outputs "out") + "/lib/security")) + (mkdir-p (string-append (assoc-ref outputs "jdk") + "/jre/lib/security")) + + ;; The cacerts files we are going to overwrite are chmod'ed as + ;; read-only (444) in icedtea-8 (which derives from this + ;; package). We have to change this so we can overwrite them. + (chmod (string-append (assoc-ref outputs "out") + "/lib/security/" keystore) #o644) + (chmod (string-append (assoc-ref outputs "jdk") + "/jre/lib/security/" keystore) #o644) + + (install-file keystore + (string-append (assoc-ref outputs "out") + "/lib/security")) + (install-file keystore + (string-append (assoc-ref outputs "jdk") + "/jre/lib/security")) + #t)))))) (native-inputs `(("openjdk-src" ,(drop "openjdk" @@ -956,11 +784,55 @@ build process and its dependencies, whereas Make uses Makefile format.") ("hotspot-drop" ,(drop "hotspot" "16ijxy8br8dla339m4i90wr9xpf7s8z3nrhfyxm7jahr8injpzyl")) - ,@(fold alist-delete (package-native-inputs icedtea-6) - '("openjdk6-src")))) + ("ant" ,ant) + ("attr" ,attr) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("coreutils" ,coreutils) + ("diffutils" ,diffutils) ;for tests + ("gawk" ,gawk) + ("grep" ,grep) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config) + ("wget" ,wget) + ("which" ,which) + ("cpio" ,cpio) + ("zip" ,zip) + ("unzip" ,unzip) + ("fastjar" ,fastjar) + ("libxslt" ,libxslt) ;for xsltproc + ("nss-certs" ,nss-certs) + ("perl" ,perl) + ("procps" ,procps) ;for "free", even though I'm not sure we should use it + ("gcj" ,gcj))) (inputs - `(("libxcomposite" ,libxcomposite) - ,@(package-inputs icedtea-6)))))) + `(("alsa-lib" ,alsa-lib) + ("cups" ,cups) + ("libx11" ,libx11) + ("libxcomposite" ,libxcomposite) + ("libxt" ,libxt) + ("libxtst" ,libxtst) + ("libxi" ,libxi) + ("libxinerama" ,libxinerama) + ("libxrender" ,libxrender) + ("libjpeg" ,libjpeg) + ("libpng" ,libpng) + ("mit-krb5" ,mit-krb5) + ("nss" ,nss) + ("giflib" ,giflib) + ("fontconfig" ,fontconfig) + ("freetype" ,freetype) + ("lcms" ,lcms) + ("zlib" ,zlib) + ("gtk" ,gtk+-2))) + (home-page "http://icedtea.classpath.org") + (synopsis "Java development kit") + (description + "This package provides the Java development kit OpenJDK built with the +IcedTea build harness.") + ;; IcedTea is released under the GPL2 + Classpath exception, which is the + ;; same license as both GNU Classpath and OpenJDK. + (license license:gpl2+)))) (define-public icedtea-8 (let* ((version "3.3.0") From 0c729ef4e361f2fe396a44bd138a693324abfc4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 2 Mar 2017 12:38:21 +0100 Subject: [PATCH 308/436] gnu: icedtea-8: Do not embed build time. * gnu/packages/java.scm (icedtea-8)[source]: Modify snippet to erase the embedded build time. --- gnu/packages/java.scm | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index cf4ba69d6a..1ff106cb99 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2016, 2017 Roel Janssen ;;; Copyright © 2017 Carlo Zancanaro @@ -855,10 +855,15 @@ IcedTea build harness.") "02vmxa6gc6gizcri1fy797qmmm9y77vgi7gy9pwkk4agcw4zyr5p")) (modules '((guix build utils))) (snippet - '(substitute* "Makefile.am" - ;; do not leak information about the build host - (("DISTRIBUTION_ID=\"\\$\\(DIST_ID\\)\"") - "DISTRIBUTION_ID=\"\\\"guix\\\"\""))))) + '(begin + (substitute* "acinclude.m4" + ;; Do not embed build time + (("(DIST_ID=\"Custom build).*$" _ prefix) + (string-append prefix "\"\n")) + ;; Do not leak information about the build host + (("DIST_NAME=\"\\$build_os\"") + "DIST_NAME=\"guix\"")) + #t)))) (arguments (substitute-keyword-arguments (package-arguments icedtea-7) ((#:configure-flags flags) From 81635fb6800684d73fa53bb656ac4f335b4fa44e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 2 Mar 2017 23:03:45 +0100 Subject: [PATCH 309/436] gnu: password-store: Update to 1.7. * gnu/packages/password-utils.scm (password-store): Update to 1.7. [inputs]: Drop PWGEN. Add QRENCODE. [arguments]: Adjust wrapper accordingly. --- gnu/packages/password-utils.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 0a3b4b64e7..811173cae4 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -32,6 +32,7 @@ #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages admin) + #:use-module (gnu packages aidc) #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages glib) @@ -282,7 +283,7 @@ any X11 window.") (define-public password-store (package (name "password-store") - (version "1.6.5") + (version "1.7") (source (origin (method url-fetch) (uri @@ -290,7 +291,7 @@ any X11 window.") name "-" version ".tar.xz")) (sha256 (base32 - "05bk3lrp5jwg0v338lvylp7glpliydzz4jf5pjr6k3kagrv3jyik")))) + "002mw7j0m33bw483rllzhcf41wp3ixka8yma6kqrfaj57jyw66hn")))) (build-system gnu-build-system) (arguments '(#:phases @@ -302,7 +303,7 @@ any X11 window.") (let ((out (assoc-ref outputs "out")) (path (map (lambda (pkg) (string-append (assoc-ref inputs pkg) "/bin")) - '("coreutils" "getopt" "git" "gnupg" "pwgen" + '("coreutils" "getopt" "git" "gnupg" "qrencode" "sed" "tree" "which" "xclip")))) (wrap-program (string-append out "/bin/pass") `("PATH" ":" prefix (,(string-join path ":")))) @@ -325,7 +326,7 @@ any X11 window.") `(("getopt" ,util-linux) ("git" ,git) ("gnupg" ,gnupg) - ("pwgen" ,pwgen) + ("qrencode" ,qrencode) ("sed" ,sed) ("tree" ,tree) ("which" ,which) From 374474225421ffbd2d0420dc94fb88cea4d679dd Mon Sep 17 00:00:00 2001 From: Mekeor Melire Date: Fri, 3 Mar 2017 00:22:47 +0100 Subject: [PATCH 310/436] gnu: Add dzen. * gnu/packages/xdisorg.scm (dzen): New variable. Signed-off-by: Leo Famulari --- gnu/packages/xdisorg.scm | 53 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index a9c2e06b44..3667797abd 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2016 Alex Kost ;;; Copyright © 2016 Marius Bakke ;;; Copyright © 2016 Petter +;;; Copyright © 2017 Mekeor Melire ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,6 +37,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) @@ -1023,6 +1025,57 @@ border, and background. It also supports multihead setups, customized mouse actions, a built-in clock, a battery monitor and a system tray.") (license license:gpl2))) +(define-public dzen + (let ((commit "488ab66019f475e35e067646621827c18a879ba1") + (revision "1")) + (package + (name "dzen") + (version (string-append "0.9.5-" ; Taken from `config.mk`. + revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/robm/dzen.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "0y47d6ii87vf4a517gi4fh0yl06f8b085sra77immnsasbq9pxnw")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; No test suite. + #:make-flags ; Replacement for `config.mk`. + (list + (string-append "VERSION = " ,version) + (string-append "PREFIX = " %output) + "MANPREFIX = ${PREFIX}/share/man" + "INCS = -I." + "LIBS = -lc -lX11 -lXinerama -lXpm $(shell pkg-config --libs xft)" + "CFLAGS = -Wall -Os ${INCS} -DVERSION=\\\"${VERSION}\\\"\ + -DDZEN_XINERAMA -DDZEN_XPM -DDZEN_XFT $(shell pkg-config --cflags xft)" + "LDFLAGS = ${LIBS}" + "CC = gcc" + "LD = ${CC}") + #:phases + (modify-phases %standard-phases + (delete 'configure) ; No configuration script. + ;; Use own make-flags instead of `config.mk`. + (add-before 'build 'dont-include-config-mk + (lambda _ + (substitute* "Makefile" (("include config.mk") "")) + #t))))) + (inputs + `(("libx11" ,libx11) + ("libxft" ,libxft) + ("libxpm" ,libxpm) + ("libxinerama" ,libxinerama))) + (native-inputs `(("pkg-config" ,pkg-config))) + (synopsis "General purpose messaging, notification and menuing program for X11") + (description "Dzen is a general purpose messaging, notification and menuing +program for X11. It was designed to be fast, tiny and scriptable in any language.") + (home-page "https://github.com/robm/dzen") + (license license:expat)))) + (define-public xcb-util-xrm (package (name "xcb-util-xrm") From f0f77eb5e47115726d588e618ea5fb856e406a5a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 21:49:09 +0100 Subject: [PATCH 311/436] gnu: youtube-dl: Update to 2017.03.02. * gnu/packages/video.scm (youtube-dl): Update to 2017.03.02. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index c609eadeec..006341644b 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -975,7 +975,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2017.02.28") + (version "2017.03.02") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -983,7 +983,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "194np8s2khzkdlpn6bmif5w9rzlwvdfapi1jnpg0wyq6mscasnj9")))) + "0f86qnppxnbh2c8bmpf0c1xhwk5vqjdzz7pqh9sydhscv8r0209g")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion From 9baab9aeeda394408290613c597bff1d96004dfb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 22:02:59 +0100 Subject: [PATCH 312/436] gnu: snappy: Update to 1.1.4. * gnu/packages/compression.scm (snappy): Update to 1.1.4. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 73b2b846ea..88f8f0d84e 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -945,7 +945,7 @@ well as bzip2.") (define-public snappy (package (name "snappy") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (string-append @@ -953,7 +953,7 @@ well as bzip2.") version "/" name "-" version ".tar.gz")) (sha256 (base32 - "1wzf8yif5ym2gj52db6v5m1pxnmn258i38x7llk9x346y2nq47ig")))) + "0mq0nz8gbi1sp3y6xcg0a6wbvnd6gc717f3vh2xrjmfj5w9gwjqk")))) (build-system gnu-build-system) (home-page "https://github.com/google/snappy") (synopsis "Fast compressor/decompressor") From 6f23e2fb023c921d03be1f3aef0e1f305ae63764 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 18:35:04 +0100 Subject: [PATCH 313/436] gnu: ruby-arel: Remove duplicate definition. * gnu/packages/ruby.scm (ruby-arel): Remove shadowed 6.0.0 version. [description]: Use the older description & expand some acronyms. --- gnu/packages/ruby.scm | 25 +++---------------------- 1 file changed, 3 insertions(+), 22 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 972bd230d2..73eefe8dde 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1020,26 +1020,6 @@ features.") (home-page "https://github.com/chneukirchen/bacon") (license license:expat))) -(define-public ruby-arel - (package - (name "ruby-arel") - (version "6.0.0") - (source (origin - (method url-fetch) - (uri (rubygems-uri "arel" version)) - (sha256 - (base32 - "18wnfnzr2i5p3fygsddjbi1cimws6823nbk8drxidmnj8jz7h0ar")))) - (build-system ruby-build-system) - (arguments - '(#:tests? #f)) ; no test suite - (synopsis "SQL AST manager for Ruby") - (description "Arel is a SQL AST manager for Ruby. It simplifies the -generation of complex SQL queries and adapts to various relational database -implementations.") - (home-page "https://github.com/rails/arel") - (license license:expat))) - (define-public ruby-connection-pool (package (name "ruby-connection-pool") @@ -1854,8 +1834,9 @@ net/http library.") (arguments '(#:tests? #f)) ; no tests (home-page "https://github.com/rails/arel") (synopsis "SQL AST manager for Ruby") - (description "Arel is a SQL AST manager for Ruby. It simplifies the -generation of complex SQL queries and is compatible with various RDBMSes.") + (description "Arel is an SQL @dfn{Abstract Syntax Tree} (AST) manager for +Ruby. It simplifies the generation of complex SQL queries and adapts to +various relational database implementations.") (license license:expat))) (define-public ruby-minitar From fe08b1a75953aa7153442dcffdcfd3a6d8c752a1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 18:42:53 +0100 Subject: [PATCH 314/436] gnu: r-codetools: Remove duplicate definition. * gnu/packages/statistics.scm (r-codetools): Remove shadowed 0.2-14 version. [home-page]: Use HTTPS. --- gnu/packages/statistics.scm | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 133ce41c43..b5aeaa4578 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1068,22 +1068,6 @@ from knitr Rmarkdown.") the execution time of R expressions.") (license license:bsd-2))) -(define-public r-codetools - (package - (name "r-codetools") - (version "0.2-14") - (source (origin - (method url-fetch) - (uri (cran-uri "codetools" version)) - (sha256 - (base32 - "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397")))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/codetools/index.html") - (synopsis "Code analysis tools for R") - (description "This package provides code analysis tools for R.") - (license license:gpl3+))) - (define-public r-pryr (package (name "r-pryr") @@ -2568,7 +2552,7 @@ data.") (base32 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/codetools") + (home-page "https://cran.r-project.org/web/packages/codetools") (synopsis "Code analysis tools for R") (description "This package provides code analysis tools for R to check R code for possible problems.") From 9c53993fb279456f032a843f23fa546e90305910 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 18:47:02 +0100 Subject: [PATCH 315/436] gnu: r-gtable: Remove duplicate definition. * gnu/packages/statistics.scm (r-gtable): Remove shadowed 0.1.2 version. [home-page]: Use HTTPS. [synopsis, description]: Use those of the removed version. --- gnu/packages/statistics.scm | 26 ++++---------------------- 1 file changed, 4 insertions(+), 22 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b5aeaa4578..139ac71834 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -346,24 +346,6 @@ functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly.") (license license:gpl2+))) -(define-public r-gtable - (package - (name "r-gtable") - (version "0.1.2") - (source - (origin - (method url-fetch) - (uri (cran-uri "gtable" version)) - (sha256 - (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh")))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/gtable") - (synopsis "R library to arrange grobs in tables") - (description - "Gtable is a collection of tools to make it easier to work with -\"tables\" of grobs.") - (license license:gpl2+))) - (define-public r-pheatmap (package (name "r-pheatmap") @@ -2230,11 +2212,11 @@ variety of formats.") "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0")))) (properties `((upstream-name . "gtable"))) (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/gtable") - (synopsis "Arrange grobs in tables") + (home-page "https://cran.r-project.org/web/packages/gtable") + (synopsis "R library to arrange grobs in tables") (description - "This package provides tools to make it easier to work with tables of -grobs.") + "Gtable is a collection of tools to make it easier to work with +\"tables\" of grobs.") (license license:gpl2+))) (define-public r-gridextra From 7967efc18cbd3e862026cd2d30366b6428d0bcae Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 21:22:07 +0100 Subject: [PATCH 316/436] gnu: arc-theme: Update to 20170302. * gnu/packages/gnome.scm (arc-theme): Update to 20170302. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index b673b3d402..650ab4f36e 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5606,7 +5606,7 @@ functionality and behavior.") (define-public arc-theme (package (name "arc-theme") - (version "20161119") + (version "20170302") (source (origin (method url-fetch) (uri (string-append "https://github.com/horst3180/arc-theme" @@ -5614,7 +5614,7 @@ functionality and behavior.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1kbhaxmydyip3vdw4kf8rk776jcd9wf0w7z6h2i4naxdn4rsnw54")))) + "0igxpngnkf1wpsg872a9jg3c9f5z8afm312yfbillz16mk8w39cw")))) (build-system gnu-build-system) (arguments '(#:phases From c41802401c410d4d06d15a1b7cfe43e2db3755f3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 21:23:36 +0100 Subject: [PATCH 317/436] gnu: arc-icon-theme: Update to 20161122. * gnu/packages/gnome.scm (arc-icon-theme): Update to 20161122. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 650ab4f36e..6a0a9037a8 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5674,7 +5674,7 @@ simple and consistent.") (define-public arc-icon-theme (package (name "arc-icon-theme") - (version "20160605") + (version "20161122") (source (origin (method url-fetch) (uri (string-append "https://github.com/horst3180/arc-icon-theme" @@ -5682,7 +5682,7 @@ simple and consistent.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1npf0ki0j0llrw9wbffhxxa1cdms0q7b8xlg9m943dd9g7pgdm2p")))) + "1ya1cqvv8q847c0rpcg6apzky87q3h04y8jz5nmi52qk6kg8si0b")))) (build-system gnu-build-system) (arguments '(#:phases From 0f9bb61bfa1bf7276eb96dd29c4dc94ea23e8fad Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 2 Mar 2017 21:22:52 +0100 Subject: [PATCH 318/436] gnu: moka-icon-theme: Update to 5.3.5. * gnu/packages/gnome.scm (moka-icon-theme): Update to 5.3.5. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 6a0a9037a8..cfd8b24290 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5639,7 +5639,7 @@ like GNOME, Unity, Budgie, Pantheon, XFCE, Mate, etc.") (define-public moka-icon-theme (package (name "moka-icon-theme") - (version "5.3.1") + (version "5.3.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/moka-project" @@ -5648,7 +5648,7 @@ like GNOME, Unity, Budgie, Pantheon, XFCE, Mate, etc.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1lnk7p8dsd9xh6cgz5krvlcr457w8yl4m6p6s5c2g5narsjswzrm")))) + "062rab0ggmgb3y0d6b3k5d47wsadi28cdnyyr2vqbjhza01dglci")))) (build-system gnu-build-system) (arguments '(#:phases From 1e5c056ca1faf8e7457713a480eeee7c201de554 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 3 Mar 2017 02:04:06 +0100 Subject: [PATCH 319/436] gnu: catimg: Update to 2.2.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/image-viewers.scm (catimg): Update to 2.2.2. [arguments]: Add ‘-DMAN_OUTPUT_PATH’ to the cmake arguments. --- gnu/packages/image-viewers.scm | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index c3f6de8057..05b9472395 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -212,7 +212,7 @@ your images. Among its features are: (define-public catimg (package (name "catimg") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) @@ -221,10 +221,10 @@ your images. Among its features are: (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "14g90zwh2d3s13hgyxypx2vc0rj1g58l6zcxhgc84wsyxfxd6xpb")))) + "1abkhrhw4r221lwn2vb8in3vmp6gxn3qlv34cqndr55v5gdpb9qz")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; No check target + `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases (replace 'configure @@ -234,20 +234,22 @@ your images. Among its features are: (substitute* "catimg" ;; By replacing "convert", we also replace the "convert" ;; in the message 'The version of convert is too old, don't - ;; expect good results :('. This should not happen, but in + ;; expect good results :('. This should not happen, but in ;; practice this error message should not affect us. (("convert") convert)) #t))) (replace 'build (lambda _ - (zero? (system* "cmake" "-D" - (string-append "CMAKE_INSTALL_PREFIX=" - (assoc-ref %outputs "out")) - ".")) - (zero? (system* "make")))) + (let* ((out (assoc-ref %outputs "out")) + (man (string-append out "/share/man/man1"))) + (zero? (system* "cmake" + (string-append "-DCMAKE_INSTALL_PREFIX=" out) + (string-append "-DMAN_OUTPUT_PATH=" man) + ".")) + (zero? (system* "make"))))) (add-before 'install 'install-script (lambda* (#:key outputs #:allow-other-keys) - ;; The bashscript lacks an file extension, we have to rename + ;; The bash script lacks an file extension. We have to rename ;; it so that the C program and the bash script can be happy ;; side by side. (let* ((out (assoc-ref outputs "out")) @@ -257,7 +259,7 @@ your images. Among its features are: (string-append bin "/catimg.sh")) #t)))))) (inputs - `(("imagemagick" ,imagemagick))) ; For the bash script version + `(("imagemagick" ,imagemagick))) ; for the bash script version (home-page "https://github.com/posva/catimg") (synopsis "Render images in the terminal") (description From 95b80db637f2c7cb1c71d695324b81636f1a0e35 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 3 Mar 2017 02:06:57 +0100 Subject: [PATCH 320/436] gnu: cmark: Update to 0.27.1. * gnu/packages/markdown.scm (cmark): Update to 0.27.1. --- gnu/packages/markdown.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/markdown.scm b/gnu/packages/markdown.scm index ae54b0b172..4a020198e4 100644 --- a/gnu/packages/markdown.scm +++ b/gnu/packages/markdown.scm @@ -104,7 +104,7 @@ convert it to structurally valid XHTML (or HTML).") (define-public cmark (package (name "cmark") - (version "0.26.1") + (version "0.27.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/jgm/cmark/archive/" @@ -112,7 +112,7 @@ convert it to structurally valid XHTML (or HTML).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1mpmcy4bbmc8m058zqs9dwx49lcfi7bdnfszsr9y66cwgylia1mm")))) + "1da62ispca9aal2a36gaj87175rv5013pl7x740vk32y6lclr6v6")))) (build-system cmake-build-system) (arguments '(#:test-target "test")) From 488a373451595c82e9be21da8456ba2cfe2ef4b1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 3 Mar 2017 05:29:12 +0100 Subject: [PATCH 321/436] gnu: libseccomp: Update to 2.3.2. * gnu/packages/linux.scm (libseccomp): Update to 2.3.2. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 6ff6d0b64e..d239d4e4c4 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3229,7 +3229,7 @@ of flash storage.") (define-public libseccomp (package (name "libseccomp") - (version "2.3.1") + (version "2.3.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/seccomp/libseccomp/" @@ -3237,7 +3237,7 @@ of flash storage.") "/libseccomp-" version ".tar.gz")) (sha256 (base32 - "0asnlkzqms520r0dra08dzcz5hh6hs7lkajfw9wij3vrd0hxsnzz")))) + "18dwfxzsw3agiy2dxbflrkhmjgvlji0wwkk636nabh2ng41qrp1x")))) (build-system gnu-build-system) (native-inputs `(("which" ,which))) From 84e36a562bd16dcc2dc1e18abf2a96a3b0d968af Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 3 Mar 2017 17:55:16 +1000 Subject: [PATCH 322/436] gnu: googletest: Update to 1.8.0. * gnu/packages/check.scm (googletest): Update to 1.8.0. [build-system]: Use cmake-build-system. [arguments]: Remove field. [native-inputs]: Remove autoconf, automake, libtool. --- gnu/packages/check.scm | 44 ++++-------------------------------------- 1 file changed, 4 insertions(+), 40 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 9ad03cd558..372f1c4fea 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -201,7 +201,7 @@ normally do not detect. The goal is to detect only real errors in the code (define-public googletest (package (name "googletest") - (version "1.7.0") + (version "1.8.0") (source (origin (method url-fetch) @@ -210,46 +210,10 @@ normally do not detect. The goal is to detect only real errors in the code (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1k0nf1l9cb3prdmsvaajl5i31bx86c1mw0d5jgzykz7rzm36afpp")))) - (build-system gnu-build-system) + "1n5p1m2m3fjrjdj752lf92f9wq3pl5cbsfrb49jqbg52ghkz99jq")))) + (build-system cmake-build-system) (native-inputs - `(("python-2" ,python-2) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'configure 'autoconf - (lambda _ - (zero? (system* "autoreconf" "-vfi")))) - (add-before 'autoconf 'generate-headers - (lambda _ - (begin - (delete-file "include/gtest/gtest-param-test.h") - (system* "python2" "scripts/pump.py" - "include/gtest/gtest-param-test.h.pump") - (delete-file "include/gtest/internal/gtest-tuple.h") - (system* "python2" "scripts/pump.py" - "include/gtest//internal/gtest-tuple.h.pump") - (delete-file - "include/gtest/internal/gtest-param-util-generated.h") - (system* - "python2" "scripts/pump.py" - "include/gtest/internal/gtest-param-util-generated.h.pump") - (delete-file "include/gtest/internal/gtest-type-util.h") - (system* "python2" "scripts/pump.py" - "include/gtest/internal/gtest-type-util.h.pump")))) - (replace 'install - (lambda _ - (let ((out (assoc-ref %outputs "out"))) - (begin - (install-file "lib/.libs/libgtest_main.a" - (string-append out "/lib")) - (install-file "lib/.libs/libgtest.a" - (string-append out "/lib")) - (copy-recursively "include" - (string-append out "/include"))))))))) + `(("python-2" ,python-2))) (home-page "https://github.com/google/googletest/") (synopsis "Test discovery and XUnit test framework") (description "Google Test features an XUnit test framework, automated test From da5db9880e4ca48bb229d71fe3217695f92c106f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 3 Mar 2017 03:46:44 -0500 Subject: [PATCH 323/436] gnu: python-requests: Update to 2.13.0. * gnu/packages/python.scm (python-requests, python2-requests): Update to 2.13.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0bfc8598ff..05ce8d72a9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2476,13 +2476,13 @@ installed with a newer @code{pip} or with wheel's own command line utility.") (define-public python-requests (package (name "python-requests") - (version "2.9.1") + (version "2.13.0") (source (origin (method url-fetch) (uri (pypi-uri "requests" version)) (sha256 (base32 - "0zsqrzlybf25xscgi7ja4s48y2abf9wvjkn47wh984qgs1fq2xy5")))) + "1s0wg4any4dsv5l3hqjxqk2zgb7pdbqhy9rhc8kh3aigfq4ws8jp")))) (build-system python-build-system) (native-inputs `(("python-py" ,python-py) From 89d42ac17cdcffd21c5f192a90ef799d4dcb969f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 3 Mar 2017 03:01:42 -0500 Subject: [PATCH 324/436] gnu: certbot, python-acme: Update to 0.12.0. * gnu/packages/tls.scm (python-acme, python2-acme): Update to 0.12.0. (certbot): Update to 0.12.0. --- gnu/packages/tls.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index c24c8e7387..318bb21614 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -4,7 +4,6 @@ ;;; Copyright © 2014 Ian Denhardt ;;; Copyright © 2013, 2015 Andreas Enge ;;; Copyright © 2015 David Thompson -;;; Copyright © 2015, 2016 Leo Famulari ;;; Copyright © 2015, 2016, 2017 Leo Famulari ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 ng0 @@ -507,13 +506,13 @@ security, and applying best practice development processes.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.11.1") + (version "0.12.0") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "0kk95iqxygrg0cd66kq8kbyalg2x5pz9hn1175cgwgf1vy72adfv")))) + "1pzv8fcfwdqzvvpyhgjz412is0b98yj9495k8sidzzqgbdmvlp50")))) (build-system python-build-system) (arguments `(#:phases @@ -564,7 +563,7 @@ security, and applying best practice development processes.") (uri (pypi-uri name version)) (sha256 (base32 - "1wis5kgqcsrs60kkcmbrbx8z9yasmwa6lg9ir5im232hdm4285vc")))) + "1dw86gb8lyap5ckjawmli1hxgbchw2g62g1lqfvxyqjv0df94waa")))) (build-system python-build-system) (arguments `(#:python ,python-2 From 92ae98e2a0c2ffc807111dbf7616df47a9d3b31c Mon Sep 17 00:00:00 2001 From: Alex Vong Date: Thu, 2 Mar 2017 19:59:05 +0800 Subject: [PATCH 325/436] gnu: mupdf: Fix CVE-2017-{5896,5991}. * gnu/packages/patches/mupdf-CVE-2017-5896.patch, gnu/packages/patches/mupdf-CVE-2017-5991.patch: New files. * gnu/packages/pdf.scm (mupdf/fixed)[source]: Add patches. * gnu/local.mk (dist_patch_DATA): Add them. Signed-off-by: Leo Famulari --- gnu/local.mk | 2 + .../patches/mupdf-CVE-2017-5896.patch | 63 +++++++++++ .../patches/mupdf-CVE-2017-5991.patch | 101 ++++++++++++++++++ gnu/packages/pdf.scm | 5 +- 4 files changed, 170 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/mupdf-CVE-2017-5896.patch create mode 100644 gnu/packages/patches/mupdf-CVE-2017-5991.patch diff --git a/gnu/local.mk b/gnu/local.mk index 406e0dc963..584ab75a57 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -764,6 +764,8 @@ dist_patch_DATA = \ %D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch \ %D%/packages/patches/mupdf-mujs-CVE-2016-10132.patch \ %D%/packages/patches/mupdf-mujs-CVE-2016-10133.patch \ + %D%/packages/patches/mupdf-CVE-2017-5896.patch \ + %D%/packages/patches/mupdf-CVE-2017-5991.patch \ %D%/packages/patches/mupen64plus-ui-console-notice.patch \ %D%/packages/patches/musl-CVE-2016-8859.patch \ %D%/packages/patches/mutt-store-references.patch \ diff --git a/gnu/packages/patches/mupdf-CVE-2017-5896.patch b/gnu/packages/patches/mupdf-CVE-2017-5896.patch new file mode 100644 index 0000000000..1537ecc896 --- /dev/null +++ b/gnu/packages/patches/mupdf-CVE-2017-5896.patch @@ -0,0 +1,63 @@ +Fix CVE-2017-5896: + +https://bugs.ghostscript.com/show_bug.cgi?id=697515 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5896 +http://www.openwall.com/lists/oss-security/2017/02/10/1 +https://security-tracker.debian.org/tracker/CVE-2017-5896 +https://blogs.gentoo.org/ago/2017/02/09/mupdf-use-after-free-in-fz_subsample_pixmap-pixmap-c/ + +Patch lifted from upstream source repository: + +http://git.ghostscript.com/?p=mupdf.git;h=2c4e5867ee699b1081527bc6c6ea0e99a35a5c27 + +From 2c4e5867ee699b1081527bc6c6ea0e99a35a5c27 Mon Sep 17 00:00:00 2001 +From: Robin Watts +Date: Thu, 9 Feb 2017 07:12:16 -0800 +Subject: [PATCH] bug 697515: Fix out of bounds read in fz_subsample_pixmap + +Pointer arithmetic for final special case was going wrong. +--- + source/fitz/pixmap.c | 6 ++++-- + 1 file changed, 4 insertions(+), 2 deletions(-) + +diff --git a/source/fitz/pixmap.c b/source/fitz/pixmap.c +index a8317127..f1291dc2 100644 +--- a/source/fitz/pixmap.c ++++ b/source/fitz/pixmap.c +@@ -1104,6 +1104,7 @@ fz_subsample_pixmap_ARM(unsigned char *ptr, int w, int h, int f, int factor, + "@STACK:r1,<9>,factor,n,fwd,back,back2,fwd2,divX,back4,fwd4,fwd3,divY,back5,divXY\n" + "ldr r4, [r13,#4*22] @ r4 = divXY \n" + "ldr r5, [r13,#4*11] @ for (nn = n; nn > 0; n--) { \n" ++ "ldr r8, [r13,#4*17] @ r8 = back4 \n" + "18: @ \n" + "mov r14,#0 @ r14= v = 0 \n" + "sub r5, r5, r1, LSL #8 @ for (xx = x; xx > 0; x--) { \n" +@@ -1120,7 +1121,7 @@ fz_subsample_pixmap_ARM(unsigned char *ptr, int w, int h, int f, int factor, + "mul r14,r4, r14 @ r14= v *= divX \n" + "mov r14,r14,LSR #16 @ r14= v >>= 16 \n" + "strb r14,[r9], #1 @ *d++ = r14 \n" +- "sub r0, r0, r8 @ s -= back2 \n" ++ "sub r0, r0, r8 @ s -= back4 \n" + "subs r5, r5, #1 @ n-- \n" + "bgt 18b @ } \n" + "21: @ \n" +@@ -1249,6 +1250,7 @@ fz_subsample_pixmap(fz_context *ctx, fz_pixmap *tile, int factor) + x += f; + if (x > 0) + { ++ int back4 = x * n - 1; + div = x * y; + for (nn = n; nn > 0; nn--) + { +@@ -1263,7 +1265,7 @@ fz_subsample_pixmap(fz_context *ctx, fz_pixmap *tile, int factor) + s -= back5; + } + *d++ = v / div; +- s -= back2; ++ s -= back4; + } + } + } +-- +2.12.0 + diff --git a/gnu/packages/patches/mupdf-CVE-2017-5991.patch b/gnu/packages/patches/mupdf-CVE-2017-5991.patch new file mode 100644 index 0000000000..1fa6dc3466 --- /dev/null +++ b/gnu/packages/patches/mupdf-CVE-2017-5991.patch @@ -0,0 +1,101 @@ +Fix CVE-2017-5991: + +https://bugs.ghostscript.com/show_bug.cgi?id=697500 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5991 +https://security-tracker.debian.org/tracker/CVE-2017-5991 + +Patch lifted from upstream source repository: + +http://git.ghostscript.com/?p=mupdf.git;h=1912de5f08e90af1d9d0a9791f58ba3afdb9d465 + +From 1912de5f08e90af1d9d0a9791f58ba3afdb9d465 Mon Sep 17 00:00:00 2001 +From: Robin Watts +Date: Thu, 9 Feb 2017 15:49:15 +0000 +Subject: [PATCH] Bug 697500: Fix NULL ptr access. + +Cope better with errors during rendering - avoid letting the +gstate stack get out of sync. + +This avoids us ever getting into the situation of popping +a clip when we should be popping a mask or a group. This was +causing an unexpected case in the painting. +--- + source/pdf/pdf-op-run.c | 26 ++++++++++++++++++-------- + 1 file changed, 18 insertions(+), 8 deletions(-) + +diff --git a/source/pdf/pdf-op-run.c b/source/pdf/pdf-op-run.c +index a3ea895d..f1eac8d3 100644 +--- a/source/pdf/pdf-op-run.c ++++ b/source/pdf/pdf-op-run.c +@@ -1213,6 +1213,7 @@ pdf_run_xobject(fz_context *ctx, pdf_run_processor *proc, pdf_xobject *xobj, pdf + pdf_run_processor *pr = (pdf_run_processor *)proc; + pdf_gstate *gstate = NULL; + int oldtop = 0; ++ int oldbot = -1; + fz_matrix local_transform = *transform; + softmask_save softmask = { NULL }; + int gparent_save; +@@ -1232,16 +1233,17 @@ pdf_run_xobject(fz_context *ctx, pdf_run_processor *proc, pdf_xobject *xobj, pdf + fz_var(cleanup_state); + fz_var(gstate); + fz_var(oldtop); ++ fz_var(oldbot); + + gparent_save = pr->gparent; + pr->gparent = pr->gtop; ++ oldtop = pr->gtop; + + fz_try(ctx) + { + pdf_gsave(ctx, pr); + + gstate = pr->gstate + pr->gtop; +- oldtop = pr->gtop; + + pdf_xobject_bbox(ctx, xobj, &xobj_bbox); + pdf_xobject_matrix(ctx, xobj, &xobj_matrix); +@@ -1302,12 +1304,25 @@ pdf_run_xobject(fz_context *ctx, pdf_run_processor *proc, pdf_xobject *xobj, pdf + + doc = pdf_get_bound_document(ctx, xobj->obj); + ++ oldbot = pr->gbot; ++ pr->gbot = pr->gtop; ++ + pdf_process_contents(ctx, (pdf_processor*)pr, doc, resources, xobj->obj, NULL); + } + fz_always(ctx) + { ++ /* Undo any gstate mismatches due to the pdf_process_contents call */ ++ if (oldbot != -1) ++ { ++ while (pr->gtop > pr->gbot) ++ { ++ pdf_grestore(ctx, pr); ++ } ++ pr->gbot = oldbot; ++ } ++ + if (cleanup_state >= 3) +- pdf_grestore(ctx, pr); /* Remove the clippath */ ++ pdf_grestore(ctx, pr); /* Remove the state we pushed for the clippath */ + + /* wrap up transparency stacks */ + if (transparency) +@@ -1341,13 +1356,8 @@ pdf_run_xobject(fz_context *ctx, pdf_run_processor *proc, pdf_xobject *xobj, pdf + pr->gstate[pr->gparent].ctm = gparent_save_ctm; + pr->gparent = gparent_save; + +- if (gstate) +- { +- while (oldtop < pr->gtop) +- pdf_grestore(ctx, pr); +- ++ while (oldtop < pr->gtop) + pdf_grestore(ctx, pr); +- } + + pdf_unmark_obj(ctx, xobj->obj); + } +-- +2.12.0 + diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index a229d689dd..13dbd0ecd1 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -11,6 +11,7 @@ ;;; Coypright © 2016 Julien Lepiller ;;; Copyright © 2016 Arun Isaac ;;; Copyright © 2017 Leo Famulari +;;; Copyright © 2017 Alex Vong ;;; ;;; This file is part of GNU Guix. ;;; @@ -550,7 +551,9 @@ and examining the file structure (pdfshow).") (append (origin-patches (package-source mupdf)) (search-patches "mupdf-mujs-CVE-2016-10132.patch" - "mupdf-mujs-CVE-2016-10133.patch"))))))) + "mupdf-mujs-CVE-2016-10133.patch" + "mupdf-CVE-2017-5896.patch" + "mupdf-CVE-2017-5991.patch"))))))) (define-public qpdf (package From 6b2afac9d5be65b2f7b677a9d70b76f91ba23a60 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 3 Mar 2017 11:29:41 +0100 Subject: [PATCH 326/436] gnu: stellarium: Fix package formatting. * gnu/packages/astronomy.scm (stellarium): Fix package formatting. --- gnu/packages/astronomy.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 73fbb09d10..43506a7bc2 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -127,10 +127,12 @@ programs for the manipulation and analysis of astronomical data.") (base32 "04avigz8i8mi2x6x71bqr9np85n1p9qnvbj2hxr947f1jv22zr8g")))) (build-system cmake-build-system) - (inputs `(("qt" ,qt) - ("zlib" ,zlib))) - (native-inputs `(("gettext" ,gettext-minimal) ; xgettext is used at compile time - ("perl" ,perl))) ; For pod2man + (inputs + `(("qt" ,qt) + ("zlib" ,zlib))) + (native-inputs + `(("gettext" ,gettext-minimal) ; xgettext is used at compile time + ("perl" ,perl))) ; For pod2man (arguments `(#:test-target "tests" #:phases (modify-phases %standard-phases From 7109e0fff8e9a235251e4610b9663d1985ca7924 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 3 Mar 2017 12:06:11 +0100 Subject: [PATCH 327/436] build-system/cargo: Export %cargo-build-system-modules. * guix/build-system/cargo.scm (%cargo-build-system-modules): Export. --- guix/build-system/cargo.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/guix/build-system/cargo.scm b/guix/build-system/cargo.scm index 3582f0e328..578c4446a4 100644 --- a/guix/build-system/cargo.scm +++ b/guix/build-system/cargo.scm @@ -29,7 +29,8 @@ #:use-module (guix build-system gnu) #:use-module (ice-9 match) #:use-module (srfi srfi-26) - #:export (cargo-build-system + #:export (%cargo-build-system-modules + cargo-build-system crate-url crate-url? crate-uri)) From 42a3293a645a497980780e0ffe24a20af58caf82 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 3 Mar 2017 14:25:52 +0100 Subject: [PATCH 328/436] gnu: tor: Update to 0.2.9.10. * gnu/packages/tor.scm (tor): Update to 0.2.9.10. --- gnu/packages/tor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 9339dcdd70..e48017e640 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -40,14 +40,14 @@ (define-public tor (package (name "tor") - (version "0.2.9.9") + (version "0.2.9.10") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "0hqdk5p6dw4bpn7c8gmhyi8jjkhc37112pfw5nx4gl0g4lmmscik")))) + "0h8kpn42mgpkzmnga143hi8nh0ai65ypxh7qhkwbb15j3wz2h4fn")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--enable-expensive-hardening" From aada6f371edf3f6f974111e7c3ddab06bd29efc7 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 7 Feb 2017 13:30:16 +0100 Subject: [PATCH 329/436] pari-gp: Update to 2.9.1. * gnu/packages/algebra.scm (pari-gp): Update to 2.9.1. --- gnu/packages/algebra.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 544b62a1da..57f97e604a 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -128,7 +128,7 @@ solve the shortest vector problem.") (define-public pari-gp (package (name "pari-gp") - (version "2.7.6") + (version "2.9.1") (source (origin (method url-fetch) (uri (string-append @@ -136,7 +136,7 @@ solve the shortest vector problem.") version ".tar.gz")) (sha256 (base32 - "04dqi697czd8mmw8aiwzrkgbvkjassqagg6lfy3lkf1k5qi9g9rr")))) + "0rq7wz9df1xs4acdzzb5dapx8vs6m5py39n2wynw2qv4d2b0ylfw")))) (build-system gnu-build-system) (native-inputs `(("texlive" ,texlive-minimal))) (inputs `(("gmp" ,gmp) From 0a77fdf4b8732598e341a6793503ea4847e0c760 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 7 Feb 2017 13:32:03 +0100 Subject: [PATCH 330/436] gp2c: Update to 0.10.0. * gnu/packages/algebra.scm (gp2c): Update to 0.10.0. --- gnu/packages/algebra.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 57f97e604a..be4c48f72d 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -168,7 +168,7 @@ PARI is also available as a C library to allow for faster computations.") (define-public gp2c (package (name "gp2c") - (version "0.0.9pl5") + (version "0.0.10") (source (origin (method url-fetch) (uri (string-append @@ -176,7 +176,7 @@ PARI is also available as a C library to allow for faster computations.") version ".tar.gz")) (sha256 (base32 - "1q003mkagc5ib6lqb2xfay7j4ffkwv7xlnznp6wdrq2sbqq4vyak")))) + "1xhpz5p81iw261ay1kip283ggr0ir8ydz8qx3v24z8jfms1r3y70")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (inputs `(("pari-gp" ,pari-gp))) From 608afe067ee4e43ca209f3d4b47b0789ed1f6707 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 3 Mar 2017 17:10:30 +0100 Subject: [PATCH 331/436] gnu: maim: Update to 4.4.61. * gnu/packages/xdisorg.scm (maim): Update to 4.4.61. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 3667797abd..3e0b441128 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -471,7 +471,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "4.4.60") + (version "4.4.61") (source (origin (method url-fetch) (uri (string-append @@ -480,7 +480,7 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1j8czhbgilmv9c9hlind1w847yk856dzvxx1sj17fx89xkg8nixk")))) + "14jksv05xyydbpb9v8k3jgq7sl72bh356iapymg02vwg519i1d5k")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target From aa6738ddb63279da58ff790ed73a19951943bb68 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 3 Mar 2017 17:07:00 +0100 Subject: [PATCH 332/436] gnu: jasper: Update to 2.0.12. * gnu/packages/image.scm (jasper): Update to 2.0.12. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 54b7dd6e22..53ed69a84e 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -901,14 +901,14 @@ convert, manipulate, filter and display a wide variety of image formats.") (define-public jasper (package (name "jasper") - (version "2.0.10") + (version "2.0.12") (source (origin (method url-fetch) (uri (string-append "https://www.ece.uvic.ca/~frodo/jasper" "/software/jasper-" version ".tar.gz")) (sha256 (base32 - "1s022mfxyw8jw60fgyj60lbm9h6bc4nk2751b0in8qsjwcl59n2l")))) + "1njdbxv7d4anzrd476wjww2qsi96dd8vfnp4hri0srrqxpszl92v")))) (build-system cmake-build-system) (inputs `(("libjpeg" ,libjpeg))) (synopsis "JPEG-2000 library") From 728f36202d2a2d4bbcc525f6a79c5e3cbf9cbd0f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 6 Jan 2017 13:08:47 -0500 Subject: [PATCH 333/436] gnu: nspr: Update to 4.13.1. * gnu/packages/gnuzilla.scm (nspr): Update to 4.13.1. --- gnu/packages/gnuzilla.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 9279c46b5d..45a6f9338b 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -152,7 +152,7 @@ in C/C++.") (define-public nspr (package (name "nspr") - (version "4.12") + (version "4.13.1") (source (origin (method url-fetch) (uri (string-append @@ -160,7 +160,7 @@ in C/C++.") version "/src/nspr-" version ".tar.gz")) (sha256 (base32 - "1pk98bmc5xzbl62q5wf2d6mryf0v95z6rsmxz27nclwiaqg0mcg0")))) + "1arkg08l6zlp8v44shqbk2c8qzwd913lgh60fb3yfxls6d8ifk2y")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) From 3b175eab84f9899804b466506a57b5807285150a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 3 Mar 2017 17:21:58 +0100 Subject: [PATCH 334/436] gnu: nss, nss-certs: Update to 3.29.2. * gnu/packages/certs.scm (nss-certs): Update to 3.29.2. * gnu/packages/gnuzilla.scm (nss): Update to 3.29.2. * gnu/packages/patches/nss-pkgconfig.patch: Adapt to context changes. --- gnu/packages/certs.scm | 4 ++-- gnu/packages/gnuzilla.scm | 4 ++-- gnu/packages/patches/nss-pkgconfig.patch | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/certs.scm b/gnu/packages/certs.scm index b27577bbec..246e5ca14a 100644 --- a/gnu/packages/certs.scm +++ b/gnu/packages/certs.scm @@ -73,7 +73,7 @@ (define-public nss-certs (package (name "nss-certs") - (version "3.27.1") + (version "3.29.2") (source (origin (method url-fetch) (uri (let ((version-with-underscores @@ -84,7 +84,7 @@ "nss-" version ".tar.gz"))) (sha256 (base32 - "0sraxk26swlgl7rl742rkfp5k251v5z3lqw9k8ikin0cjfhkfdpx")))) + "149807rmzb76hnh48rw4m9jw83iw0168njzchz0hmbsgc8mk0i5w")))) (build-system gnu-build-system) (outputs '("out")) (native-inputs diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 45a6f9338b..c4543aa7d9 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -186,7 +186,7 @@ in the Mozilla clients.") (define-public nss (package (name "nss") - (version "3.27.1") + (version "3.29.2") (source (origin (method url-fetch) (uri (let ((version-with-underscores @@ -197,7 +197,7 @@ in the Mozilla clients.") "nss-" version ".tar.gz"))) (sha256 (base32 - "0sraxk26swlgl7rl742rkfp5k251v5z3lqw9k8ikin0cjfhkfdpx")) + "149807rmzb76hnh48rw4m9jw83iw0168njzchz0hmbsgc8mk0i5w")) ;; Create nss.pc and nss-config. (patches (search-patches "nss-pkgconfig.patch")))) (build-system gnu-build-system) diff --git a/gnu/packages/patches/nss-pkgconfig.patch b/gnu/packages/patches/nss-pkgconfig.patch index e611f69bea..a33e05fcf2 100644 --- a/gnu/packages/patches/nss-pkgconfig.patch +++ b/gnu/packages/patches/nss-pkgconfig.patch @@ -221,5 +221,5 @@ Later adapted to apply cleanly to nss-3.21. RELEASE = nss --DIRS = coreconf lib cmd external_tests -+DIRS = coreconf lib cmd external_tests config +-DIRS = coreconf lib cmd gtests ++DIRS = coreconf lib cmd gtests config From 169a438c0f8eca3d1582066f9285b542ea2c07bc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 3 Mar 2017 17:57:11 +0100 Subject: [PATCH 335/436] gnu: acpid: Update to 2.0.28. * gnu/packages/linux.scm (acpid): Update to 2.0.28. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d239d4e4c4..6e08473ec3 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2338,14 +2338,14 @@ about ACPI devices.") (define-public acpid (package (name "acpid") - (version "2.0.23") + (version "2.0.28") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/acpid2/acpid-" version ".tar.xz")) (sha256 (base32 - "1vl7c6vc724v4jwki17czgj6lnrknnj1a6llm8gkl32i2gnam5j3")))) + "043igasvp1l6nv5rzh4sksmymay2qn20anl4zm4zvwnkn1a3l34q")))) (build-system gnu-build-system) (home-page "https://sourceforge.net/projects/acpid2/") (synopsis "Daemon for delivering ACPI events to user-space programs") From 21abf092a49f0ce80cbfff5cccabb7dbf53abf96 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Fri, 3 Mar 2017 17:02:12 +0100 Subject: [PATCH 336/436] gnu: arb: Update to 2.10.0. * gnu/packages/algebra.scm (arb): Update to 2.10.0. * gnu/packages/patches/arb-ldconfig.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 3 +-- gnu/packages/algebra.scm | 7 +++---- gnu/packages/patches/arb-ldconfig.patch | 22 ---------------------- 3 files changed, 4 insertions(+), 28 deletions(-) delete mode 100644 gnu/packages/patches/arb-ldconfig.patch diff --git a/gnu/local.mk b/gnu/local.mk index 15003bcab0..ce8ea3d37b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1,6 +1,6 @@ # GNU Guix --- Functional package management for GNU # Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès -# Copyright © 2013, 2014, 2015, 2016 Andreas Enge +# Copyright © 2013, 2014, 2015, 2016, 2017 Andreas Enge # Copyright © 2016 Mathieu Lirzin # Copyright © 2013, 2014, 2015, 2016 Mark H Weaver # Copyright © 2016 Chris Marusich @@ -482,7 +482,6 @@ dist_patch_DATA = \ %D%/packages/patches/alsa-lib-mips-atomic-fix.patch \ %D%/packages/patches/antiword-CVE-2014-8123.patch \ %D%/packages/patches/apr-skip-getservbyname-test.patch \ - %D%/packages/patches/arb-ldconfig.patch \ %D%/packages/patches/artanis-fix-Makefile.in.patch \ %D%/packages/patches/ath9k-htc-firmware-binutils.patch \ %D%/packages/patches/ath9k-htc-firmware-gcc.patch \ diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index be4c48f72d..e244644c40 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016 Andreas Enge +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Andreas Enge ;;; Copyright © 2013, 2015, 2017 Ludovic Courtès ;;; Copyright © 2016 Nicolas Goaziou ;;; Copyright © 2014 Mark H Weaver @@ -311,7 +311,7 @@ fast arithmetic.") (define-public arb (package (name "arb") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (string-append @@ -320,8 +320,7 @@ fast arithmetic.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "04hhcpshfkcq9fr4hixbhpps50yf9drk62xgkvlcaj5kb4nyrx7l")) - (patches (search-patches "arb-ldconfig.patch")))) + "0jwcv9ssvi8axb1y7m2h4ykgyl015cl6g28gfl92l4dgnag585ak")))) (build-system gnu-build-system) (propagated-inputs `(("flint" ,flint))) ; flint.h is included by arf.h diff --git a/gnu/packages/patches/arb-ldconfig.patch b/gnu/packages/patches/arb-ldconfig.patch deleted file mode 100644 index 478ec5a6f0..0000000000 --- a/gnu/packages/patches/arb-ldconfig.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -u -r arb-2.8.1.orig/configure arb-2.8.1/configure ---- arb-2.8.1.orig/configure 2015-12-31 17:30:01.000000000 +0100 -+++ arb-2.8.1/configure 2016-01-20 16:41:41.336726596 +0100 -@@ -647,6 +647,7 @@ - echo "ARB_SHARED=$SHARED" >> Makefile - echo "ARB_LIB=$ARB_LIB" >> Makefile - echo "ARB_LIBNAME=$ARB_LIBNAME" >> Makefile -+echo "ARB_MAJOR=$ARB_MAJOR" >> Makefile - echo "ARB_SOLIB=$ARB_SOLIB" >> Makefile - echo "EXEEXT=$EXEEXT" >> Makefile - echo "PREFIX=$PREFIX" >> Makefile -diff -u -r arb-2.8.1.orig/Makefile.in arb-2.8.1/Makefile.in ---- arb-2.8.1.orig/Makefile.in 2015-12-31 17:30:01.000000000 +0100 -+++ arb-2.8.1/Makefile.in 2016-01-20 16:30:32.575298517 +0100 -@@ -101,6 +101,7 @@ - $(LDCONFIG) -n "$(CURDIR)"; \ - fi - ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME)"; \ -+ ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME).$(ARB_MAJOR)"; \ - - libarb.a: $(OBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) | build build/interfaces - $(AT)$(foreach ext, $(EXTENSIONS), $(foreach dir, $(patsubst $(ext)/%.h, %, $(wildcard $(ext)/*.h)), mkdir -p build/$(dir); BUILD_DIR=$(CURDIR)/build/$(dir); export BUILD_DIR; MOD_DIR=$(dir); export MOD_DIR; $(MAKE) -f $(CURDIR)/Makefile.subdirs -C $(ext)/$(dir) static || exit $$?;)) From b2e3d59c50d1d367799886318f0e38f4fb9fc0aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Sat, 4 Mar 2017 17:05:49 +0800 Subject: [PATCH 337/436] gnu: glulxe: Update to 0.5.4. * gnu/packages/games.scm (glulxe): Update to 0.5.4. [license]: Change to 'expat'. --- gnu/packages/games.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index d26669e68f..7333cfca00 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -883,15 +883,15 @@ using the curses.h library for screen control.") (define-public glulxe (package (name "glulxe") - (version "0.5.2") + (version "0.5.4") (source (origin (method url-fetch) (uri (string-append "http://www.ifarchive.org/if-archive/programming/" - "glulx/interpreters/glulxe/glulxe-052.tar.gz")) + "glulx/interpreters/glulxe/glulxe-054.tar.gz")) (sha256 (base32 - "19iw6kl8ncqcy9pv4gsqfh3xsa1n94zd234rqavvmxccnf3nj19g")))) + "0vipydg6ra90yf9b3ipgppwxyb2xdhcxwvirgjy0v20wlf56zhhz")))) (build-system gnu-build-system) (inputs `(("glk" ,glkterm))) (arguments @@ -916,7 +916,7 @@ using the curses.h library for screen control.") playing interactive fiction. It was designed by Andrew Plotkin to relieve some of the restrictions in the venerable Z-machine format. This is the reference interpreter, using Glk API.") - (license (license:fsf-free "file://README")))) + (license license:expat))) (define-public fizmo (package From 5bbf31ccba8c86730fac1dbe081032b1995ce31b Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 3 Mar 2017 12:35:17 +0100 Subject: [PATCH 338/436] gnu: stellarium: Use modular Qt. * gnu/packages/astronomy.scm (stellarium)[inputs]: Remove qt. Add qtbase, qtmultimedia, qtscript, qtserialport. [native-inputs]: Add qtbase, qttools. --- gnu/packages/astronomy.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 43506a7bc2..2695530fee 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -128,11 +128,16 @@ programs for the manipulation and analysis of astronomical data.") "04avigz8i8mi2x6x71bqr9np85n1p9qnvbj2hxr947f1jv22zr8g")))) (build-system cmake-build-system) (inputs - `(("qt" ,qt) + `(("qtbase" ,qtbase) + ("qtmultimedia" ,qtmultimedia) + ("qtscript" ,qtscript) + ("qtserialport" ,qtserialport) ("zlib" ,zlib))) (native-inputs `(("gettext" ,gettext-minimal) ; xgettext is used at compile time - ("perl" ,perl))) ; For pod2man + ("perl" ,perl) ; For pod2man + ("qtbase" ,qtbase) ; Qt MOC is needed at compile time + ("qttools" ,qttools))) (arguments `(#:test-target "tests" #:phases (modify-phases %standard-phases From 885227386855e446e653d958c38b6bbcfc2a24ca Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 19:09:34 +0000 Subject: [PATCH 339/436] gnu: Add mbedtls-apache. * gnu/packages/tls.scm (mbedtls-apache): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/tls.scm | 31 ++++++++++++++++++++++++++++++- 1 file changed, 30 insertions(+), 1 deletion(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 318bb21614..8f428b3d6b 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2015 David Thompson ;;; Copyright © 2015, 2016, 2017 Leo Famulari ;;; Copyright © 2016 Efraim Flashner -;;; Copyright © 2016 ng0 +;;; Copyright © 2016, 2017 ng0 ;;; Copyright © 2016 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. @@ -32,6 +32,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system cmake) #:use-module (gnu packages compression) #:use-module (gnu packages) #:use-module (gnu packages guile) @@ -793,3 +794,31 @@ then ported to the GNU / Linux environment.") ;; acme-client is distributed under the ISC license, but the files 'jsmn.h' ;; and 'jsmn.c' are distributed under the Expat license. (license (list license:isc license:expat)))) + +;; The "-apache" variant is the upstreamed prefered variant. A "-gpl" +;; variant exists in addition to the "-apache" one. +(define-public mbedtls-apache + (package + (name "mbedtls-apache") + (version "2.4.0") + (source + (origin + (method url-fetch) + ;; XXX: The download links on the website are script redirection links + ;; which effectively lead to the format listed in the uri here. + (uri (string-append "https://tls.mbed.org/download/mbedtls-" + version "-apache.tgz")) + (sha256 + (base32 + "03bzbfidigljva6xj49k38q3kwlbj75lrky4a0ainylzsfg5bhy1")))) + (build-system cmake-build-system) + (native-inputs + `(("perl" ,perl))) + (synopsis "Small TLS library") + (description + "@code{mbed TLS}, formerly known as PolarSSL, makes it trivially easy +for developers to include cryptographic and SSL/TLS capabilities in their +(embedded) products, facilitating this functionality with a minimal +coding footprint.") + (home-page "https://tls.mbed.org") + (license license:asl2.0))) From 3190c307f95fc5f289c1aa8a3955a58e1a5ca4b2 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 14 Feb 2017 19:09:35 +0000 Subject: [PATCH 340/436] gnu: Add hiawatha. * gnu/packages/web.scm (hiawatha): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/web.scm | 55 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index f63a3eb9da..dab30df13d 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4410,6 +4410,61 @@ developers can integrate into their applications to make use of the functions of Tidy.") (license l:bsd-3))) +(define-public hiawatha + (package + (name "hiawatha") + (version "10.4") + (source + (origin + (method url-fetch) + (uri (string-append "https://www.hiawatha-webserver.org/files/" + "hiawatha-" version ".tar.gz")) + (modules '((guix build utils))) + (snippet + ;; We use our packaged mbedtls, so delete the included copy. + '(delete-file-recursively "mbedtls")) + (sha256 + (base32 + "0m2llzm72s29c32abnj03532m85fawvi8ybjpx6s3mgvx2yvq3p4")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; No tests included + #:configure-flags (list (string-append "-DUSE_SYSTEM_MBEDTLS=on") + (string-append "-DENABLE_TOMAHAWK=on") + (string-append "-DWEBROOT_DIR=" + (assoc-ref %outputs "out") + "/share/hiawatha/html")) + #:phases + (modify-phases %standard-phases + (add-after 'install 'remove-empty-dirs + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + ;; The directories in "var" are empty, remove them. + (delete-file-recursively (string-append out "/var")) + #t))) + (add-after 'install 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Make sure 'hiawatha' finds 'mbedtls'. + (let* ((out (assoc-ref outputs "out")) + (sbin (string-append out "/sbin")) + (mbed (assoc-ref inputs "mbedtls-apache"))) + (wrap-program (string-append sbin "/hiawatha") + `("PATH" ":" prefix (,mbed))))))))) + (inputs + ;; TODO: package "hiawatha-monitor", an optional dependency of "hiawatha" + `(("mbedtls-apache" ,mbedtls-apache) ;Hiawatha includes this version. + ("zlib" ,zlib) + ("libxslt" ,libxslt) + ("libxml2" ,libxml2))) + (home-page "https://www.hiawatha-webserver.org") + (synopsis "Webserver with focus on security") + (description + "Hiawatha has been written with security in mind. This resulted in a +highly secure webserver in both code and features. Hiawatha can stop SQL +injections, XSS and CSRF attacks and exploit attempts. Via a specially +crafted monitoring tool, you can keep track of all your webservers.") + (license l:gpl2))) + (define-public qutebrowser (package (name "qutebrowser") From 52c14bb6ec6fbd532b1e03a512d133e2499186b9 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 2 Mar 2017 01:00:35 +0100 Subject: [PATCH 341/436] gnu: pugixml: Build relocatable library. * gnu/packages/xml.scm (pugixml): Add "-shared -fPIC" to ensure the library is relocatable. Signed-off-by: Kei Kebreau --- gnu/packages/xml.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 9a22535c28..6ec2b1fdc9 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -803,7 +803,9 @@ the form of functions.") "0fcgggry5x5bn0zhb09ij9hb0p45nb0sv0d9fw3cm1cf62hp9n80")))) (build-system cmake-build-system) (arguments - `(#:tests? #f)) ; no tests + `(#:configure-flags '("-DCMAKE_CXX_FLAGS=-shared -fPIC" + "-DCMAKE_C_FLAGS=-shared -fPIC") + #:tests? #f)) ; no tests (home-page "http://pugixml.org") (synopsis "Light-weight, simple and fast XML parser for C++ with XPath support") (description From 34ba7cd4ebbaf0a597a0254cd7d675be23e28ccc Mon Sep 17 00:00:00 2001 From: ng0 Date: Sat, 4 Mar 2017 14:09:31 +0000 Subject: [PATCH 342/436] gnu: gitolite: Update to 3.6.6. * gnu/packages/version-control.scm (gitolite): Update to 3.6.6. Signed-off-by: Leo Famulari --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 1c3ffb040c..1076c18905 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -591,7 +591,7 @@ also walk each side of a merge and test those changes individually.") (define-public gitolite (package (name "gitolite") - (version "3.6.5") + (version "3.6.6") (source (origin (method url-fetch) (uri (string-append @@ -600,7 +600,7 @@ also walk each side of a merge and test those changes individually.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0xpqg04gyr4dhdhxx5lbk61lwwd5ml32530bigg2qy663icngwqm")))) + "07q33f86694s0x3k9lcmy1vzfw9appdrlmmb9j3bz4qkrxqdnwb9")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no tests From d0c16adb190c7244ee3ef1329cba78a015ae5d10 Mon Sep 17 00:00:00 2001 From: ng0 Date: Sat, 4 Mar 2017 14:09:32 +0000 Subject: [PATCH 343/436] gnu: gitolite: Fix shebangs in hooks. Fixes . * gnu/packages/version-control.scm (gitolite)[arguments]: Add 'fix-hooks-shebangs' phase to fix references to '/usr/bin/perl'. Signed-off-by: Leo Famulari --- gnu/packages/version-control.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 1076c18905..ccda00173d 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -616,6 +616,17 @@ also walk each side of a merge and test those changes individually.") (substitute* (find-files "." ".*") ((" perl -") (string-append " " perl " -")))))) + (add-before 'install 'fix-hooks-shebangs + (lambda* (#:key inputs #:allow-other-keys) + (let ((perl (string-append (assoc-ref inputs "perl") + "/bin/perl"))) + ;; The files in 'lib/Gitolite/Hooks' keep references to + ;; '/usr/bin/perl', without this fix it is impossible to + ;; to run gitolite in production. + (substitute* (find-files "src/lib/Gitolite/Hooks" ".*") + (("/usr/bin/perl") + perl)) + #t))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((output (assoc-ref outputs "out")) From f1710d8da0b794f93624ba0a880ba4850d2305bf Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 5 Mar 2017 09:15:00 +1000 Subject: [PATCH 344/436] gnu: ruby-pry: Update to 0.10.4. * gnu/packages/ruby.scm (ruby-pry): Update to 0.10.4. --- gnu/packages/ruby.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 73eefe8dde..fba0978e44 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1993,14 +1993,14 @@ for select languages.") (define-public ruby-pry (package (name "ruby-pry") - (version "0.10.1") + (version "0.10.4") (source (origin (method url-fetch) (uri (rubygems-uri "pry" version)) (sha256 (base32 - "1j0r5fm0wvdwzbh6d6apnp7c0n150hpm9zxpm5xvcgfqr36jaj8z")))) + "05xbzyin63aj2prrv8fbq2d5df2mid93m81hz5bvf2v4hnzs42ar")))) (build-system ruby-build-system) (arguments '(#:tests? #f)) ; no tests From 5e0535a7e6b0ca292a792c45bf3e432059a06a2b Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 5 Mar 2017 09:17:12 +1000 Subject: [PATCH 345/436] gnu: ruby-coderay: Update to 1.1.1. * gnu/packages/ruby.scm (ruby-coderay): Update to 1.1.1. --- gnu/packages/ruby.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index fba0978e44..4d839bcdf1 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1973,14 +1973,14 @@ extract comments.") (define-public ruby-coderay (package (name "ruby-coderay") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (rubygems-uri "coderay" version)) (sha256 (base32 - "059wkzlap2jlkhg460pkwc1ay4v4clsmg1bp4vfzjzkgwdckr52s")))) + "1x6z923iwr1hi04k6kz5a6llrixflz8h5sskl9mhaaxy9jx2x93r")))) (build-system ruby-build-system) (arguments '(#:tests? #f)) ; missing test files From c35745edc4e78defba4a82e32974d729cf159c34 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 2 Mar 2017 17:35:43 -0500 Subject: [PATCH 346/436] gnu: kio: Fix CVE-2017-6410. * gnu/packages/patches/kio-CVE-2017-6410.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/kde-frameworks.scm (kio)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/kde-frameworks.scm | 1 + gnu/packages/patches/kio-CVE-2017-6410.patch | 53 ++++++++++++++++++++ 3 files changed, 55 insertions(+) create mode 100644 gnu/packages/patches/kio-CVE-2017-6410.patch diff --git a/gnu/local.mk b/gnu/local.mk index ce8ea3d37b..a44c4072b0 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -648,6 +648,7 @@ dist_patch_DATA = \ %D%/packages/patches/jq-CVE-2015-8863.patch \ %D%/packages/patches/kdbusaddons-kinit-file-name.patch \ %D%/packages/patches/khmer-use-libraries.patch \ + %D%/packages/patches/kio-CVE-2017-6410.patch \ %D%/packages/patches/kmod-module-directory.patch \ %D%/packages/patches/kobodeluxe-paths.patch \ %D%/packages/patches/kobodeluxe-enemies-pipe-decl.patch \ diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 36c2851567..ba4ead2d67 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2206,6 +2206,7 @@ makes starting KDE applications faster and reduces memory consumption.") "mirror://kde/stable/frameworks/" (version-major+minor version) "/" name "-" version ".tar.xz")) + (patches (search-patches "kio-CVE-2017-6410.patch")) (sha256 (base32 "1hqc88c2idi9fkb7jy82csb0i740lghv0p2fg1gaglcarjdz7nia")))) diff --git a/gnu/packages/patches/kio-CVE-2017-6410.patch b/gnu/packages/patches/kio-CVE-2017-6410.patch new file mode 100644 index 0000000000..748636f806 --- /dev/null +++ b/gnu/packages/patches/kio-CVE-2017-6410.patch @@ -0,0 +1,53 @@ +Fix CVE-2017-6410, "Information Leak when accessing https when using a +malicious PAC file": + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-6410 +https://www.kde.org/info/security/advisory-20170228-1.txt + +Patch copied from upstream source repository: + +https://cgit.kde.org/kio.git/commit/?id=f9d0cb47cf94e209f6171ac0e8d774e68156a6e4 + +From f9d0cb47cf94e209f6171ac0e8d774e68156a6e4 Mon Sep 17 00:00:00 2001 +From: Albert Astals Cid +Date: Tue, 28 Feb 2017 19:00:48 +0100 +Subject: Sanitize URLs before passing them to FindProxyForURL + +Remove user/password information +For https: remove path and query + +Thanks to safebreach.com for reporting the problem + +CCMAIL: yoni.fridburg@safebreach.com +CCMAIL: amit.klein@safebreach.com +CCMAIL: itzik.kotler@safebreach.com +--- + src/kpac/script.cpp | 11 +++++++++-- + 1 file changed, 9 insertions(+), 2 deletions(-) + +diff --git a/src/kpac/script.cpp b/src/kpac/script.cpp +index a0235f7..2485c54 100644 +--- a/src/kpac/script.cpp ++++ b/src/kpac/script.cpp +@@ -754,9 +754,16 @@ QString Script::evaluate(const QUrl &url) + } + } + ++ QUrl cleanUrl = url; ++ cleanUrl.setUserInfo(QString()); ++ if (cleanUrl.scheme() == QLatin1String("https")) { ++ cleanUrl.setPath(QString()); ++ cleanUrl.setQuery(QString()); ++ } ++ + QScriptValueList args; +- args << url.url(); +- args << url.host(); ++ args << cleanUrl.url(); ++ args << cleanUrl.host(); + + QScriptValue result = func.call(QScriptValue(), args); + if (result.isError()) { +-- +cgit v0.11.2 + From 07302d1ab4fae67117476a51a1031de02b05b519 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 4 Mar 2017 18:07:26 -0500 Subject: [PATCH 347/436] gnu: gnupg: Update to 2.1.19. * gnu/packages/gnupg.scm (gnupg): Update to 2.1.19. [arguments]: Add 'patch-test-paths' phase and remove 'set-gnupg-home' phase. Add '--enable-gnupg-builddir-envvar' to #:configure-flags. --- gnu/packages/gnupg.scm | 36 ++++++++++++++++++++++++++++-------- 1 file changed, 28 insertions(+), 8 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index befd29961c..d76fcc2d3c 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -217,14 +217,14 @@ compatible to GNU Pth.") (define-public gnupg (package (name "gnupg") - (version "2.1.18") + (version "2.1.19") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) (sha256 (base32 - "157rrv3ly9j2k0acz43nhiba5hfl6h7048jvj55wwqjmgsmnyk6h")))) + "1w4vccmb5l50lm4yrz9vkdj7whbfvzx543r55362kkj1aqgyvk26")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -243,7 +243,11 @@ compatible to GNU Pth.") ("sqlite" ,sqlite) ("zlib" ,zlib))) (arguments - `(#:configure-flags '("--enable-gpg2-is-gpg") + `(#:configure-flags '("--enable-gpg2-is-gpg" + ;; Otherwise, the test suite looks for the `gpg` + ;; executable in its installation directory in + ;; /gnu/store before it has been installed. + "--enable-gnupg-builddir-envvar") #:phases (modify-phases %standard-phases (add-before 'configure 'patch-paths @@ -259,11 +263,27 @@ compatible to GNU Pth.") (("/usr/bin/env gpgscm") (string-append (getcwd) "/tests/gpgscm/gpgscm"))) #t)) - ;; If this variable is undefined, /bin/pwd is invoked. - (add-before 'check 'set-gnupg-home - (lambda _ - (setenv "GNUPGHOME" (getcwd)) - #t))))) + (add-before 'build 'patch-test-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((coreutils (assoc-ref inputs "coreutils")) + (cat (string-append coreutils "/bin/cat")) + (pwd (string-append coreutils "/bin/pwd")) + (true (string-append coreutils "/bin/true")) + (false (string-append coreutils "/bin/false"))) + (substitute* '("tests/inittests" + "tests/pkits/inittests" + "tests/Makefile" + "tests/pkits/common.sh" + "tests/pkits/Makefile" + ) + (("/bin/pwd") pwd)) + (substitute* "common/t-exectool.c" + (("/bin/cat") cat)) + (substitute* "common/t-exectool.c" + (("/bin/true") true)) + (substitute* "common/t-exectool.c" + (("/bin/false") false)) + #t)))))) (home-page "https://gnupg.org/") (synopsis "GNU Privacy Guard") (description From 9f86202ba1fda3f22ff5044420658e16b18edfd2 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sat, 4 Mar 2017 22:13:22 -0500 Subject: [PATCH 348/436] gnu: starfighter: Update to 1.7. * gnu/packages/games.scm (starfighter): Update to 1.7. [arguments]: Remove obsolete make flags. Re-enable configure and test phases. --- gnu/packages/games.scm | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 7333cfca00..550652eefd 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -2617,7 +2617,7 @@ tactics.") (define-public starfighter (package (name "starfighter") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (string-append @@ -2626,18 +2626,8 @@ tactics.") name "-" version "-src.tar.gz")) (sha256 (base32 - "1qb5nk0b3d0ia5zszmg4a3ydf4fiy39fmymb66vwkqn4djajdhzq")))) + "1646hpjq8bz2fkfkja1dah511hn7zd2r7da4w9c9blhad3p5732v")))) (build-system gnu-build-system) - (arguments - '(#:tests? #f ; no check target - #:make-flags - (let ((out (assoc-ref %outputs "out"))) - (list (string-append "PREFIX=" out) - (string-append "BINDIR=" out "/bin/"))) - #:phases - (modify-phases %standard-phases - ;; no configure script - (delete 'configure)))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs From 40c611a41df35877c91a6b1ef66bdc84e6355ec7 Mon Sep 17 00:00:00 2001 From: rennes Date: Fri, 17 Feb 2017 19:16:36 -0600 Subject: [PATCH 349/436] gnu: wxwidgets: Fix for Filezilla client. * gnu/packages/patches/wxwidgets-fix-windowGTK.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Leo Famulari --- gnu/local.mk | 3 ++- .../patches/wxwidgets-fix-windowGTK.patch | 18 ++++++++++++++++++ gnu/packages/wxwidgets.scm | 5 ++++- 3 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/wxwidgets-fix-windowGTK.patch diff --git a/gnu/local.mk b/gnu/local.mk index a44c4072b0..c88892df54 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -5,7 +5,7 @@ # Copyright © 2013, 2014, 2015, 2016 Mark H Weaver # Copyright © 2016 Chris Marusich # Copyright © 2016, 2017 Kei Kebreau -# Copyright © 2016 Rene Saavedra +# Copyright © 2016, 2017 Rene Saavedra # Copyright © 2016 Adonay "adfeno" Felipe Nogueira # Copyright © 2016, 2017 Ricardo Wurmus # Copyright © 2016 Ben Woodcroft @@ -976,6 +976,7 @@ dist_patch_DATA = \ %D%/packages/patches/wordnet-CVE-2008-2149.patch \ %D%/packages/patches/wordnet-CVE-2008-3908-pt1.patch \ %D%/packages/patches/wordnet-CVE-2008-3908-pt2.patch \ + %D%/packages/patches/wxwidgets-fix-windowGTK.patch \ %D%/packages/patches/xdotool-fix-makefile.patch \ %D%/packages/patches/xf86-video-ark-remove-mibstore.patch \ %D%/packages/patches/xf86-video-ast-remove-mibstore.patch \ diff --git a/gnu/packages/patches/wxwidgets-fix-windowGTK.patch b/gnu/packages/patches/wxwidgets-fix-windowGTK.patch new file mode 100644 index 0000000000..1255835d01 --- /dev/null +++ b/gnu/packages/patches/wxwidgets-fix-windowGTK.patch @@ -0,0 +1,18 @@ +This patch allow Filezilla client to resize window. +The patch was adapted from upstream source repository: +'' + +--- a/src/gtk/toplevel.cpp 2014-10-06 16:33:44.000000000 -0500 ++++ b/src/gtk/toplevel.cpp 2017-02-16 21:33:27.779907810 -0600 +@@ -1216,8 +1216,9 @@ + int hints_mask = GDK_HINT_MIN_SIZE | GDK_HINT_MAX_SIZE; + hints.min_width = 1; + hints.min_height = 1; +- hints.max_width = INT_MAX; +- hints.max_height = INT_MAX; ++ // using INT_MAX for size will lead to integer overflow with HiDPI scaling ++ hints.max_width = INT_MAX / 16; ++ hints.max_height = INT_MAX / 16; + const int decorSize_x = m_decorSize.left + m_decorSize.right; + const int decorSize_y = m_decorSize.top + m_decorSize.bottom; + if (minSize.x > decorSize_x) diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm index 5285037ffe..52fa8184dd 100644 --- a/gnu/packages/wxwidgets.scm +++ b/gnu/packages/wxwidgets.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2016 Ricardo Wurmus ;;; Copyright © 2016 Theodoros Foradis ;;; Copyright © 2016 Danny Milosavljevic +;;; Copyright © 2017 Rene Saavedra ;;; ;;; This file is part of GNU Guix. ;;; @@ -50,7 +51,9 @@ "releases/download/v" version "/wxWidgets-" version ".tar.bz2")) (sha256 - (base32 "0paq27brw4lv8kspxh9iklpa415mxi8zc117vbbbhfjgapf7js1l")))) + (base32 "0paq27brw4lv8kspxh9iklpa415mxi8zc117vbbbhfjgapf7js1l")) + (patches (search-patches + "wxwidgets-fix-windowGTK.patch")))) (build-system glib-or-gtk-build-system) (inputs `(("glu" ,glu) From afa595350bdfab8f65bece34d7303bf8c9b981da Mon Sep 17 00:00:00 2001 From: rennes Date: Tue, 14 Feb 2017 23:22:07 -0600 Subject: [PATCH 350/436] gnu: Add libfilezilla. * gnu/packages/ftp.scm (libfilezilla): New variable. Signed-off-by: Leo Famulari --- gnu/packages/ftp.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 7380fcfc3b..3f3a0491ca 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2016 Tobias Geerinckx-Rice +;;; Copyright © 2017 Rene Saavedra ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,6 +27,10 @@ #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages autotools) + #:use-module (gnu packages check) + #:use-module (gnu packages compression) + #:use-module (gnu packages databases) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) #:use-module (gnu packages ncurses) #:use-module (gnu packages readline) @@ -159,3 +164,25 @@ maintaining a web page or other FTP archive. It synchronizes a set of local files to a remote server by performing uploads and remote deletes as required.") (license gpl2+))) + +(define-public libfilezilla + (package + (name "libfilezilla") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (string-append "http://download.filezilla-project.org/" + name "/" name "-" version ".tar.bz2")) + (sha256 + (base32 + "0340v5xs48f28q2d16ldb9359dkzlhl4l449mgyv3qabnlz2pl21")))) + (build-system gnu-build-system) + (native-inputs + `(("cppunit" ,cppunit))) + (home-page "https://lib.filezilla-project.org") + (synopsis "Cross-platform C++ library used by Filezilla client") + (description + "This package provides some basic functionality to build high-performing, +platform-independent programs.") + (license gpl2+))) From 0bc26f66c747b65888ab12538b60469c0190e14a Mon Sep 17 00:00:00 2001 From: rennes Date: Tue, 14 Feb 2017 23:27:11 -0600 Subject: [PATCH 351/436] gnu: Add filezilla. * gnu/packages/ftp.scm (filezilla): New variable. --- gnu/packages/ftp.scm | 47 ++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 45 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 3f3a0491ca..bb2e746942 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -32,11 +32,16 @@ #:use-module (gnu packages databases) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) + #:use-module (gnu packages glib) + #:use-module (gnu packages gtk) + #:use-module (gnu packages libidn) #:use-module (gnu packages ncurses) - #:use-module (gnu packages readline) + #:use-module (gnu packages nettle) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages readline) #:use-module (gnu packages tls) - #:use-module (gnu packages compression)) + #:use-module (gnu packages wxwidgets) + #:use-module (gnu packages xml)) (define-public lftp (package @@ -186,3 +191,41 @@ as required.") "This package provides some basic functionality to build high-performing, platform-independent programs.") (license gpl2+))) + +(define-public filezilla + (package + (name "filezilla") + (version "3.24.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://sourceforge.net/projects/" name + "/files/FileZilla_Client/" version + "/FileZilla_" version "_src" ".tar.bz2")) + (sha256 + (base32 + "1bacrl8lj90hqbh129hpbgqj78k1i84j83rkzn507jnykj4x8p9x")))) + (build-system gnu-build-system) + (native-inputs + `(("gettext" ,gettext-minimal) + ("pkg-config" ,pkg-config) + ("pugixml" ,pugixml) + ("xdg-utils" ,xdg-utils))) + (inputs + `(("dbus" ,dbus) + ("gnutls" ,gnutls) + ("gtk+" ,gtk+) + ("libfilezilla" ,libfilezilla) + ("libidn" ,libidn) + ("nettle" ,nettle) + ("sqlite" ,sqlite) + ("wxwidgets" ,wxwidgets))) + (home-page "https://filezilla-project.org") + (synopsis "Full-featured graphical FTP/FTPS/SFTP client") + (description + "Filezilla client supports FTP, FTP over SSL/TLS (FTPS), +SSH File Transfer Protocol (SFTP), HTTP/1.1, SOCKS5, FTP-Proxy, IPv6 +and others features such as bookmarks, drag and drop, filename filters, +directory comparison and more.") + (license gpl2+) + (properties '((upstream-name . "FileZilla"))))) From a78e0bda99fed71e43f5dd3a64e5613bd808fa92 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 4 Mar 2017 23:02:51 -0500 Subject: [PATCH 352/436] gnu: filezilla: Update to 3.24.1. * gnu/packages/ftp.scm (filezilla): Update to 3.24.1. [arguments]: Add '--disable-autoupdatecheck' to #:configure-flags. --- gnu/packages/ftp.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index bb2e746942..49e7214991 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -195,7 +195,7 @@ platform-independent programs.") (define-public filezilla (package (name "filezilla") - (version "3.24.0") + (version "3.24.1") (source (origin (method url-fetch) @@ -204,8 +204,11 @@ platform-independent programs.") "/FileZilla_" version "_src" ".tar.bz2")) (sha256 (base32 - "1bacrl8lj90hqbh129hpbgqj78k1i84j83rkzn507jnykj4x8p9x")))) + "0ahcld3g6jj92nakm5i58wgmcv6f4l9yisw3aqbc2ry0gs679pg6")))) (build-system gnu-build-system) + (arguments + ;; Don't let filezilla phone home to check for updates. + '(#:configure-flags '("--disable-autoupdatecheck"))) (native-inputs `(("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config) From 9ee4c9ab6f1aa6592a234918dc3946e79317c6dd Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 14 Feb 2017 11:28:04 -0500 Subject: [PATCH 353/436] services: Add agetty service. * gnu/services/base.scm (): New record type. (agetty-shepherd-service, agetty-service): New procedures. (agetty-service-type): New variable. * doc/guix.texi (Base Services): Document it. [mingetty-configuration],[kmscon-configuration]: Specify the types of supported consoles. --- doc/guix.texi | 170 +++++++++++++++++++++++++++++++- gnu/services/base.scm | 222 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 390 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index be11096a43..7c7729859b 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8391,7 +8391,7 @@ other things. @deftp {Data Type} mingetty-configuration This is the data type representing the configuration of Mingetty, which -implements console log-in. +provides the default implementation of virtual console log-in. @table @asis @@ -8418,6 +8418,172 @@ The Mingetty package to use. @end table @end deftp +@deffn {Scheme Procedure} agetty-service @var{config} +Return a service to run agetty according to @var{config}, an +@code{} object, which specifies the tty to run, +among other things. +@end deffn + +@deftp {Data Type} agetty-configuration +This is the data type representing the configuration of agetty, which +implements virtual and serial console log-in. See the @code{agetty(8)} +man page for more information. + +@table @asis + +@item @code{tty} +The name of the console this agetty runs on, as a string---e.g., +@code{"ttyS0"}. This argument is mandatory. + +@item @code{baud-rate} (default: @code{#f}) +A string containing a comma-separated list of one or more baud rates, in +descending order. + +@item @code{term} (default: @code{#f}) +A string containing the value used for the @code{TERM} environment +variable. + +@item @code{eight-bits?} (default: @code{#f}) +When @code{#t}, the tty is assumed to be 8-bit clean, and parity detection is +disabled. + +@item @code{auto-login} (default: @code{#f}) +When passed a login name, as a string, the specified user will be logged +in automatically without prompting for their login name or password. + +@item @code{no-reset?} (default: @code{#f}) +When @code{#t}, don't reset terminal cflags (control modes). + +@item @code{host} (default: @code{#f}) +This accepts a string containing the "login_host", which will be written +into the @file{/var/run/utmpx} file. + +@item @code{remote?} (default: @code{#f}) +When set to @code{#t} in conjunction with @var{host}, this will add an +@code{-r} fakehost option to the command line of the login program +specified in @var{login-program}. + +@item @code{flow-control?} (default: @code{#f}) +When set to @code{#t}, enable hardware (RTS/CTS) flow control. + +@item @code{no-issue?} (default: @code{#f}) +When set to @code{#t}, the contents of the @file{/etc/issue} file will +not be displayed before presenting the login prompt. + +@item @code{init-string} (default: @code{#f}) +This accepts a string that will be sent to the tty or modem before +sending anything else. It can be used to initialize a modem. + +@item @code{no-clear?} (default: @code{#f}) +When set to @code{#t}, agetty will not clear the screen before showing +the login prompt. + +@item @code{login-program} (default: (file-append shadow "/bin/login")) +This must be either a gexp denoting the name of a log-in program, or +unset, in which case the default value is the @command{login} from the +Shadow tool suite. + +@item @code{local-line} (default: @code{#f}) +Control the CLOCAL line flag. This accepts one of three symbols as +arguments, @code{'auto}, @code{'always}, or @code{'never}. If @code{#f}, +the default value chosen by agetty is @code{'auto}. + +@item @code{extract-baud?} (default: @code{#f}) +When set to @code{#t}, instruct agetty to try to extract the baud rate +from the status messages produced by certain types of modems. + +@item @code{skip-login?} (default: @code{#f}) +When set to @code{#t}, do not prompt the user for a login name. This +can be used with @var{login-program} field to use non-standard login +systems. + +@item @code{no-newline?} (default: @code{#f}) +When set to @code{#t}, do not print a newline before printing the +@file{/etc/issue} file. + +@c Is this dangerous only when used with login-program, or always? +@item @code{login-options} (default: @code{#f}) +This option accepts a string containing options that are passed to the +login program. When used with the @var{login-program}, be aware that a +malicious user could try to enter a login name containing embedded +options that could be parsed by the login program. + +@item @code{login-pause} (default: @code{#f}) +When set to @code{#t}, wait for any key before showing the login prompt. +This can be used in conjunction with @var{auto-login} to save memory by +lazily spawning shells. + +@item @code{chroot} (default: @code{#f}) +Change root to the specified directory. This option accepts a directory +path as a string. + +@item @code{hangup?} (default: @code{#f}) +Use the Linux system call @code{vhangup} to do a virtual hangup of the +specified terminal. + +@item @code{keep-baud?} (default: @code{#f}) +When set to @code{#t}, try to keep the existing baud rate. The baud +rates from @var{baud-rate} are used when agetty receives a @key{BREAK} +character. + +@item @code{timeout} (default: @code{#f}) +When set to an integer value, terminate if no user name could be read +within @var{timeout} seconds. + +@item @code{detect-case?} (default: @code{#f}) +When set to @code{#t}, turn on support for detecting an uppercase-only +terminal. This setting will detect a login name containing only +uppercase letters as indicating an uppercase-only terminal and turn on +some upper-to-lower case conversions. Note that this will not support +Unicode characters. + +@item @code{wait-cr?} (default: @code{#f}) +When set to @code{#t}, wait for the user or modem to send a +carriage-return or linefeed character before displaying +@file{/etc/issue} or login prompt. This is typically used with the +@var{init-string} option. + +@item @code{no-hints?} (default: @code{#f}) +When set to @code{#t}, do not print hints about Num, Caps, and Scroll +locks. + +@item @code{no-hostname?} (default: @code{#f}) +By default, the hostname is printed. When this option is set to +@code{#t}, no hostname will be shown at all. + +@item @code{long-hostname?} (default: @code{#f}) +By default, the hostname is only printed until the first dot. When this +option is set to @code{#t}, the fully qualified hostname by +@code{gethostname} or @code{getaddrinfo} is shown. + +@item @code{erase-characters} (default: @code{#f}) +This option accepts a string of additional characters that should be +interpreted as backspace when the user types their login name. + +@item @code{kill-characters} (default: @code{#f}) +This option accepts a string that should be interpreted to mean "ignore +all previous characters" (also called a "kill" character) when the types +their login name. + +@item @code{chdir} (default: @code{#f}) +This option accepts, as a string, a directory path that will be changed +to before login. + +@item @code{delay} (default: @code{#f}) +This options accepts, as an integer, the number of seconds to sleep +before opening the tty and displaying the login prompt. + +@item @code{nice} (default: @code{#f}) +This option accepts, as an integer, the nice value with which to run the +@command{login} program. + +@item @code{extra-options} (default: @code{'()}) +This option provides an "escape hatch" for the user to provide arbitrary +command-line arguments to @command{agetty} as a list of strings. + +@end table +@end deftp + @deffn {Scheme Procedure} kmscon-service-type @var{config} Return a service to run @uref{https://www.freedesktop.org/wiki/Software/kmscon,kmscon} according to @var{config}, a @code{} object, which @@ -8426,7 +8592,7 @@ specifies the tty to run, among other things. @deftp {Data Type} kmscon-configuration This is the data type representing the configuration of Kmscon, which -implements console log-in. +implements virtual console log-in. @table @asis diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 7ae815d4b5..5298a11f63 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -38,6 +38,7 @@ #:select (canonical-package glibc)) #:use-module (gnu packages bash) #:use-module (gnu packages package-management) + #:use-module (gnu packages linux) #:use-module (gnu packages lsof) #:use-module (gnu packages terminals) #:use-module ((gnu build file-systems) @@ -74,6 +75,11 @@ login-service-type login-service + agetty-configuration + agetty-configuration? + agetty-service + agetty-service-type + mingetty-configuration mingetty-configuration? mingetty-service @@ -730,6 +736,222 @@ Return a service that sets up Unicode support in @var{tty} and loads the message of the day, among other things." (service login-service-type config)) +(define-record-type* + agetty-configuration make-agetty-configuration + agetty-configuration? + (agetty agetty-configuration-agetty ; + (default util-linux)) + (tty agetty-configuration-tty) ;string + (term agetty-term ;string | #f + (default #f)) + (baud-rate agetty-baud-rate ;string | #f + (default #f)) + (auto-login agetty-auto-login ;list of strings | #f + (default #f)) + (login-program agetty-login-program ;gexp + (default (file-append shadow "/bin/login"))) + (login-pause? agetty-login-pause? ;Boolean + (default #f)) + (eight-bits? agetty-eight-bits? ;Boolean + (default #f)) + (no-reset? agetty-no-reset? ;Boolean + (default #f)) + (remote? agetty-remote? ;Boolean + (default #f)) + (flow-control? agetty-flow-control? ;Boolean + (default #f)) + (host agetty-host ;string | #f + (default #f)) + (no-issue? agetty-no-issue? ;Boolean + (default #f)) + (init-string agetty-init-string ;string | #f + (default #f)) + (no-clear? agetty-no-clear? ;Boolean + (default #f)) + (local-line agetty-local-line ;always | never | auto + (default #f)) + (extract-baud? agetty-extract-baud? ;Boolean + (default #f)) + (skip-login? agetty-skip-login? ;Boolean + (default #f)) + (no-newline? agetty-no-newline? ;Boolean + (default #f)) + (login-options agetty-login-options ;string | #f + (default #f)) + (chroot agetty-chroot ;string | #f + (default #f)) + (hangup? agetty-hangup? ;Boolean + (default #f)) + (keep-baud? agetty-keep-baud? ;Boolean + (default #f)) + (timeout agetty-timeout ;integer | #f + (default #f)) + (detect-case? agetty-detect-case? ;Boolean + (default #f)) + (wait-cr? agetty-wait-cr? ;Boolean + (default #f)) + (no-hints? agetty-no-hints? ;Boolean + (default #f)) + (no-hostname? agetty-no hostname? ;Boolean + (default #f)) + (long-hostname? agetty-long-hostname? ;Boolean + (default #f)) + (erase-characters agetty-erase-characters ;string | #f + (default #f)) + (kill-characters agetty-kill-characters ;string | #f + (default #f)) + (chdir agetty-chdir ;string | #f + (default #f)) + (delay agetty-delay ;integer | #f + (default #f)) + (nice agetty-nice ;integer | #f + (default #f)) + ;; "Escape hatch" for passing arbitrary command-line arguments. + (extra-options agetty-extra-options ;list of strings + (default '())) +;;; XXX Unimplemented for now! +;;; (issue-file agetty-issue-file ;file-like +;;; (default #f)) + ) + +(define agetty-shepherd-service + (match-lambda + (($ agetty tty term baud-rate auto-login + login-program login-pause? eight-bits? no-reset? remote? flow-control? + host no-issue? init-string no-clear? local-line extract-baud? + skip-login? no-newline? login-options chroot hangup? keep-baud? timeout + detect-case? wait-cr? no-hints? no-hostname? long-hostname? + erase-characters kill-characters chdir delay nice extra-options) + (list + (shepherd-service + (documentation "Run agetty on a tty.") + (provision (list (symbol-append 'term- (string->symbol tty)))) + + ;; Since the login prompt shows the host name, wait for the 'host-name' + ;; service to be done. Also wait for udev essentially so that the tty + ;; text is not lost in the middle of kernel messages (see also + ;; mingetty-shepherd-service). + (requirement '(user-processes host-name udev)) + + (start #~(make-forkexec-constructor + (list #$(file-append util-linux "/sbin/agetty") + #$@extra-options + #$@(if eight-bits? + #~("--8bits") + #~()) + #$@(if no-reset? + #~("--noreset") + #~()) + #$@(if remote? + #~("--remote") + #~()) + #$@(if flow-control? + #~("--flow-control") + #~()) + #$@(if host + #~("--host" #$host) + #~()) + #$@(if no-issue? + #~("--noissue") + #~()) + #$@(if init-string + #~("--init-string" #$init-string) + #~()) + #$@(if no-clear? + #~("--noclear") + #~()) +;;; FIXME This doesn't work as expected. According to agetty(8), if this option +;;; is not passed, then the default is 'auto'. However, in my tests, when that +;;; option is selected, agetty never presents the login prompt, and the +;;; term-ttyS0 service respawns every few seconds. + #$@(if local-line + #~(#$(match local-line + ('auto "--local-line=auto") + ('always "--local-line=always") + ('never "-local-line=never"))) + #~()) + #$@(if extract-baud? + #~("--extract-baud") + #~()) + #$@(if skip-login? + #~("--skip-login") + #~()) + #$@(if no-newline? + #~("--nonewline") + #~()) + #$@(if login-options + #~("--login-options" #$login-options) + #~()) + #$@(if chroot + #~("--chroot" #$chroot) + #~()) + #$@(if hangup? + #~("--hangup") + #~()) + #$@(if keep-baud? + #~("--keep-baud") + #~()) + #$@(if timeout + #~("--timeout" #$(number->string timeout)) + #~()) + #$@(if detect-case? + #~("--detect-case") + #~()) + #$@(if wait-cr? + #~("--wait-cr") + #~()) + #$@(if no-hints? + #~("--nohints?") + #~()) + #$@(if no-hostname? + #~("--nohostname") + #~()) + #$@(if long-hostname? + #~("--long-hostname") + #~()) + #$@(if erase-characters + #~("--erase-chars" #$erase-characters) + #~()) + #$@(if kill-characters + #~("--kill-chars" #$kill-characters) + #~()) + #$@(if chdir + #~("--chdir" #$chdir) + #~()) + #$@(if delay + #~("--delay" #$(number->string delay)) + #~()) + #$@(if nice + #~("--nice" #$(number->string nice)) + #~()) + #$@(if auto-login + (list "--autologin" auto-login) + '()) + #$@(if login-program + #~("--login-program" #$login-program) + #~()) + #$@(if login-pause? + #~("--login-pause") + #~()) + #$tty + #$@(if baud-rate + #~(#$baud-rate) + #~()) + #$@(if term + #~(#$term) + #~())))) + (stop #~(make-kill-destructor))))))) + +(define agetty-service-type + (service-type (name 'agetty) + (extensions (list (service-extension shepherd-root-service-type + agetty-shepherd-service))))) + +(define* (agetty-service config) + "Return a service to run agetty according to @var{config}, which specifies +the tty to run, among other things." + (service agetty-service-type config)) + (define-record-type* mingetty-configuration make-mingetty-configuration mingetty-configuration? From 3df18d6144818b81c97318269355817e472c8c89 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 5 Mar 2017 11:41:34 +0200 Subject: [PATCH 354/436] gnu: obs: Update to 18.0.0. * gnu/packages/video.scm (obs): Update to 18.0.0. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 006341644b..ec390d4db9 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1490,7 +1490,7 @@ be used for realtime video capture via Linux-specific APIs.") (define-public obs (package (name "obs") - (version "17.0.2") + (version "18.0.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/jp9000/obs-studio" @@ -1498,7 +1498,7 @@ be used for realtime video capture via Linux-specific APIs.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "02cfhpkcsq718zwhwwsm48gjggf95qr38hqpi0kwrvsy18ll0msm")))) + "0pxrzzp8z7kmwfdp49rwrk0j3lpya6garvbbzzfvldwhyam9az5d")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no tests From 8ea42482141d3f091980d52537c3eea50ec7c91e Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sun, 19 Feb 2017 17:36:20 +0100 Subject: [PATCH 355/436] gnu: Add binutils-vc4. * gnu/packages/embedded.scm (binutils-vc4): New variable. --- gnu/packages/embedded.scm | 53 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 70de5e53b8..3e1f87d749 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -30,12 +30,14 @@ #:use-module (guix build utils) #:use-module (gnu packages) #:use-module (gnu packages autotools) + #:use-module ((gnu packages base) #:prefix base:) #:use-module (gnu packages bison) #:use-module (gnu packages cross-base) #:use-module (gnu packages dejagnu) #:use-module (gnu packages flex) #:use-module (gnu packages gcc) #:use-module (gnu packages gdb) + #:use-module (gnu packages guile) #:use-module (gnu packages libftdi) #:use-module (gnu packages libusb) #:use-module (gnu packages perl) @@ -719,3 +721,54 @@ toolchain, the loader, the Openspin compiler, the Spin2cpp tool, and the Spin simulator.") (home-page (package-home-page propeller-gcc)) (license (package-license propeller-gcc)))) + +(define-public binutils-vc4 + (let ((commit "708acc851880dbeda1dd18aca4fd0a95b2573b36")) + (package + (name "binutils-vc4") + (version (string-append "2.23.51-0." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/puppeh/binutils-vc4.git") + (commit commit))) + (sha256 + (base32 + "1kdrz6fki55lm15rwwamn74fnqpy0zlafsida2zymk76n3656c63")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--target=vc4-elf" + "--disable-werror" + "--enable-cgen-maint") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-cgen + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (string-append (assoc-ref inputs "cgen") + "/cgen") "cgen") + #t)) + (add-after 'unpack-cgen 'fix-cgen-guile + (lambda _ + (substitute* "opcodes/Makefile.in" + (("guile\\{,-\\}1.8") "guile")) + (zero? (system* "which" "guile"))))))) + (native-inputs + `(("cgen" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/puppeh/cgen.git") + (commit "d8e2a9eb70425f180fdd5bfd032884b0855f2032"))) + (sha256 + (base32 + "14b3h2ji740s8zq5vwm4qdcxs4aa4wxi6wb9di3bv1h39x14nyr9")))) + ("texinfo" ,texinfo) + ("flex" ,flex) + ("bison" ,bison) + ("guile-1.8" ,guile-1.8) + ("which" ,base:which))) + (synopsis "Binutils for VC4") + (description "This package provides @code{binutils} for VideoCore IV, +the Raspberry Pi chip.") + (license license:gpl3+) + (home-page "https://github.com/puppeh/vc4-toolchain/")))) From 67a8298c098dd4235af4c9d53aea404cd57146d5 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sun, 5 Mar 2017 12:53:27 -0500 Subject: [PATCH 356/436] gnu: libmp3splt: Update to 0.9.2. * gnu/packages/mp3.scm (libmp3splt): Update to 0.9.2. --- gnu/packages/mp3.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index e60bd5c5c1..800faee6ce 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -230,7 +230,7 @@ pre-defined or user-specifiable output format.") (define-public libmp3splt (package (name "libmp3splt") - (version "0.8.1a") + (version "0.9.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/mp3splt/libmp3splt/" @@ -238,7 +238,7 @@ pre-defined or user-specifiable output format.") version ".tar.gz")) (sha256 (base32 - "0d20r1bd4fgp9kp7w3qixjgll34czck9dgw59mx2kbhb0mhh00d8")))) + "1p1mn2hsmj5cp40fnc8g1yfvk72p8pjxi866gjdkgjsqrr7xdvih")))) (build-system gnu-build-system) (inputs `(("libid3tag" ,libid3tag) ("libmad" ,libmad) From 2041f9019ee56e281a4d8bb8937583733089c8a6 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sun, 5 Mar 2017 13:12:03 -0500 Subject: [PATCH 357/436] gnu: mp3splt: Update to 2.6.2. * gnu/packages/mp3.scm (mp3splt): Update to 2.6.2. [native-inputs]: Add pkg-config. --- gnu/packages/mp3.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index 800faee6ce..78c2b2f73b 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -263,7 +263,7 @@ This package contains the library.") (define-public mp3splt (package (name "mp3splt") - (version "2.5.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/mp3splt/mp3splt/" @@ -271,8 +271,9 @@ This package contains the library.") version ".tar.gz")) (sha256 (base32 - "106dnka56prlc9nsfh300f8841am2lmkwlzgl9lkr25mgnc35wwh")))) + "1aiv20gypb6r84qabz8gblk8vi42cg3x333vk2pi3fyqvl82phry")))) (build-system gnu-build-system) + (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("libmp3splt" ,libmp3splt))) (synopsis "Utility for splitting mp3 and ogg vorbis files") (description From 461160c530df6d08dfe7287443496d750045758c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 5 Mar 2017 10:58:29 +0100 Subject: [PATCH 358/436] gnu: ardour: Update to 5.8. * gnu/packages/audio.scm (ardour): Update to 5.8. --- gnu/packages/audio.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 312fdd4e99..cce52732d6 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2015 Alex Kost @@ -186,7 +186,7 @@ streams from live audio.") (define-public ardour (package (name "ardour") - (version "5.6") + (version "5.8") (source (origin (method git-fetch) (uri (git-reference @@ -203,7 +203,7 @@ streams from live audio.") namespace ARDOUR { const char* revision = \"" version "\" ; }"))))) (sha256 (base32 - "1fgvjmvdyh61qn8azpmh19ac58ps5sl2dywwshr56v0svakhwwh9")) + "1lcvslrcw6g4kp9w0h1jx46x6ilz4nzz0k2yrw4gd545k1rwx0c1")) (file-name (string-append name "-" version)))) (build-system waf-build-system) (arguments From ba5c85679db3f7cf976b5edfbabb7cfe19a329c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 5 Mar 2017 11:34:38 +0100 Subject: [PATCH 359/436] gnu: ardour: Generate freedesktop files. * gnu/packages/audio.scm (ardour)[arguments]: Add "--freedesktop" configure flag. [native-inputs]: Add itstool and gettext-minimal. --- gnu/packages/audio.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index cce52732d6..3d943dc01c 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -208,7 +208,8 @@ namespace ARDOUR { const char* revision = \"" version "\" ; }"))))) (build-system waf-build-system) (arguments `(#:configure-flags '("--cxx11" ; required by gtkmm - "--no-phone-home") ; don't contact ardour.org + "--no-phone-home" ; don't contact ardour.org + "--freedesktop") ; install .desktop file #:phases (modify-phases %standard-phases (add-after @@ -256,6 +257,8 @@ namespace ARDOUR { const char* revision = \"" version "\" ; }"))))) (native-inputs `(("perl" ,perl) ("cppunit" ,cppunit) + ("itstool" ,itstool) + ("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config))) (home-page "http://ardour.org") (synopsis "Digital audio workstation") From 5f0c649683aeba9f7272d81277cec37fd36af880 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 5 Mar 2017 19:42:52 +0100 Subject: [PATCH 360/436] gnu: ardour: Enable tests. * gnu/packages/audio.scm (ardour)[arguments]: Enable unit tests. --- gnu/packages/audio.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 3d943dc01c..2b11a32caf 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -209,13 +209,14 @@ namespace ARDOUR { const char* revision = \"" version "\" ; }"))))) (arguments `(#:configure-flags '("--cxx11" ; required by gtkmm "--no-phone-home" ; don't contact ardour.org - "--freedesktop") ; install .desktop file + "--freedesktop" ; install .desktop file + "--test") ; build unit tests #:phases (modify-phases %standard-phases (add-after 'unpack 'set-rpath-in-LDFLAGS ,(ardour-rpath-phase (version-prefix version 1)))) - #:tests? #f ; no check target + #:test-target "test" #:python ,python-2)) (inputs `(("alsa-lib" ,alsa-lib) From 5af1a381334d70d771b317f363e617a9011465c8 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 5 Mar 2017 11:21:15 +0100 Subject: [PATCH 361/436] gnu: wireshark: Update to 2.2.5. * gnu/packages/networking.scm (wireshark): Update to 2.2.5. Signed-off-by: Leo Famulari --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index eb3047c81b..fe9e6a5933 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -470,7 +470,7 @@ which can be used to encrypt a password with @code{crypt(3)}.") (define-public wireshark (package (name "wireshark") - (version "2.2.4") + (version "2.2.5") (synopsis "Network traffic analyzer") (source (origin @@ -479,7 +479,7 @@ which can be used to encrypt a password with @code{crypt(3)}.") version ".tar.bz2")) (sha256 (base32 - "049r5962yrajhhz9r4dsnx403dab50d6091y2mw298ymxqszp9s2")))) + "1j4sc3pmy8l6k41007spglcqiabjlzc7f85pn3jmjr9ksv9qipbm")))) (build-system glib-or-gtk-build-system) (inputs `(("bison" ,bison) ("c-ares" ,c-ares) From 33c93ea33ed9ab35f9432665f931285898ca75c7 Mon Sep 17 00:00:00 2001 From: ng0 Date: Sun, 5 Mar 2017 16:14:43 -0500 Subject: [PATCH 362/436] gnu: rxvt-unicode: Add '.desktop' files. This fixes . * gnu/packages/xdisorg.scm (rxvt-unicode)[arguments]: Add 'install-desktop-urxvt' and 'install-desktop-urxvtc' phases. --- gnu/packages/xdisorg.scm | 43 ++++++++++++++++++++++++++++++++++++++-- 1 file changed, 41 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 3e0b441128..7d4209d126 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2016 Marius Bakke ;;; Copyright © 2016 Petter ;;; Copyright © 2017 Mekeor Melire +;;; Copyright © 2017 ng0 ;;; ;;; This file is part of GNU Guix. ;;; @@ -689,9 +690,47 @@ compact configuration syntax.") ;; This sets the destination when installing the necessary terminal ;; capability data, which are not provided by 'ncurses'. See ;; https://lists.gnu.org/archive/html/bug-ncurses/2009-10/msg00031.html - '(#:make-flags (list (string-append "TERMINFO=" + `(#:make-flags (list (string-append "TERMINFO=" (assoc-ref %outputs "out") - "/share/terminfo")))) + "/share/terminfo")) + #:phases + (modify-phases %standard-phases + (add-after 'install 'install-desktop-urxvt + (lambda* (#:key outputs #:allow-other-keys) + (let* ((output (assoc-ref outputs "out")) + (desktop (string-append output "/share/applications"))) + (mkdir-p desktop) + (with-output-to-file + (string-append desktop "/urxvt.desktop") + (lambda _ + (format #t + "[Desktop Entry]~@ + Name=rxvt-unicode~@ + Comment=~@ + Exec=~a/bin/urxvt~@ + TryExec=~@*~a/bin/urxvt~@ + Icon=~@ + Type=Application~%" + output))) + #t))) + (add-after 'install 'install-desktop-urxvtc + (lambda* (#:key outputs #:allow-other-keys) + (let* ((output (assoc-ref outputs "out")) + (desktop (string-append output "/share/applications"))) + (mkdir-p desktop) + (with-output-to-file + (string-append desktop "/urxvtc.desktop") + (lambda _ + (format #t + "[Desktop Entry]~@ + Name=rxvt-unicode~@ + Comment=Rxvt clone with XFT and unicode support~@ + Exec=~a/bin/urxvtc~@ + TryExec=~@*~a/bin/urxvtc~@ + Icon=~@ + Type=Application~%" + output))) + #t)))))) (inputs `(("libXft" ,libxft) ("libX11" ,libx11))) From 7bc19c92054b7b6d5a9268a7f2d3344adf04cce4 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 5 Mar 2017 20:17:50 -0500 Subject: [PATCH 363/436] gnu: xmlto: Fix source URL. Works around . * gnu/packages/xml.scm (xmlto)[source]: Update URL. [file-name]: New field. --- gnu/packages/xml.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 6ec2b1fdc9..66eb63ade4 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -849,9 +849,11 @@ code for classes that correspond to data structures defined by XMLSchema.") (source (origin (method url-fetch) - (uri (string-append - "https://fedorahosted.org/releases/x/m/xmlto/xmlto-" - version ".tar.bz2")) + ;; The old source on fedorahosted.org is offline permanently: + ;; + (uri (string-append "mirror://debian/pool/main/x/xmlto/" + "xmlto_" version ".orig.tar.bz2")) + (file-name (string-append name "-" version ".tar.bz2")) (sha256 (base32 "0xhj8b2pwp4vhl9y16v3dpxpsakkflfamr191mprzsspg4xdyc0i")))) From ec0742133297ac02b684ee1e81d1143de06956f7 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 21 Feb 2017 13:33:20 +0100 Subject: [PATCH 364/436] gnu: Add python2-backports-shutil-get-terminal-size. * gnu/packages/python.scm (python2-backports-shutil-get-terminal-size): New variable. Signed-off-by: Danny Milosavljevic --- gnu/packages/python.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5631c7ac0b..0d1dd18a58 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -33,7 +33,7 @@ ;;; Copyright © 2016 Arun Isaac ;;; Copyright © 2016, 2017 Julien Lepiller ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice -;;; Copyright © 2016 Thomas Danckaert +;;; Copyright © 2016, 2017 Thomas Danckaert ;;; Copyright © 2017 Carlo Zancanaro ;;; Copyright © 2017 Frederick M. Muriithi ;;; @@ -6087,6 +6087,29 @@ connection to each user.") (define-public python2-backports-abc (package-with-python2 python-backports-abc)) +(define-public python2-backports-shutil-get-terminal-size + (package + (name "python2-backports-shutil-get-terminal-size") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "backports.shutil_get_terminal_size" version)) + (sha256 + (base32 + "107cmn7g3jnbkp826zlj8rrj19fam301qvaqf0f3905f5217lgki")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2)) + (home-page "https://github.com/chrippa/backports.shutil_get_terminal_size") + (synopsis "Backport of Python 3.3's @code{shutil.get_terminal_size}") + (description + "This package provides a backport of the @code{get_terminal_size +function} from Python 3.3's @code{shutil}. +Unlike the original version it is written in pure Python rather than C, +so it might be a tiny bit slower.") + (license license:expat))) + (define-public python-waf (package (name "python-waf") From 2aa6d3aeeb49f116aab2757b217cd25fab71d7d6 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 21 Feb 2017 21:33:02 +0100 Subject: [PATCH 365/436] gnu: Add python-colorspacious. * gnu/packages/python.scm (python-colorspacious, python2-colorspacious): New variables. Signed-off-by: Danny Milosavljevic --- gnu/packages/python.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0d1dd18a58..181436e399 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3826,6 +3826,30 @@ To address this and enable easy cycling over arbitrary @code{kwargs}, the (define-public python2-cycler (package-with-python2 python-cycler)) +(define-public python-colorspacious + (package + (name "python-colorspacious") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/njsmith/colorspacious/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version)) + (sha256 + (base32 "1vflh5jm32qb0skza2i8pjacv09w6gq84fqpp2nj77s0rbmzgr4k")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numpy" ,python-numpy))) + (home-page "https://github.com/njsmith/colorspacious") + (synopsis "Python library for colorspace conversions") + (description "@code{colorspacious} is a Python library that lets you +convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.") + (license license:expat))) + +(define-public python2-colorspacious + (package-with-python2 python-colorspacious)) + (define-public python-matplotlib (package (name "python-matplotlib") From b320f7bf06213087886d4f7fb12baccbc399f3e3 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Fri, 24 Feb 2017 17:07:27 +0100 Subject: [PATCH 366/436] gnu: python-testpath: Fix library location for python2 version. * gnu/packages/python.scm (python-testpath)[arguments]: Install module in the proper "lib/pythonx.y" location for all Python versions. Signed-off-by: Danny Milosavljevic --- gnu/packages/python.scm | 26 ++++++++++++++++---------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 181436e399..3066c88549 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5183,20 +5183,26 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (build-system python-build-system) (arguments `(#:tests? #f ; this package does not even have a setup.py + #:modules ((guix build python-build-system) + (guix build utils) + (srfi srfi-1)) + #:imported-modules (,@%python-build-system-modules + (srfi srfi-1)) #:phases (modify-phases %standard-phases (delete 'install) (replace 'build - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((dir (string-append - (assoc-ref outputs "out") - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages/testpath"))) - (mkdir-p dir) - (copy-recursively "testpath" dir)) - #t))))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((version (last + (string-split (assoc-ref inputs "python") #\-))) + (x.y (string-join (take (string-split version #\.) 2) + ".")) + (dir (string-append + (assoc-ref outputs "out") + "/lib/python" x.y "/site-packages/testpath"))) + (mkdir-p dir) + (copy-recursively "testpath" dir)) + #t))))) (home-page "https://github.com/takluyver/testpath") (synopsis "Test utilities for code working with files and commands") (description From 350932536a2e04bf4644cdad7ce2b91d8b12cd10 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 21 Feb 2017 11:45:06 +0100 Subject: [PATCH 367/436] gnu: python-scipy: Update to 0.18.1. * gnu/packages/python.scm (python-scipy): Update to 0.18.1. [source]: Use github instead of sourceforge. [native-inputs]: Add python-cython. Signed-off-by: Danny Milosavljevic --- gnu/packages/python.scm | 104 +++++++++++++++++++--------------------- 1 file changed, 48 insertions(+), 56 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3066c88549..7f60680fdc 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4079,16 +4079,16 @@ functions.") (define-public python-scipy (package (name "python-scipy") - (version "0.16.0") + (version "0.18.1") (source (origin (method url-fetch) -; http://downloads.sourceforge.net/project/scipy/scipy/0.16.1/scipy-0.16.1.tar.gz - (uri (string-append "mirror://sourceforge/scipy/scipy/" version - "/scipy-" version ".tar.xz")) + (uri (string-append "https://github.com/scipy/scipy/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0wa0a4skpda3gx7lb12yn19nhbairlyxrvda2lz2bcawk3x5qzz2")))) + "17slsrfawjp7if6qrlx03zhgp05350ginxx8ddpw9zqx43x905sn")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy) @@ -4098,21 +4098,16 @@ functions.") `(("lapack" ,lapack) ("openblas" ,openblas))) (native-inputs - `(("python-nose" ,python-nose) - ("python-sphinx" ,python-sphinx-1.2.3) + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-sphinx" ,python-sphinx) ("python-numpydoc" ,python-numpydoc) ("gfortran" ,gfortran) - ("texlive" ,texlive) ("perl" ,perl))) (outputs '("out" "doc")) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-tests - (lambda _ - (substitute* "scipy/integrate/tests/test_quadpack.py" - (("libm.so") "libm.so.6")) - #t)) (add-before 'build 'configure-openblas (lambda* (#:key inputs #:allow-other-keys) (call-with-output-file "site.cfg" @@ -4132,40 +4127,44 @@ atlas_libs = openblas (assoc-ref inputs "openblas") (assoc-ref inputs "openblas")))) #t)) - (delete 'check) - (add-after 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html")) - (pyver ,(string-append "PYVER="))) - ;; Make installed package available for building the - ;; documentation - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "doc" - ;; Fix generation of images for mathematical expressions. - (substitute* (find-files "source" "conf\\.py") - (("pngmath_use_preview = True") - "pngmath_use_preview = False")) - (mkdir-p html) - (system* "make" "html" pyver) - (system* "make" "latex" "PAPER=a4" pyver) - (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver) - (copy-file "build/latex/scipy-ref.pdf" - (string-append doc "/scipy-ref.pdf")) - (with-directory-excursion "build/html" - (for-each (lambda (file) - (let* ((dir (dirname file)) - (tgt-dir (string-append html "/" dir))) - (install-file file html))) - (find-files "." ".*")))) - #t))) - (add-after 'install-doc 'check - (lambda _ - ;; Tests can only be run after the library has been installed and not - ;; within the source directory. - (with-directory-excursion "/tmp" - (zero? (system* "python" "-c" "import scipy; scipy.test()")))))))) + (add-after 'install 'install-doc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "doc") "/share")) + (doc (string-append data "/doc/" ,name "-" ,version)) + (html (string-append doc "/html")) + (pyver ,(string-append "PYVER="))) + ;; Make installed package available for building the + ;; documentation + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "doc" + ;; Fix generation of images for mathematical expressions. + (substitute* (find-files "source" "conf\\.py") + (("pngmath_use_preview = True") + "pngmath_use_preview = False")) + (mkdir-p html) + (system* "make" "html" pyver) + (with-directory-excursion "build/html" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append html "/" dir))) + (install-file file html))) + (find-files "." ".*"))))) + #t)) + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "scipy/integrate/tests/test_quadpack.py" + (("libm.so") "libm.so.6")) + #t)) + ;; Tests can only be run after the library has been installed and not + ;; within the source directory. + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "/tmp" + (zero? (system* "python" "-c" + "import scipy; scipy.test('full')"))) + #t))))) (home-page "http://www.scipy.org/") (synopsis "The Scipy library provides efficient numerical routines") (description "The SciPy library is one of the core packages that make up @@ -4175,15 +4174,8 @@ routines such as routines for numerical integration and optimization.") (license license:bsd-3))) (define-public python2-scipy - (let ((scipy (package-with-python2 - (strip-python2-variant python-scipy)))) - (package (inherit scipy) - ;; Make sure to use special packages for Python 2 instead - ;; of those automatically rewritten by package-with-python2. - (native-inputs - `(("python2-sphinx" ,python2-sphinx-1.2.3) - ,@(fold alist-delete (package-native-inputs scipy) - '("python-sphinx"))))))) + (package-with-python2 + (strip-python2-variant python-scipy))) (define-public python-socksipy-branch (package From fb25d348ddc2cecbb5dd8ec402c7a506a9f99f91 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 21 Feb 2017 12:41:09 +0100 Subject: [PATCH 368/436] gnu: python-ipython: Update to 5.2.2. * gnu/packages/python.scm (python-ipython): Update to 5.2.2. [propagated-inputs]: Add pyhon-prompt-toolkit and python-nbformat. (python2-ipython) [arguments]: Enable tests. [propagated-inputs]: Add python2-backports-shutil-get-terminal-size. [native-inputs]: Add graphviz. Signed-off-by: Danny Milosavljevic --- gnu/packages/python.scm | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7f60680fdc..e94aa812b1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5209,17 +5209,18 @@ tools for mocking system commands and recording calls to those.") (define-public python-ipython (package (name "python-ipython") - (version "4.0.3") + (version "5.2.2") (source (origin (method url-fetch) (uri (pypi-uri "ipython" version ".tar.gz")) (sha256 - (base32 "1h2gp1p06sww9rzfkfzqy489bh47gj3910y2b1wdk3dcx1cqz4is")))) + (base32 "1qhjwa9cyz1np7rhv3p4ip13lkgbqsad62l24xkwiq1ic2gwiqbf")))) (build-system python-build-system) (outputs '("out" "doc")) (propagated-inputs `(("python-pyzmq" ,python-pyzmq) + ("python-prompt-toolkit" ,python-prompt-toolkit) ("python-terminado" ,python-terminado) ("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) @@ -5232,16 +5233,19 @@ tools for mocking system commands and recording calls to those.") ("python-jsonschema" ,python-jsonschema) ("python-traitlets" ,python-traitlets) ("python-ipykernel" ,python-ipykernel) + ("python-nbformat" ,python-nbformat) ("python-pygments" ,python-pygments))) (inputs `(("readline" ,readline) ("which" ,which))) (native-inputs - `(("pkg-config" ,pkg-config) + `(("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) ("python-requests" ,python-requests) ;; for tests ("python-testpath" ,python-testpath) ("python-nose" ,python-nose) ("python-sphinx" ,python-sphinx) + ("python-shpinx-rtd-theme" ,python-sphinx-rtd-theme) ("texlive" ,texlive) ("texinfo" ,texinfo))) (arguments @@ -5255,15 +5259,16 @@ tools for mocking system commands and recording calls to those.") (html (string-append doc "/html")) (man1 (string-append data "/man/man1")) (info (string-append data "/info")) - (examples (string-append doc "/examples"))) + (examples (string-append doc "/examples")) + (python-arg (string-append "PYTHON=" (which "python")))) (setenv "LANG" "en_US.utf8") ;; Make installed package available for running the tests (add-installed-pythonpath inputs outputs) (with-directory-excursion "docs" ;; FIXME: pdf fails to build ;;(system* "make" "pdf" "PAPER=a4") - (system* "make" "html") - (system* "make" "info")) + (system* "make" python-arg "html") + (system* "make" python-arg "info")) (copy-recursively "docs/man" man1) (copy-recursively "examples" examples) (copy-recursively "docs/build/html" html) @@ -5313,10 +5318,12 @@ computing.") (let ((ipython (package-with-python2 (strip-python2-variant python-ipython)))) (package (inherit ipython) - ;; FIXME: some tests are failing - (arguments - `(#:tests? #f ,@(package-arguments ipython))) ;; FIXME: add pyreadline once available. + (propagated-inputs + `(("python2-backports-shutil-get-terminal-size" + ,python2-backports-shutil-get-terminal-size) + ("python2-pathlib2" ,python2-pathlib2) + ,@(package-propagated-inputs ipython))) (native-inputs `(("python2-mock" ,python2-mock) ,@(package-native-inputs ipython)))))) From d701f8bdb247121753289d2d0b7059530cd9442d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 6 Mar 2017 13:02:20 +0100 Subject: [PATCH 369/436] gnu: libosinfo: Update to 1.0.0. * gnu/packages/qemu.scm (libosinfo): Update to 1.0.0. [source]: Use new release location as fedorahosted.org is defunct. [arguments]: Replace phase "copy-ids" with configure flags; add phase "disable-broken-test" to disable the "isodetect" test. [native-inputs]: Update origin for "pci.ids" and "usb.ids". --- gnu/packages/qemu.scm | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/gnu/packages/qemu.scm b/gnu/packages/qemu.scm index 9afcd83049..3aa4128be0 100644 --- a/gnu/packages/qemu.scm +++ b/gnu/packages/qemu.scm @@ -207,23 +207,29 @@ server and embedded PowerPC, and S390 guests.") (define-public libosinfo (package (name "libosinfo") - (version "0.3.1") + (version "1.0.0") (source (origin (method url-fetch) - (uri (string-append "https://fedorahosted.org/releases/l/i/libosinfo/libosinfo-" + (uri (string-append "https://releases.pagure.org/libosinfo/libosinfo-" version ".tar.gz")) (sha256 (base32 - "151qrzmafxww5yfamrr7phk8217xmihfhazpb597vdv87na75cjh")))) + "0srrs2m6irqd4f867g8ls6jp2dq3ql0l9d0fh80d55sivvn2bd7p")))) (build-system gnu-build-system) (arguments - `(#:phases + `(#:configure-flags + (list (string-append "--with-usb-ids-path=" + (assoc-ref %build-inputs "usb.ids")) + (string-append "--with-pci-ids-path=" + (assoc-ref %build-inputs "pci.ids"))) + #:phases (modify-phases %standard-phases - (add-after 'unpack 'copy-ids - (lambda* (#:key inputs #:allow-other-keys) - (copy-file (assoc-ref inputs "pci.ids") "data/pci.ids") - (copy-file (assoc-ref inputs "usb.ids") "data/usb.ids") + ;; This odd test fails for unknown reasons. + (add-after 'unpack 'disable-broken-test + (lambda _ + (substitute* "test/Makefile.in" + (("test-isodetect\\$\\(EXEEXT\\)") "")) #t))))) (inputs `(("libsoup" ,libsoup) @@ -240,18 +246,18 @@ server and embedded PowerPC, and S390 guests.") ("pci.ids" ,(origin (method url-fetch) - (uri "https://raw.githubusercontent.com/pciutils/pciids/f9477789526f9d380bc57aa92e357c521738d5dd/pci.ids") + (uri "https://github.com/pciutils/pciids/raw/ad02084f0bc143e3c15e31a6152a3dfb1d7a3156/pci.ids") (sha256 (base32 - "0g6dbwlamagxqxvng67xng3w2x56c0np4md1v1p1jn32qw518az0")))) + "0kfhpj5rnh24hz2714qhfmxk281vwc2w50sm73ggw5d15af7zfsw")))) ("usb.ids" ,(origin (method url-fetch) - (uri "http://linux-usb.cvs.sourceforge.net/viewvc/linux-usb/htdocs/usb.ids?revision=1.539") + (uri "http://linux-usb.cvs.sourceforge.net/viewvc/linux-usb/htdocs/usb.ids?revision=1.551") (file-name "usb.ids") (sha256 (base32 - "0w9ila7662lzpx416lqy69zx6gfwq2xiigwd5fdyqcrg3dj07m80")))))) + "17rg5i0wbyk289gr8v4kgvnc9q5bidz7ldcvv9x58l083wn16hq3")))))) (home-page "https://libosinfo.org/") (synopsis "Operating system information database") (description "libosinfo is a GObject based library API for managing From c0446791bde9117cdf7badbd033403454cec4f19 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 6 Mar 2017 13:22:51 +0100 Subject: [PATCH 370/436] gnu: python2-backports-shutil-get-terminal-size: Enable tests. * gnu/packages/python.scm (python2-backports-shutil-get-terminal-size)[arguments]: Replace 'check' phase with custom command. [native-inputs]: Add PYTHON2-PYTEST. --- gnu/packages/python.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e94aa812b1..82cae875d8 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6129,7 +6129,14 @@ connection to each user.") "107cmn7g3jnbkp826zlj8rrj19fam301qvaqf0f3905f5217lgki")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "py.test" "-v"))))))) + (native-inputs + `(("python2-pytest" ,python2-pytest))) (home-page "https://github.com/chrippa/backports.shutil_get_terminal_size") (synopsis "Backport of Python 3.3's @code{shutil.get_terminal_size}") (description From 5b1f31ffcfd529d46fddfcda0c25eeba142de4ba Mon Sep 17 00:00:00 2001 From: Troy Sankey Date: Mon, 20 Feb 2017 01:37:38 -0500 Subject: [PATCH 371/436] gnu: python-setuptools-scm: Update to 1.15.0. * gnu/packages/python.scm (python-setuptools-scm): Update to 1.15.0. Signed-off-by: Marius Bakke --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 82cae875d8..334c836d99 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4886,13 +4886,13 @@ child application and control it as if a human were typing commands.") (define-public python-setuptools-scm (package (name "python-setuptools-scm") - (version "1.11.1") + (version "1.15.0") (source (origin (method url-fetch) (uri (pypi-uri "setuptools_scm" version)) (sha256 (base32 - "1gqr73i150yzj3mz32854vj93x07yr52kn8fdckwa41ll8wgficc")))) + "0bwyc5markib0i7i2qlyhdzxhiywzxbkfiapldma8m91m82jvwfs")))) (build-system python-build-system) (home-page "https://github.com/pypa/setuptools_scm/") (synopsis "Manage Python package versions in SCM metadata") From 5f8ca95eb54d975e1a9acbe2e1abe6813e469810 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 6 Mar 2017 09:25:23 +0100 Subject: [PATCH 372/436] gnu: giac-xcas: Update to 1.2.3-25. * gnu/packages/algebra.scm (giac-xcas): Update to 1.2.3-25. Signed-off-by: Marius Bakke --- gnu/packages/algebra.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index e244644c40..7a84332dd5 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -202,7 +202,7 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.") (define-public giac-xcas (package (name "giac-xcas") - (version "1.2.3-19") + (version "1.2.3-25") (source (origin (method url-fetch) ;; "~parisse/giac" is not used because the maintainer regularly @@ -214,7 +214,7 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.") "source/giac_" version ".tar.gz")) (sha256 (base32 - "0asynsj0xcfdjn0vkyxdgdy3hfpr6gc9f92xxa1rmn7clbqmlk1y")))) + "0d6a42p8111raf7k16yvjajnpj22abiqndy3yzkrb4b8l071r24d")))) (build-system gnu-build-system) (arguments `(#:phases From b812da70594f5d40647d156f69be0eb169d6be19 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 5 Mar 2017 14:04:34 -0500 Subject: [PATCH 373/436] Revert "doc: Symlink daemon start-up files." This reverts commit b7230de54b493da5a78922b4226255763b525a98. Versions of systemd that supported symlinked service files are not yet widely deployed. See this thread for more information: http://lists.gnu.org/archive/html/guix-devel/2017-01/msg01199.html --- doc/guix.texi | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 7c7729859b..732f4312a4 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -443,8 +443,15 @@ Run the daemon, and set it to automatically start on boot. If your host distro uses the systemd init system, this can be achieved with these commands: +@c Versions of systemd that supported symlinked service files are not +@c yet widely deployed, so we should suggest that users copy the service +@c files into place. +@c +@c See this thread for more information: +@c http://lists.gnu.org/archive/html/guix-devel/2017-01/msg01199.html + @example -# ln -s ~root/.guix-profile/lib/systemd/system/guix-daemon.service \ +# cp ~root/.guix-profile/lib/systemd/system/guix-daemon.service \ /etc/systemd/system/ # systemctl start guix-daemon && systemctl enable guix-daemon @end example @@ -452,8 +459,8 @@ with these commands: If your host distro uses the Upstart init system: @example -# ln -s ~root/.guix-profile/lib/upstart/system/guix-daemon.conf /etc/init/ # initctl reload-configuration +# cp ~root/.guix-profile/lib/upstart/system/guix-daemon.conf /etc/init/ # start guix-daemon @end example From 613d0895b92c677e0639d5e77c55043e38e020c8 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 5 Mar 2017 14:33:13 -0500 Subject: [PATCH 374/436] build: Don't embed absolute paths in .service and .conf service files. Otherwise, users will be stuck running an old copy of guix and the guix-daemon if they copy the service files instead of symlinking them. * etc/guix-daemon.conf.in, etc/guix-daemon.service.in, etc/guix-publish.conf.in, etc/guix-publish.service.in: Expand @localstatedir@ instead of @bindir@. * nix/local.mk (etc/guix-%.service, etc/guix-%.conf): Use @localstatedir@ instead of @bindir@. --- etc/guix-daemon.conf.in | 2 +- etc/guix-daemon.service.in | 2 +- etc/guix-publish.conf.in | 2 +- etc/guix-publish.service.in | 2 +- nix/local.mk | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/etc/guix-daemon.conf.in b/etc/guix-daemon.conf.in index 8f833cb693..09c70cde38 100644 --- a/etc/guix-daemon.conf.in +++ b/etc/guix-daemon.conf.in @@ -9,4 +9,4 @@ stop on runlevel [016] task -exec @bindir@/guix-daemon --build-users-group=guixbuild +exec @localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix-daemon --build-users-group=guixbuild diff --git a/etc/guix-daemon.service.in b/etc/guix-daemon.service.in index ab0ce090c3..ffe4cf9bd5 100644 --- a/etc/guix-daemon.service.in +++ b/etc/guix-daemon.service.in @@ -6,7 +6,7 @@ Description=Build daemon for GNU Guix [Service] -ExecStart=@bindir@/guix-daemon --build-users-group=guixbuild +ExecStart=@localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix-daemon --build-users-group=guixbuild Environment=GUIX_LOCPATH=/root/.guix-profile/lib/locale RemainAfterExit=yes StandardOutput=syslog diff --git a/etc/guix-publish.conf.in b/etc/guix-publish.conf.in index 498fa295be..241c594559 100644 --- a/etc/guix-publish.conf.in +++ b/etc/guix-publish.conf.in @@ -9,4 +9,4 @@ stop on runlevel [016] task -exec @bindir@/guix publish --user=nobody --port=8181 +exec @localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix publish --user=nobody --port=8181 diff --git a/etc/guix-publish.service.in b/etc/guix-publish.service.in index fc4e3c21f3..8aaf09e3cd 100644 --- a/etc/guix-publish.service.in +++ b/etc/guix-publish.service.in @@ -6,7 +6,7 @@ Description=Publish the GNU Guix store [Service] -ExecStart=@bindir@/guix publish --user=nobody --port=8181 +ExecStart=@localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix publish --user=nobody --port=8181 Environment=GUIX_LOCPATH=/root/.guix-profile/lib/locale RemainAfterExit=yes StandardOutput=syslog diff --git a/nix/local.mk b/nix/local.mk index eb70d266fb..9e0c457bec 100644 --- a/nix/local.mk +++ b/nix/local.mk @@ -190,7 +190,7 @@ nodist_systemdservice_DATA = etc/guix-daemon.service etc/guix-publish.service etc/guix-%.service: etc/guix-%.service.in \ $(top_builddir)/config.status $(AM_V_GEN)$(MKDIR_P) "`dirname $@`"; \ - $(SED) -e 's|@''bindir''@|$(bindir)|' < \ + $(SED) -e 's|@''localstatedir''@|$(localstatedir)|' < \ "$<" > "$@.tmp"; \ mv "$@.tmp" "$@" @@ -201,7 +201,7 @@ nodist_upstartjob_DATA = etc/guix-daemon.conf etc/guix-publish.conf etc/guix-%.conf: etc/guix-%.conf.in \ $(top_builddir)/config.status $(AM_V_GEN)$(MKDIR_P) "`dirname $@`"; \ - $(SED) -e 's|@''bindir''@|$(bindir)|' < \ + $(SED) -e 's|@''localstatedir''@|$(localstatedir)|' < \ "$<" > "$@.tmp"; \ mv "$@.tmp" "$@" From 23f22ba8afa9d3318c8a79022216dea3b9c866df Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 5 Mar 2017 13:23:21 -0500 Subject: [PATCH 375/436] services: openssh: Parameterize the OpenSSH package used by the service. * gnu/services/ssh.scm ()[openssh]: New field. (openssh-activation, openssh-shepherd-service): Use it. --- gnu/services/ssh.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/services/ssh.scm b/gnu/services/ssh.scm index 7b2d4a8f06..c1d42e70ce 100644 --- a/gnu/services/ssh.scm +++ b/gnu/services/ssh.scm @@ -260,6 +260,8 @@ The other options should be self-descriptive." (define-record-type* openssh-configuration make-openssh-configuration openssh-configuration? + (openssh openssh-configuration-openssh ;package + (default openssh)) (pid-file openssh-configuration-pid-file (default "/var/run/sshd.pid")) (port-number openssh-configuration-port-number ;integer @@ -297,7 +299,8 @@ The other options should be self-descriptive." (mkdir-p (dirname #$(openssh-configuration-pid-file config))) ;; Generate missing host keys. - (system* (string-append #$openssh "/bin/ssh-keygen") "-A"))) + (system* (string-append #$(openssh-configuration-openssh config) + "/bin/ssh-keygen") "-A"))) (define (openssh-config-file config) "Return the sshd configuration file corresponding to CONFIG." @@ -342,7 +345,7 @@ The other options should be self-descriptive." (openssh-configuration-pid-file config)) (define openssh-command - #~(list (string-append #$openssh "/sbin/sshd") + #~(list (string-append #$(openssh-configuration-openssh config) "/sbin/sshd") "-D" "-f" #$(openssh-config-file config))) (list (shepherd-service From e2948ef5c1578b229dd849e0a15b47a18d19f662 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 6 Mar 2017 16:01:02 -0500 Subject: [PATCH 376/436] gnu: libressl: Update to 2.5.1. * gnu/packages/tls.scm (libressl): Update to 2.5.1. --- gnu/packages/tls.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 8f428b3d6b..32aa7a61dc 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -469,7 +469,7 @@ required structures.") (define-public libressl (package (name "libressl") - (version "2.5.0") + (version "2.5.1") (source (origin (method url-fetch) @@ -478,7 +478,7 @@ required structures.") version ".tar.gz")) (sha256 (base32 - "1bkfvapi4z826slycmicvs7hwgk4l82gd8w6nqvznldbammvyll6")))) + "1kc709scgd76vk7fld4jnb4wb5lxdv1cj8zsgyjb33xp4jlf06pp")))) (build-system gnu-build-system) (native-search-paths ;; FIXME: These two variables must designate a single file or directory From e20784e65efa7c783792e8a830d4b4aaf35750d5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 5 Mar 2017 20:41:36 -0500 Subject: [PATCH 377/436] gnu: texlive: Fix CVE-2016-10243. * gnu/packages/patches/texlive-texmf-CVE-2016-10243.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/tex.scm (texlive-texmf-src): Use it. --- gnu/local.mk | 1 + .../patches/texlive-texmf-CVE-2016-10243.patch | 18 ++++++++++++++++++ gnu/packages/tex.scm | 2 ++ 3 files changed, 21 insertions(+) create mode 100644 gnu/packages/patches/texlive-texmf-CVE-2016-10243.patch diff --git a/gnu/local.mk b/gnu/local.mk index c88892df54..9f83c2bcae 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -930,6 +930,7 @@ dist_patch_DATA = \ %D%/packages/patches/tcsh-fix-autotest.patch \ %D%/packages/patches/tcsh-fix-out-of-bounds-read.patch \ %D%/packages/patches/teensy-loader-cli-help.patch \ + %D%/packages/patches/texlive-texmf-CVE-2016-10243.patch \ %D%/packages/patches/texi2html-document-encoding.patch \ %D%/packages/patches/texi2html-i18n.patch \ %D%/packages/patches/tidy-CVE-2015-5522+5523.patch \ diff --git a/gnu/packages/patches/texlive-texmf-CVE-2016-10243.patch b/gnu/packages/patches/texlive-texmf-CVE-2016-10243.patch new file mode 100644 index 0000000000..3a9ae993f6 --- /dev/null +++ b/gnu/packages/patches/texlive-texmf-CVE-2016-10243.patch @@ -0,0 +1,18 @@ +Fix CVE-2016-10243: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10243 + +Patch adapted from upstream commit: + +https://www.tug.org/svn/texlive?view=revision&revision=42605 + +--- trunk/Master/texmf-dist/web2c/texmf.cnf 2016/11/29 23:10:33 42604 ++++ trunk/Master/texmf-dist/web2c/texmf.cnf 2016/11/29 23:27:53 42605 +@@ -568,7 +568,6 @@ extractbb,\ + gregorio,\ + kpsewhich,\ + makeindex,\ +-mpost,\ + repstopdf,\ + + % we'd like to allow: diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 7c84ed7194..404fd03393 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -72,6 +72,8 @@ (origin (method url-fetch) (uri "ftp://tug.org/historic/systems/texlive/2016/texlive-20160523b-texmf.tar.xz") + (patches (search-patches "texlive-texmf-CVE-2016-10243.patch")) + (patch-flags '("-p2")) (sha256 (base32 "1dv8vgfzpczqw82hv9g7a8djhhyzywljmrarlcyy6g2qi5q51glr")))) From 14807141e5fa3f59705d61280ed593eae4df2b07 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 6 Mar 2017 17:10:33 -0500 Subject: [PATCH 378/436] Revert "gnu: gnupg: Update to 2.1.19." This reverts commit 07302d1ab4fae67117476a51a1031de02b05b519. GnuPG 2.1.19 fails to build on armhf-linux and i686-linux: --- gnu/packages/gnupg.scm | 36 ++++++++---------------------------- 1 file changed, 8 insertions(+), 28 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index d76fcc2d3c..befd29961c 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -217,14 +217,14 @@ compatible to GNU Pth.") (define-public gnupg (package (name "gnupg") - (version "2.1.19") + (version "2.1.18") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) (sha256 (base32 - "1w4vccmb5l50lm4yrz9vkdj7whbfvzx543r55362kkj1aqgyvk26")))) + "157rrv3ly9j2k0acz43nhiba5hfl6h7048jvj55wwqjmgsmnyk6h")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -243,11 +243,7 @@ compatible to GNU Pth.") ("sqlite" ,sqlite) ("zlib" ,zlib))) (arguments - `(#:configure-flags '("--enable-gpg2-is-gpg" - ;; Otherwise, the test suite looks for the `gpg` - ;; executable in its installation directory in - ;; /gnu/store before it has been installed. - "--enable-gnupg-builddir-envvar") + `(#:configure-flags '("--enable-gpg2-is-gpg") #:phases (modify-phases %standard-phases (add-before 'configure 'patch-paths @@ -263,27 +259,11 @@ compatible to GNU Pth.") (("/usr/bin/env gpgscm") (string-append (getcwd) "/tests/gpgscm/gpgscm"))) #t)) - (add-before 'build 'patch-test-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ((coreutils (assoc-ref inputs "coreutils")) - (cat (string-append coreutils "/bin/cat")) - (pwd (string-append coreutils "/bin/pwd")) - (true (string-append coreutils "/bin/true")) - (false (string-append coreutils "/bin/false"))) - (substitute* '("tests/inittests" - "tests/pkits/inittests" - "tests/Makefile" - "tests/pkits/common.sh" - "tests/pkits/Makefile" - ) - (("/bin/pwd") pwd)) - (substitute* "common/t-exectool.c" - (("/bin/cat") cat)) - (substitute* "common/t-exectool.c" - (("/bin/true") true)) - (substitute* "common/t-exectool.c" - (("/bin/false") false)) - #t)))))) + ;; If this variable is undefined, /bin/pwd is invoked. + (add-before 'check 'set-gnupg-home + (lambda _ + (setenv "GNUPGHOME" (getcwd)) + #t))))) (home-page "https://gnupg.org/") (synopsis "GNU Privacy Guard") (description From 7ccb71e0ea95ae14e3b2698fe3be0738878fc93e Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 21 Feb 2017 20:28:27 +0100 Subject: [PATCH 379/436] gnu: python-numpy: Update to 1.12.0. * gnu/packages/python.scm (python-numpy): Update to 1.12.0. [source]: Use github instead of sourceforge. [native-inputs]: Add python-cython. To simplify the handling of dependency cycles (numpy documentation depends on matplotlib, which depends on numpy), we split out the documentation into a separate package: (python-numpy-bootstrap, python2-numpy-bootstrap): Remove variables. (python-numpy-documentation, python2-numpy-documentation): New variables. Signed-off-by: Marius Bakke --- gnu/packages/python.scm | 146 ++++++++++++++++++++++------------------ 1 file changed, 81 insertions(+), 65 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 334c836d99..f2c16c252a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3465,24 +3465,26 @@ between language specification and implementation aspects.") ;; This version of numpy is missing the documentation and is only used to ;; build matplotlib which is required to build numpy's documentation. -(define python-numpy-bootstrap +(define-public python-numpy (package - (name "python-numpy-bootstrap") - (version "1.10.4") + (name "python-numpy") + (version "1.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/numpy/NumPy/" version - "/numpy-" version ".tar.gz")) + (uri (string-append + "https://github.com/numpy/numpy/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1bjjhvncraka5s6i4lg644jrxij6bvycxy7an20gcz3a0m11iygp")))) + "025d4j4aakcp8w5i5diqh812cbbjgac7jszx1j56ivrbi1i8vv7d")))) (build-system python-build-system) (inputs `(("openblas" ,openblas) ("lapack" ,lapack))) (native-inputs - `(("python-nose" ,python-nose) + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) ("gfortran" ,gfortran))) (arguments `(#:phases @@ -3531,8 +3533,8 @@ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.") (license license:bsd-3))) -(define python2-numpy-bootstrap - (package-with-python2 python-numpy-bootstrap)) +(define-public python2-numpy + (package-with-python2 python-numpy)) (define-public python-munch (package @@ -3589,69 +3591,83 @@ Models, is a program for performing both single-SNP and SNP-set genome-wide association studies (GWAS) on extremely large data sets.") (license license:asl2.0))) -(define-public python-numpy - (package (inherit python-numpy-bootstrap) - (name "python-numpy") - (outputs '("out" "doc")) - (inputs - `(("which" ,which) - ,@(package-inputs python-numpy-bootstrap))) - (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-pyparsing" ,python-pyparsing) - ,@(package-propagated-inputs python-numpy-bootstrap))) +(define-public python-numpy-documentation + (package + (name "python-numpy-documentation") + (version (package-version python-numpy)) + (source (package-source python-numpy)) + (build-system python-build-system) (native-inputs - `(("pkg-config" ,pkg-config) + `(("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("pkg-config" ,pkg-config) ("python-sphinx" ,python-sphinx) ("python-numpydoc" ,python-numpydoc) ("texlive" ,texlive) ("texinfo" ,texinfo) ("perl" ,perl) - ,@(package-native-inputs python-numpy-bootstrap))) + ("scipy-sphinx-theme" + ,(origin ; The build script expects scipy-sphinx-theme as a git submodule + (method git-fetch) + (uri (git-reference + (url "https://github.com/scipy/scipy-sphinx-theme.git") + (commit "c466764e22"))) + (sha256 + (base32 + "0q2y87clwlsgc7wvlsn9pzyssybcq10plwhq2w1ydykfsyyqbmkl")))) + ,@(package-native-inputs python-numpy))) (arguments - `(,@(substitute-keyword-arguments - (package-arguments python-numpy-bootstrap) - ((#:phases phases) - `(alist-cons-after - 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make installed package available for building the - ;; documentation - (add-installed-pythonpath inputs outputs) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append - data "/doc/" ,name "-" - ,(package-version python-numpy-bootstrap))) - (info (string-append data "/info")) - (html (string-append doc "/html")) - (pyver ,(string-append "PYVER="))) - (with-directory-excursion "doc" - (mkdir-p html) - (system* "make" "html" pyver) - (system* "make" "latex" "PAPER=a4" pyver) - (system* "make" "-C" "build/latex" - "all-pdf" "PAPER=a4" pyver) - ;; FIXME: Generation of the info file fails. - ;; (system* "make" "info" pyver) - ;; (mkdir-p info) - ;; (copy-file "build/texinfo/numpy.info" - ;; (string-append info "/numpy.info")) - (for-each (lambda (file) - (copy-file (string-append "build/latex" file) - (string-append doc file))) - '("/numpy-ref.pdf" "/numpy-user.pdf")) - (with-directory-excursion "build/html" - (for-each (lambda (file) - (let* ((dir (dirname file)) - (tgt-dir (string-append html "/" dir))) - (unless (equal? "." dir) - (mkdir-p tgt-dir)) - (install-file file html))) - (find-files "." ".*")))))) - ,phases))))))) + `(#:tests? #f ; we're only generating the documentation + #:phases + (modify-phases %standard-phases + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "out") "/share")) + (doc (string-append + data "/doc/" ,name "-" + ,(package-version python-numpy))) + (info-reader (string-append data "/info")) + (html (string-append doc "/html")) + (scipy-sphinx-theme "scipy-sphinx-theme") + (sphinx-theme-checkout (assoc-ref inputs scipy-sphinx-theme)) + (pyver ,(string-append "PYVER="))) + (with-directory-excursion "doc" + (copy-recursively sphinx-theme-checkout scipy-sphinx-theme) + (mkdir-p html) + (system* "make" "html" pyver) + (system* "make" "latex" "PAPER=a4" pyver) + (system* "make" "-C" "build/latex" + "all-pdf" "PAPER=a4" pyver) + ;; FIXME: Generation of the info file fails. + ;; (system* "make" "info" pyver) + ;; (mkdir-p info) + ;; (copy-file "build/texinfo/numpy.info" + ;; (string-append info "/numpy.info")) + (for-each (lambda (file) + (copy-file (string-append "build/latex" file) + (string-append doc file))) + '("/numpy-ref.pdf" "/numpy-user.pdf")) + (with-directory-excursion "build/html" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append html "/" dir))) + (unless (equal? "." dir) + (mkdir-p tgt-dir)) + (install-file file html))) + (find-files "." ".*"))))) + #t))))) + (home-page (package-home-page python-numpy)) + (synopsis "Documentation for the python-numpy package") + (description (package-description python-numpy)) + (license (package-license python-numpy)))) -(define-public python2-numpy - (package-with-python2 python-numpy)) +(define-public python2-numpy-documentation + (let ((numpy-documentation (package-with-python2 python-numpy-documentation))) + (package + (inherit numpy-documentation) + (native-inputs `(("python2-functools32" ,python2-functools32) + ,@(package-native-inputs numpy-documentation)))))) (define-public python-pygit2 (package @@ -3872,7 +3888,7 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc. ("gobject-introspection" ,gobject-introspection) ("python-tkinter" ,python "tk") ("python-dateutil" ,python-dateutil) - ("python-numpy" ,python-numpy-bootstrap) + ("python-numpy" ,python-numpy) ("python-pillow" ,python-pillow) ("python-pytz" ,python-pytz) ("python-six" ,python-six) From 550bd98b41c2bf3bfdcf3da29a41f0933b102266 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 6 Mar 2017 21:58:19 +0100 Subject: [PATCH 380/436] gnu: Add python2-subprocess32. * gnu/packages/python.scm (python2-subprocess32): New variable. * gnu/packages/patches/python2-subprocess32-disable-input-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + ...hon2-subprocess32-disable-input-test.patch | 18 ++++++++ gnu/packages/python.scm | 41 +++++++++++++++++++ 3 files changed, 60 insertions(+) create mode 100644 gnu/packages/patches/python2-subprocess32-disable-input-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index 9f83c2bcae..5fd7c778fc 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -871,6 +871,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch \ %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \ %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch \ + %D%/packages/patches/python2-subprocess32-disable-input-test.patch \ %D%/packages/patches/qemu-CVE-2016-10155.patch \ %D%/packages/patches/qemu-CVE-2017-2615.patch \ %D%/packages/patches/qemu-CVE-2017-5525.patch \ diff --git a/gnu/packages/patches/python2-subprocess32-disable-input-test.patch b/gnu/packages/patches/python2-subprocess32-disable-input-test.patch new file mode 100644 index 0000000000..05b4eef1ba --- /dev/null +++ b/gnu/packages/patches/python2-subprocess32-disable-input-test.patch @@ -0,0 +1,18 @@ +This test tries to send a KeyboardInterrupt, which does +not work in the build environment. + +--- a/test_subprocess32.py 2017-03-06 22:21:49.334045485 +0100 ++++ b/test_subprocess32.py 2017-03-06 22:22:02.490439949 +0100 +@@ -1299,12 +1299,6 @@ + getattr(p, method)(*args) + return p + +- def test_send_signal(self): +- p = self._kill_process('send_signal', signal.SIGINT) +- _, stderr = p.communicate() +- self.assertIn('KeyboardInterrupt', stderr) +- self.assertNotEqual(p.wait(), 0) +- + def test_kill(self): + p = self._kill_process('kill') + _, stderr = p.communicate() diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f2c16c252a..56c16fd73f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9044,6 +9044,47 @@ authenticated session objects providing things like keep-alive.") 3.2.3 for use with older versions of Python and PyPy.") (license license:expat))) +(define-public python2-subprocess32 + (package + (name "python2-subprocess32") + (version "3.2.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "subprocess32" version)) + (sha256 + (base32 + "14350dhhlhyz5gqzi3lihn9m6lvskx5mcb20srx1kgsk9i50li8y")) + (patches + (search-patches "python2-subprocess32-disable-input-test.patch")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-/bin/sh + (lambda _ + (substitute* '("subprocess32.py" + "test_subprocess32.py") + (("/bin/sh") (which "sh"))) + #t)) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; For some reason this package fails to import + ;; _posixsubprocess.so when PYTHONPATH is set to the build + ;; directory. Running tests after install is easier. + (add-installed-pythonpath inputs outputs) + (zero? (system* "python" "test_subprocess32.py"))))))) + (home-page "https://github.com/google/python-subprocess32") + (synopsis "Backport of the subprocess module from Python 3.2") + (description + "This is a backport of the @code{subprocess} standard library module +from Python 3.2 and 3.3 for use on Python 2. It includes bugfixes and some +new features. On POSIX systems it is guaranteed to be reliable when used +in threaded applications. It includes timeout support from Python 3.3 but +otherwise matches 3.2’s API.") + (license license:psfl))) + (define-public python2-futures (package (name "python2-futures") From 4535a93adb225a8b0ed777b922e45bd59068f440 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 21 Feb 2017 22:18:45 +0100 Subject: [PATCH 381/436] gnu: python-matplotlib: Update to 2.0.0. * gnu/packages/python.scm (python-matplotlib, python2-matplotlib): Update to 2.0.0. [source]: Remove Tk backend patch, use Github instead of Sourceforge. [outputs]: Remove "doc" output. [inputs]: Add python-pyqt. [propagated-inputs]: Add python-cycler. [native-inputs]: Remove python-sphinx, python-numpydoc, texlive and texinfo. (python2-matplotlib)[native-inputs]: Add python2-functools32 and python2-subprocess32. (python-matplotlib-documentation, python2-matplotlib-documentation): New variables. * gnu/packages/patches/matplotlib-setupext-tk.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Signed-off-by: Marius Bakke --- gnu/local.mk | 1 - .../patches/matplotlib-setupext-tk.patch | 34 ----- gnu/packages/python.scm | 120 ++++++++++-------- 3 files changed, 69 insertions(+), 86 deletions(-) delete mode 100644 gnu/packages/patches/matplotlib-setupext-tk.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5fd7c778fc..5dec691d01 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -746,7 +746,6 @@ dist_patch_DATA = \ %D%/packages/patches/make-impure-dirs.patch \ %D%/packages/patches/mars-install.patch \ %D%/packages/patches/mars-sfml-2.3.patch \ - %D%/packages/patches/matplotlib-setupext-tk.patch \ %D%/packages/patches/maxima-defsystem-mkdir.patch \ %D%/packages/patches/mcron-install.patch \ %D%/packages/patches/mcrypt-CVE-2012-4409.patch \ diff --git a/gnu/packages/patches/matplotlib-setupext-tk.patch b/gnu/packages/patches/matplotlib-setupext-tk.patch deleted file mode 100644 index 37c3d686e0..0000000000 --- a/gnu/packages/patches/matplotlib-setupext-tk.patch +++ /dev/null @@ -1,34 +0,0 @@ -Use 'pkg-config' instead of heuristics to find 'tk' flags. - ---- matplotlib-1.4.3/setupext.py.orig 2015-12-01 14:21:19.554417453 +0100 -+++ matplotlib-1.4.3/setupext.py 2015-12-02 10:39:47.282363530 +0100 -@@ -1457,7 +1457,7 @@ - p = subprocess.Popen( - '. %s ; eval echo ${%s}' % (file, varname), - shell=True, -- executable="/bin/sh", -+ executable="sh", - stdout=subprocess.PIPE) - result = p.communicate()[0] - return result.decode('ascii') -@@ -1601,8 +1601,19 @@ - # of distros. - - # Query Tcl/Tk system for library paths and version string -+ def getoutput(s): -+ ret = os.popen(s).read().strip() -+ return ret - try: -- tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk() -+ pkg_config_libs = getoutput('pkg-config --libs-only-L tk').split() -+ # drop '-L' part of strings -+ pkg_config_libs = [s[2:] for s in pkg_config_libs] -+ pkg_config_ver = getoutput('pkg-config --modversion tk') -+ tk_ver = re.match(r"(\d+.\d+)[\d.]*", pkg_config_ver).group(1) -+ tcl_lib_dir = next(s for s in pkg_config_libs -+ if re.match(r".*-tcl-.*", s)) + '/tcl' + tk_ver -+ tk_lib_dir = next(s for s in pkg_config_libs -+ if re.match(r".*-tk-.*", s)) + '/tk' + tk_ver - except: - tk_ver = '' - result = self.hardcoded_tcl_config() diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 56c16fd73f..7315df7325 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -89,6 +89,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) + #:use-module (gnu packages qt) #:use-module (gnu packages readline) #:use-module (gnu packages sdl) #:use-module (gnu packages shells) @@ -3869,21 +3870,20 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc. (define-public python-matplotlib (package (name "python-matplotlib") - (version "1.4.3") + (version "2.0.0") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/matplotlib/matplotlib" - "/matplotlib-" version - "/matplotlib-" version ".tar.gz")) + (uri (string-append + "https://github.com/matplotlib/matplotlib/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1dn05cvd0g984lzhh72wa0z93psgwshbbg93fkab6slx5m3l95av")) - (patches (search-patches "matplotlib-setupext-tk.patch")))) + "0w3k5m5qb3wsd7yhvmg042xddvligklvcq2visk2c5wnph3hhsln")))) (build-system python-build-system) - (outputs '("out" "doc")) (propagated-inputs ; the following packages are all needed at run time - `(("python-pyparsing" ,python-pyparsing) + `(("python-cycler" ,python-cycler) + ("python-pyparsing" ,python-pyparsing) ("python-pygobject" ,python-pygobject) ("gobject-introspection" ,gobject-introspection) ("python-tkinter" ,python "tk") @@ -3915,17 +3915,13 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc. ("glib" ,glib) ;; FIXME: Add backends when available. ;("python-wxpython" ,python-wxpython) - ;("python-pyqt" ,python-pyqt) + ("python-pyqt" ,python-pyqt) ("tcl" ,tcl) ("tk" ,tk))) (native-inputs `(("pkg-config" ,pkg-config) - ("python-sphinx" ,python-sphinx-1.2.3) - ("python-numpydoc" ,python-numpydoc) ("python-nose" ,python-nose) - ("python-mock" ,python-mock) - ("texlive" ,texlive) - ("texinfo" ,texinfo))) + ("python-mock" ,python-mock))) (arguments `(#:phases (modify-phases %standard-phases @@ -3944,26 +3940,68 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc. basedirlist = ~a,~a~% [rc_options]~% backend = TkAgg~%" - (assoc-ref inputs "tcl") - (assoc-ref inputs "tk")))) - #t))) - (add-after 'install 'install-doc + (assoc-ref inputs "tcl") + (assoc-ref inputs "tk"))))) + #t))))) + (home-page "http://matplotlib.org") + (synopsis "2D plotting library for Python") + (description + "Matplotlib is a Python 2D plotting library which produces publication +quality figures in a variety of hardcopy formats and interactive environments +across platforms. Matplotlib can be used in Python scripts, the python and +ipython shell, web application servers, and six graphical user interface +toolkits.") + (license license:psfl) + (properties `((python2-variant . ,(delay python2-matplotlib)))))) + +(define-public python2-matplotlib + (let ((matplotlib (package-with-python2 + (strip-python2-variant python-matplotlib)))) + (package (inherit matplotlib) + ;; Make sure to use special packages for Python 2 instead + ;; of those automatically rewritten by package-with-python2. + (propagated-inputs + `(("python2-pycairo" ,python2-pycairo) + ("python2-functools32" ,python2-functools32) + ("python2-pygobject-2" ,python2-pygobject-2) + ("python2-subprocess32" ,python2-subprocess32) + ("python2-tkinter" ,python-2 "tk") + ,@(fold alist-delete (package-propagated-inputs matplotlib) + '("python-pycairo" "python-pygobject" "python-tkinter"))))))) + +(define-public python-matplotlib-documentation + (package + (name "python-matplotlib-documentation") + (version (package-version python-matplotlib)) + (source (package-source python-matplotlib)) + (build-system python-build-system) + (native-inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-colorspacious" ,python-colorspacious) + ("python-sphinx" ,python-sphinx) + ("python-numpydoc" ,python-numpydoc) + ("python-ipython" ,python-ipython) + ("texlive" ,texlive) + ("texinfo" ,texinfo) + ,@(package-native-inputs python-matplotlib))) + (arguments + `(#:tests? #f ; we're only generating documentation + #:phases + (modify-phases %standard-phases + (delete 'build) + (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) + (let* ((data (string-append (assoc-ref outputs "out") "/share")) (doc (string-append data "/doc/" ,name "-" ,version)) (info (string-append data "/info")) (html (string-append doc "/html"))) ;; Make installed package available for building the ;; documentation - (add-installed-pythonpath inputs outputs) (with-directory-excursion "doc" ;; Produce pdf in 'A4' format. (substitute* (find-files "." "conf\\.py") (("latex_paper_size = 'letter'") "latex_paper_size = 'a4'")) - (substitute* "users/intro.rst" - ;; Fix reST markup error (see ) - (("[[][*][]]") "[#]")) (mkdir-p html) (mkdir-p info) ;; The doc recommends to run the 'html' target twice. @@ -3985,35 +4023,15 @@ backend = TkAgg~%" (copy-file "build/texinfo/matplotlib.info" (string-append info "/matplotlib.info")) (copy-file "build/latex/Matplotlib.pdf" - (string-append doc "/Matplotlib.pdf"))) - #t)))))) - (home-page "http://matplotlib.org") - (synopsis "2D plotting library for Python") - (description - "Matplotlib is a Python 2D plotting library which produces publication -quality figures in a variety of hardcopy formats and interactive environments -across platforms. Matplotlib can be used in Python scripts, the python and -ipython shell, web application servers, and six graphical user interface -toolkits.") - (license license:psfl) - (properties `((python2-variant . ,(delay python2-matplotlib)))))) + (string-append doc "/Matplotlib.pdf")))) + #t))))) + (home-page (package-home-page python-matplotlib)) + (synopsis "Documentation for the python-matplotlib package") + (description (package-description python-matplotlib)) + (license (package-license python-matplotlib)))) -(define-public python2-matplotlib - (let ((matplotlib (package-with-python2 - (strip-python2-variant python-matplotlib)))) - (package (inherit matplotlib) - ;; Make sure to use special packages for Python 2 instead - ;; of those automatically rewritten by package-with-python2. - (native-inputs - `(("python2-sphinx" ,python2-sphinx-1.2.3) - ,@(fold alist-delete (package-native-inputs matplotlib) - '("python-sphinx")))) - (propagated-inputs - `(("python2-pycairo" ,python2-pycairo) - ("python2-pygobject-2" ,python2-pygobject-2) - ("python2-tkinter" ,python-2 "tk") - ,@(fold alist-delete (package-propagated-inputs matplotlib) - '("python-pycairo" "python-pygobject" "python-tkinter"))))))) +(define-public python2-matplotlib-documentation + (package-with-python2 python-matplotlib-documentation)) (define-public python2-pysnptools (package From 8e08604814d32f6f934932d5516f111bc2bb6d12 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 6 Mar 2017 15:46:06 +0100 Subject: [PATCH 382/436] gnu: python-pandas: Update to 0.19.2. * gnu/packages/python.scm (python-pandas, python2-pandas): Update to 0.19.2. [source]: Use 'pypi-uri'. --- gnu/packages/python.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7315df7325..f1cf98a527 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1165,16 +1165,13 @@ datetime module, available in Python 2.3+.") (define-public python-pandas (package (name "python-pandas") - (version "0.18.1") + (version "0.19.2") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/11/09/" - "e66eb844daba8680ddff26335d5b4fead77f60f957678243549a8dd4830d/" - "pandas-" version ".tar.gz")) + (uri (pypi-uri "pandas" version)) (sha256 - (base32 "1ckpxrvvjj6zxmn68icd9hib8qcpx9b35f6izxnr25br5ilq7r6j")))) + (base32 "0540cnbwy2hc4hv2sxfs8i47xi91qzvzxfn80dl785ibiicly3vg")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy) From 6cb747769915e8ecef04fd5c5a625d535f4db1d7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 6 Mar 2017 16:09:23 +0100 Subject: [PATCH 383/436] gnu: python-statsmodels: Update to 0.8.0. * gnu/packages/statistics.scm (python-statsmodels, python2-statsmodels): Update to 0.8.0. [source]: Use 'pypi-uri'. [arguments]: Add more files to matplotlib backend substitution. * gnu/packages/patches/python-statsmodels-fix-tests.patch: Drop test that fails with numpy 1.12. Remove previous contents. --- .../python-statsmodels-fix-tests.patch | 220 +++--------------- gnu/packages/statistics.scm | 11 +- 2 files changed, 32 insertions(+), 199 deletions(-) diff --git a/gnu/packages/patches/python-statsmodels-fix-tests.patch b/gnu/packages/patches/python-statsmodels-fix-tests.patch index 3315ddbd5f..f910b4b5a5 100644 --- a/gnu/packages/patches/python-statsmodels-fix-tests.patch +++ b/gnu/packages/patches/python-statsmodels-fix-tests.patch @@ -1,196 +1,28 @@ -This patch fixes a couple of test failures introduced by changes to the pandas -package. It was extracted from this pull request: +This drops a test that fails with numpy 1.12. -https://github.com/statsmodels/statsmodels/pull/2675 +Upstream bug URL: https://github.com/statsmodels/statsmodels/issues/3541 - -From c9ef60a7bc4407766ab9e9f12c8a6b89013046ee Mon Sep 17 00:00:00 2001 -From: Ralf Gommers -Date: Tue, 20 Oct 2015 07:34:11 +0200 -Subject: [PATCH 1/4] MAINT: fix use of old_behavior kw for numpy.correlate. - Was removed in 1.10.0 - -Numpy PR that removed it: https://github.com/numpy/numpy/pull/5991 - -Closes gh-2667. ---- - statsmodels/tsa/ar_model.py | 6 ++---- - 1 file changed, 2 insertions(+), 4 deletions(-) - -diff --git a/statsmodels/tsa/ar_model.py b/statsmodels/tsa/ar_model.py -index 087a9e0..02984bd 100644 ---- a/statsmodels/tsa/ar_model.py -+++ b/statsmodels/tsa/ar_model.py -@@ -261,10 +261,8 @@ def _presample_varcov(self, params): - - Vpinv = np.zeros((p, p), dtype=params.dtype) - for i in range(1, p1): -- Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i], -- old_behavior=False)[:-1] -- Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0, -- old_behavior=False)[:-1] -+ Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i],)[:-1] -+ Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0,)[:-1] - - Vpinv = Vpinv + Vpinv.T - np.diag(Vpinv.diagonal()) - return Vpinv - -From f1dc8979b09bc1736149993f895943b3158ee2db Mon Sep 17 00:00:00 2001 -From: Ralf Gommers -Date: Wed, 21 Oct 2015 22:05:52 +0200 -Subject: [PATCH 2/4] MAINT: fix graphics module for changes in recent pandas - versions. - ---- - statsmodels/graphics/tests/test_mosaicplot.py | 2 +- - statsmodels/graphics/tests/test_tsaplots.py | 6 +++--- - statsmodels/graphics/tsaplots.py | 2 +- - 3 files changed, 5 insertions(+), 5 deletions(-) - -diff --git a/statsmodels/graphics/tests/test_mosaicplot.py b/statsmodels/graphics/tests/test_mosaicplot.py -index cb9bbbe..e41020e 100644 ---- a/statsmodels/graphics/tests/test_mosaicplot.py -+++ b/statsmodels/graphics/tests/test_mosaicplot.py -@@ -113,7 +113,7 @@ def test_mosaic(): - # sort by the marriage quality and give meaningful name - # [rate_marriage, age, yrs_married, children, - # religious, educ, occupation, occupation_husb] -- datas = datas.sort(['rate_marriage', 'religious']) -+ datas = datas.sort_values(by=['rate_marriage', 'religious']) - num_to_desc = {1: 'awful', 2: 'bad', 3: 'intermediate', - 4: 'good', 5: 'wonderful'} - datas['rate_marriage'] = datas['rate_marriage'].map(num_to_desc) -diff --git a/statsmodels/graphics/tests/test_tsaplots.py b/statsmodels/graphics/tests/test_tsaplots.py -index 511f18f..365be82 100644 ---- a/statsmodels/graphics/tests/test_tsaplots.py -+++ b/statsmodels/graphics/tests/test_tsaplots.py -@@ -1,4 +1,4 @@ --from statsmodels.compat.python import lmap, lzip, map -+from statsmodels.compat.python import lmap, map - import numpy as np - import pandas as pd - from numpy.testing import dec -@@ -51,8 +51,8 @@ def test_plot_month(): - dta = sm.datasets.elnino.load_pandas().data - dta['YEAR'] = dta.YEAR.astype(int).apply(str) - dta = dta.set_index('YEAR').T.unstack() -- dates = lmap(lambda x : pd.datetools.parse('1 '+' '.join(x)), -- dta.index.values) -+ dates = lmap(lambda x : pd.datetools.parse_time_string('1 '+' '.join(x))[0], -+ dta.index.values) - - # test dates argument - fig = month_plot(dta.values, dates=dates, ylabel='el nino') -diff --git a/statsmodels/graphics/tsaplots.py b/statsmodels/graphics/tsaplots.py -index 3d04692..94626c9 100644 ---- a/statsmodels/graphics/tsaplots.py -+++ b/statsmodels/graphics/tsaplots.py -@@ -200,7 +200,7 @@ def seasonal_plot(grouped_x, xticklabels, ylabel=None, ax=None): - ticks = [] - for season, df in grouped_x: - df = df.copy() # or sort balks for series. may be better way -- df.sort() -+ df.sort_values(inplace=True) - nobs = len(df) - x_plot = np.arange(start, start + nobs) - ticks.append(x_plot.mean()) - -From 4cfbef6af137629c6953f1f025d9cfc781874256 Mon Sep 17 00:00:00 2001 -From: Ralf Gommers -Date: Wed, 21 Oct 2015 22:15:25 +0200 -Subject: [PATCH 3/4] MAINT: work around pandas breaking backwards compat for - pandas.version - ---- - setup.py | 5 ++++- - statsmodels/tools/testing.py | 6 ++---- - 2 files changed, 6 insertions(+), 5 deletions(-) - -diff --git a/setup.py b/setup.py -index 0002840..74aefb8 100644 ---- a/setup.py -+++ b/setup.py -@@ -134,7 +134,10 @@ def check_dependency_versions(min_versions): - (spversion, min_versions['scipy'])) - - try: -- from pandas.version import short_version as pversion -+ import pandas -+ #FIXME: this will break for pandas 1.0.0. Needs elaborate parsing now, -+ # due to pandas removing version.short_version -+ pversion = pandas.__version__[:6] - except ImportError: - install_requires.append('pandas') - else: -diff --git a/statsmodels/tools/testing.py b/statsmodels/tools/testing.py -index e207e44..643f79f 100644 ---- a/statsmodels/tools/testing.py -+++ b/statsmodels/tools/testing.py -@@ -16,10 +16,8 @@ def strip_rc(version): - - - def is_pandas_min_version(min_version): -- '''check whether pandas is at least min_version -- ''' -- from pandas.version import short_version as pversion -- return StrictVersion(strip_rc(pversion)) >= min_version -+ '''check whether pandas is at least min_version ''' -+ return StrictVersion((pandas.__version__[:6])) >= min_version - - - # local copies, all unchanged - -From c894c3f4882d570efb517950069d83afa9794db8 Mon Sep 17 00:00:00 2001 -From: Ralf Gommers -Date: Mon, 26 Oct 2015 20:47:51 +0100 -Subject: [PATCH 4/4] BUG: fix use of Series.sort_values for older pandas. - -Some failing tests in the previous commits because older ``pandas`` versions -don't have ``Series.sort_values``. That method was only added in pandas 0.17, -in https://github.com/pydata/pandas/pull/10726 ---- - statsmodels/graphics/tests/test_mosaicplot.py | 6 +++++- - statsmodels/graphics/tsaplots.py | 6 +++++- - 2 files changed, 10 insertions(+), 2 deletions(-) - -diff --git a/statsmodels/graphics/tests/test_mosaicplot.py b/statsmodels/graphics/tests/test_mosaicplot.py -index e41020e..2a873e7 100644 ---- a/statsmodels/graphics/tests/test_mosaicplot.py -+++ b/statsmodels/graphics/tests/test_mosaicplot.py -@@ -113,7 +113,11 @@ def test_mosaic(): - # sort by the marriage quality and give meaningful name - # [rate_marriage, age, yrs_married, children, - # religious, educ, occupation, occupation_husb] -- datas = datas.sort_values(by=['rate_marriage', 'religious']) -+ if pandas.__version__ < '0.17.0': -+ datas = datas.sort(['rate_marriage', 'religious']) -+ else: -+ datas = datas.sort_values(by=['rate_marriage', 'religious']) -+ - num_to_desc = {1: 'awful', 2: 'bad', 3: 'intermediate', - 4: 'good', 5: 'wonderful'} - datas['rate_marriage'] = datas['rate_marriage'].map(num_to_desc) -diff --git a/statsmodels/graphics/tsaplots.py b/statsmodels/graphics/tsaplots.py -index 94626c9..217724f 100644 ---- a/statsmodels/graphics/tsaplots.py -+++ b/statsmodels/graphics/tsaplots.py -@@ -2,6 +2,7 @@ - - - import numpy as np -+import pandas - - from statsmodels.graphics import utils - from statsmodels.tsa.stattools import acf, pacf -@@ -200,7 +201,10 @@ def seasonal_plot(grouped_x, xticklabels, ylabel=None, ax=None): - ticks = [] - for season, df in grouped_x: - df = df.copy() # or sort balks for series. may be better way -- df.sort_values(inplace=True) -+ if pandas.__version__ < '0.17.0': -+ df.sort() -+ else: -+ df.sort_values(inplace=True) - nobs = len(df) - x_plot = np.arange(start, start + nobs) - ticks.append(x_plot.mean()) +--- a/statsmodels/discrete/tests/test_discrete.py 2017-03-06 15:29:19.947343331 +0000 ++++ b/statsmodels/discrete/tests/test_discrete.py 2017-03-06 15:29:37.759328845 +0000 +@@ -1329,21 +1329,6 @@ + res = mod.fit(start_params=-np.ones(4), method='newton', disp=0) + assert_(not res.mle_retvals['converged']) + +-def test_issue_339(): +- # make sure MNLogit summary works for J != K. +- data = sm.datasets.anes96.load() +- exog = data.exog +- # leave out last exog column +- exog = exog[:,:-1] +- exog = sm.add_constant(exog, prepend=True) +- res1 = sm.MNLogit(data.endog, exog).fit(method="newton", disp=0) +- # strip the header from the test +- smry = "\n".join(res1.summary().as_text().split('\n')[9:]) +- cur_dir = os.path.dirname(os.path.abspath(__file__)) +- test_case_file = os.path.join(cur_dir, 'results', 'mn_logit_summary.txt') +- test_case = open(test_case_file, 'r').read() +- np.testing.assert_equal(smry, test_case[:-1]) +- + def test_issue_341(): + data = sm.datasets.anes96.load() + exog = data.exog diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 139ac71834..bfa4cafe1e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1437,15 +1437,14 @@ building design matrices.") (define-public python-statsmodels (package (name "python-statsmodels") - (version "0.6.1") + (version "0.8.0") (source (origin (method url-fetch) - (uri (string-append "https://pypi.python.org/packages/source/" - "s/statsmodels/statsmodels-" version ".tar.gz")) + (uri (pypi-uri "statsmodels" version)) (sha256 (base32 - "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy")) + "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6")) (patches (search-patches "python-statsmodels-fix-tests.patch")))) (build-system python-build-system) (arguments @@ -1457,7 +1456,9 @@ building design matrices.") (lambda _ ;; Set the matplotlib backend to Agg to avoid problems using the ;; GTK backend without a display. - (substitute* (find-files "statsmodels/graphics/tests" "\\.py") + (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py") + '("statsmodels/tsa/vector_ar/tests/test_var.py" + "statsmodels/duration/tests/test_survfunc.py")) (("import matplotlib\\.pyplot as plt" line) (string-append "import matplotlib;matplotlib.use('Agg');" line))) From 5eefa50abdc9e0bc1c2cd9b5bd624592e6c1f07a Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Sat, 25 Feb 2017 23:35:22 +0100 Subject: [PATCH 384/436] gnu: Remove python-sphinx-1.2.3. * gnu/packages/python.scm (python-sphinx-1.2.3, python2-sphinx-1.2.3): Remove variables. Signed-off-by: Marius Bakke --- gnu/packages/python.scm | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f1cf98a527..876ce900a1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3089,24 +3089,6 @@ sources.") (propagated-inputs `(("python2-pytz" ,python2-pytz) ,@(package-propagated-inputs base)))))) -;; This is needed for python-matplotlib@1.4 and python-scipy@0.16, at least. -;; Try removing this when they are updated. -(define-public python-sphinx-1.2.3 - (package (inherit python-sphinx) - (version "1.2.3") - (source (origin - (method url-fetch) - (uri (pypi-uri "Sphinx" version)) - (sha256 - (base32 - "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl")))) - ;; XXX: "'NoneType' object has no attribute 'split'". - (arguments '(#:tests? #f)))) - -(define-public python2-sphinx-1.2.3 - (package (inherit (package-with-python2 - (strip-python2-variant python-sphinx-1.2.3))))) - (define-public python-sphinx-rtd-theme (package (name "python-sphinx-rtd-theme") From 46d6219d41e98d20797fc075becdeecec73c7327 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 4 Mar 2017 17:23:14 +0100 Subject: [PATCH 385/436] gnu: rofi: Fix test failure. * gnu/packages/xdisorg.scm (rofi)[arguments]: Disable parallel tests. --- gnu/packages/xdisorg.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 7d4209d126..5afc495ad7 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1003,7 +1003,8 @@ connectivity of the X server running on a particular @code{DISPLAY}.") (native-inputs `(("pkg-config" ,pkg-config))) (arguments - `(#:phases + `(#:parallel-tests? #f ; May fail in some circumstances. + #:phases (modify-phases %standard-phases (add-before 'configure 'adjust-tests (lambda _ From ba062b3ec4367919daf3ad458b88b710042fc678 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Mon, 6 Mar 2017 15:33:34 +0100 Subject: [PATCH 386/436] gnu: python-colorspacious: Run tests. * gnu/packages/python.scm (python-colorspacious, python2-colorspacious)[native-inputs]: Add python-nose. [arguments]: Add custom 'check phase which runs nosetests. Signed-off-by: Marius Bakke --- gnu/packages/python.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 876ce900a1..a271ad46b7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3837,6 +3837,14 @@ To address this and enable easy cycling over arbitrary @code{kwargs}, the (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy))) + (native-inputs + `(("python-nose" ,python-nose))) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "nosetests" "--all-modules" "-v" "colorspacious"))))))) (home-page "https://github.com/njsmith/colorspacious") (synopsis "Python library for colorspace conversions") (description "@code{colorspacious} is a Python library that lets you From ecc4324fef26b5ba14031fe203ebdec1b2cd1fec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 6 Mar 2017 22:51:22 +0100 Subject: [PATCH 387/436] system: grub: Add missing URL in comment. * gnu/system/grub.scm (grub-root-search): Add missing URL in comment. --- gnu/system/grub.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/system/grub.scm b/gnu/system/grub.scm index b18b8be6d7..1f2cd08ff0 100644 --- a/gnu/system/grub.scm +++ b/gnu/system/grub.scm @@ -255,7 +255,7 @@ code." "" (match device ;; Preferably refer to DEVICE by its UUID or label. This is more - ;; efficient and less ambiguous, see <>. + ;; efficient and less ambiguous, see . ((? bytevector? uuid) (format #f "search --fs-uuid --set ~a" (uuid->string device))) From 909de139e7f6ab474e6e510a3c15bb4b4731b8cf Mon Sep 17 00:00:00 2001 From: David Craven Date: Tue, 14 Feb 2017 16:28:33 +0100 Subject: [PATCH 388/436] vm: Fix full-boot? option. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/system/vm.scm (virtualized-operating-system): Add full-boot? option. Don't add a %store-mapping when full-boot? is passed. This leads the grub-configuration-file procedure to look for the kernel and initrd in / instead of /gnu/store. Signed-off-by: Ludovic Courtès --- gnu/system/vm.scm | 34 +++++++++++++++++++++------------- 1 file changed, 21 insertions(+), 13 deletions(-) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 103af37c9a..5c6e7f684a 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -365,7 +365,7 @@ of the GNU system as described by OS." (check? #f) (create-mount-point? #t))))) -(define (virtualized-operating-system os mappings) +(define* (virtualized-operating-system os mappings #:optional (full-boot? #f)) "Return an operating system based on OS suitable for use in a virtualized environment with the store shared with the host. MAPPINGS is a list of to realize in the virtualized OS." @@ -381,6 +381,15 @@ environment with the store shared with the host. MAPPINGS is a list of (string-prefix? "/dev/" source))))) (operating-system-file-systems os))) + (define virtual-file-systems + (cons (file-system + (mount-point "/") + (device "/dev/vda1") + (type "ext4")) + + (append (map mapping->file-system mappings) + user-file-systems))) + (operating-system (inherit os) (initrd (lambda (file-systems . rest) (apply base-initrd file-systems @@ -391,17 +400,16 @@ environment with the store shared with the host. MAPPINGS is a list of ;; Disable swap. (swap-devices '()) - (file-systems (cons* (file-system - (mount-point "/") - (device "/dev/vda1") - (type "ext4")) - - (file-system (inherit - (mapping->file-system %store-mapping)) - (needed-for-boot? #t)) - - (append (map mapping->file-system mappings) - user-file-systems))))) + ;; XXX: When FULL-BOOT? is true, do not add a 9p mount for /gnu/store + ;; since that would lead the bootloader config to look for the kernel and + ;; initrd in it. + (file-systems (if full-boot? + virtual-file-systems + (cons + (file-system + (inherit (mapping->file-system %store-mapping)) + (needed-for-boot? #t)) + virtual-file-systems))))) (define* (system-qemu-image/shared-store os @@ -474,7 +482,7 @@ When FULL-BOOT? is true, the returned script runs everything starting from the bootloader; otherwise it directly starts the operating system kernel. The DISK-IMAGE-SIZE parameter specifies the size in bytes of the root disk image; it is mostly useful when FULL-BOOT? is true." - (mlet* %store-monad ((os -> (virtualized-operating-system os mappings)) + (mlet* %store-monad ((os -> (virtualized-operating-system os mappings full-boot?)) (os-drv (operating-system-derivation os)) (image (system-qemu-image/shared-store os From 45321beb7d6cc92ff20ef1811bcc8119bb822ed9 Mon Sep 17 00:00:00 2001 From: Mekeor Melire Date: Mon, 6 Mar 2017 20:07:45 +0100 Subject: [PATCH 389/436] gnu: surf: Add 'dmenu' and 'xprop' to 'inputs'. 'dmenu' and 'xprop' are necessary to open a new URL in surf. * gnu/packages/suckless.scm (surf)[inputs]: Add dmenu and xprop. [arguments]: Add 'set-dmenu-and-xprop-file-name' phase to patch the paths to the 'dmenu' and 'xprop' binaries in surf's configuration file. Signed-off-by: Kei Kebreau --- gnu/packages/suckless.scm | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/gnu/packages/suckless.scm b/gnu/packages/suckless.scm index e30a0883a3..80a02e1718 100644 --- a/gnu/packages/suckless.scm +++ b/gnu/packages/suckless.scm @@ -255,11 +255,20 @@ drawing.") (string-append "PREFIX=" %output)) #:phases (modify-phases %standard-phases - (delete 'configure)))) + (delete 'configure) + ;; Use the right file name for dmenu and xprop. + (add-before 'build 'set-dmenu-and-xprop-file-name + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "config.def.h" + (("dmenu") (string-append (assoc-ref inputs "dmenu") "/bin/dmenu")) + (("xprop") (string-append (assoc-ref inputs "xprop") "/bin/xprop"))) + #t))))) (inputs - `(("glib-networking" ,glib-networking) + `(("dmenu" ,dmenu) + ("glib-networking" ,glib-networking) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("webkitgtk" ,webkitgtk/gtk+-2))) + ("webkitgtk" ,webkitgtk/gtk+-2) + ("xprop" ,xprop))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://surf.suckless.org/") From c402743579e3ba745c3f759889c00b52acae05fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Sun, 5 Mar 2017 19:08:25 +0800 Subject: [PATCH 390/436] gnu: Add blind. * gnu/packages/suckless.scm (blind): New package. --- gnu/packages/suckless.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/suckless.scm b/gnu/packages/suckless.scm index 80a02e1718..ca4cbec91f 100644 --- a/gnu/packages/suckless.scm +++ b/gnu/packages/suckless.scm @@ -47,6 +47,33 @@ #:use-module (gnu packages base) #:use-module (gnu packages libbsd)) +(define-public blind + (package + (name "blind") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append "http://dl.suckless.org/tools/blind-" + version ".tar.gz")) + (sha256 + (base32 + "1b36k8fg2gmabm69jckqja49i8y4rcbccgvv2wija15ciszrm1x9")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ; no check target + #:make-flags (list + "CC=gcc" + (string-append "PREFIX=" %output)) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) ; no configure script + (synopsis "Command line video editing utilities") + (home-page "http://tools.suckless.org/blind/") + (description + "Blind is a collection of command line video editing utilities. It uses +a custom raw video format with a simple container.") + (license license:isc))) + (define-public dwm (package (name "dwm") From eaa72e3a1112251b9ed39f51d5964263614b5747 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 5 Mar 2017 10:53:34 +0100 Subject: [PATCH 391/436] gnu: asymptote: Update to 2.40. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/plotutils.scm (asymptote): Update to 2.40. Signed-off-by: 宋文武 --- gnu/packages/plotutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm index bf993c66a7..6d84bf2db6 100644 --- a/gnu/packages/plotutils.scm +++ b/gnu/packages/plotutils.scm @@ -173,14 +173,14 @@ colors, styles, options and details.") (define-public asymptote (package (name "asymptote") - (version "2.39") + (version "2.40") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/asymptote/" version "/asymptote-" version ".src.tgz")) (sha256 (base32 - "187q81yw06x4gv2spfn0hcs1064ym3a8l6mdgawymfhqd60yhrs3")))) + "08hy8hgh217df9kwznr22mg8vxxh3rbmbxgx3nqhxyggc9xqy544")))) (build-system gnu-build-system) ;; Note: The 'asy' binary retains a reference to docdir for use with its ;; "help" command in interactive mode, so adding a "doc" output is not From af1268752216829127b12d2043c36e64f0c48173 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 4 Mar 2017 22:10:41 -0800 Subject: [PATCH 392/436] gnu: guile-lib: Update to 0.2.5 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The build was broken since the URL of version 0.2.3 was changed. The archive was moved into an "old" subdirectory of the original location. * gnu/packages/guile.scm (guile-lib): Update to 0.2.5. [make-flags]: Add GUILE_AUTO_COMPILE to prevent guild errors. [phases]: Remove 'check replacement since it is no longer needed. Signed-off-by: Ludovic Courtès --- gnu/packages/guile.scm | 41 +++++++++++++++++++---------------------- 1 file changed, 19 insertions(+), 22 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 293579b1be..4440c6c602 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -632,32 +632,29 @@ The library is shipped with documentation in Info format and usage examples.") (define-public guile-lib (package (name "guile-lib") - (version "0.2.3") + (version "0.2.5") (source (origin - (method url-fetch) - (uri (string-append "mirror://savannah/guile-lib/guile-lib-" - version ".tar.gz")) - (sha256 - (base32 - "0pwdd52vakni1fabaiav8v0ad7xp3bx8x3brijbr1mpgamm9dxqc")))) + (method url-fetch) + (uri (string-append "mirror://savannah/guile-lib/guile-lib-" + version ".tar.gz")) + (sha256 + (base32 + "1qbk485djgxqrbfjvk4b7w7y4x9xygf2qb8dqnl7885kajasx8qg")))) (build-system gnu-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (add-before 'configure 'patch-module-dir - (lambda _ - (substitute* "src/Makefile.in" - (("^moddir = ([[:graph:]]+)") - "moddir = $(datadir)/guile/site/@GUILE_EFFECTIVE_VERSION@\n") - (("^godir = ([[:graph:]]+)") - "godir = \ + '(#:make-flags + '("GUILE_AUTO_COMPILE=0") ;to prevent guild errors + #:phases + (modify-phases %standard-phases + (add-before 'configure 'patch-module-dir + (lambda _ + (substitute* "src/Makefile.in" + (("^moddir = ([[:graph:]]+)") + "moddir = $(datadir)/guile/site/@GUILE_EFFECTIVE_VERSION@\n") + (("^godir = ([[:graph:]]+)") + "godir = \ $(libdir)/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n")) - #t)) - (replace 'check - (lambda _ - ;; Work around a harmless test failure involving - ;; two-spaces-after-period rendering. - (zero? (system* "make" "check" ;"-C" "unit-tests" - "XFAIL_TESTS=texinfo.serialize.scm"))))))) + #t))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("guile" ,guile-2.0))) (home-page "http://www.nongnu.org/guile-lib/") From 92966847130557ee99029d89b715a1701e5b04df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 7 Mar 2017 14:51:48 +0100 Subject: [PATCH 393/436] gnu: java-xz: Update to 1.6. * gnu/packages/java.scm (java-xz): Update to 1.6. --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 1ff106cb99..1d18a0b066 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -958,13 +958,13 @@ IcedTea build harness.") (define-public java-xz (package (name "java-xz") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (string-append "http://tukaani.org/xz/xz-java-" version ".zip")) (sha256 (base32 - "0x6vn9dp9kxk83x2fp3394n95dk8fx9yg8jns9371iqsn0vy8ih1")))) + "1z3p1ri1gvl07inxn0agx44ck8n7wrzfmvkz8nbq3njn8r9wba8x")))) (build-system ant-build-system) (arguments `(#:tests? #f ; There are no tests to run. From d6abd094fcffdbd5b693ba509e2de3da28c849ec Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 7 Mar 2017 10:28:57 +0000 Subject: [PATCH 394/436] gnu: python-rpy2: Propagate python2-singledispatch. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python.scm (python-rp2)[native-inputs]: Rename to... [propagated-inputs]: ... this. Signed-off-by: Ludovic Courtès --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a271ad46b7..1ce0cc47e3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4093,9 +4093,9 @@ functions.") (define-public python2-rpy2 (let ((rpy2 (package-with-python2 python-rpy2))) (package (inherit rpy2) - (native-inputs + (propagated-inputs `(("python2-singledispatch" ,python2-singledispatch) - ,@(package-native-inputs rpy2)))))) + ,@(package-propagated-inputs rpy2)))))) (define-public python-scipy (package From 605fec783f630b8aa92bbfeb510f716144de90d8 Mon Sep 17 00:00:00 2001 From: Sergei Trofimovich Date: Sun, 19 Feb 2017 19:31:58 +0000 Subject: [PATCH 395/436] gnu: Add basic support for "alpha-linux" systems. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/bootstrap.scm (glibc-dynamic-linker): Add "/lib/ld-linux.so.2" as "alpha-linux" ld.so. * gnu/packages/linux.scm (system->linux-architecture): Add "alpha" arch. Signed-off-by: Sergei Trofimovich Signed-off-by: Ludovic Courtès --- gnu/packages/bootstrap.scm | 1 + gnu/packages/linux.scm | 1 + 2 files changed, 2 insertions(+) diff --git a/gnu/packages/bootstrap.scm b/gnu/packages/bootstrap.scm index c8d94c8303..b4847094ba 100644 --- a/gnu/packages/bootstrap.scm +++ b/gnu/packages/bootstrap.scm @@ -167,6 +167,7 @@ successful, or false to signal an error." ((string=? system "i586-gnu") "/lib/ld.so.1") ((string=? system "i686-gnu") "/lib/ld.so.1") ((string=? system "aarch64-linux") "/lib/ld-linux-aarch64.so.1") + ((string=? system "alpha-linux") "/lib/ld-linux.so.2") ;; XXX: This one is used bare-bones, without a libc, so add a case ;; here just so we can keep going. diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 6e08473ec3..de0fd71776 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -106,6 +106,7 @@ ((string-prefix? "mips" arch) "mips") ((string-prefix? "arm" arch) "arm") ((string-prefix? "aarch64" arch) "arm64") + ((string-prefix? "alpha" arch) "alpha") (else arch)))) (define (linux-libre-urls version) From c1029f86e3a11518ee26c8fc994fb401fe2e581c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 7 Mar 2017 08:28:28 +0100 Subject: [PATCH 396/436] gnu: Add emacs-yasnippet. * gnu/packages/emacs.scm (emacs-yasnippet): New variable. --- gnu/packages/emacs.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index cc8d9c0d0c..1daf8e4e68 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -3832,3 +3832,23 @@ mode-line.") (description "Emacs minor mode for redisplaying parts of the buffer as pretty symbols.") (license license:gpl3+))) + +(define-public emacs-yasnippet + (package + (name "emacs-yasnippet") + (version "0.11.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/joaotavora/yasnippet/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "15di6mkkf09b7qddpsrm0qln02hji3sx8blya5jxssi9wxxx9iq5")))) + (build-system emacs-build-system) + (home-page "http://github.com/joaotavora/yasnippet") + (synopsis "Yet another snippet extension for Emacs") + (description + "YASnippet is a template system for Emacs. It allows you to type an +abbreviation and automatically expand it into function templates.") + (license license:gpl3+))) From f11275c9e52bca7964c86f3c7d9daee2dd4771a0 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 4 Mar 2017 18:07:26 -0500 Subject: [PATCH 397/436] gnu: gnupg: Update to 2.1.19. * gnu/packages/gnupg.scm (gnupg): Update to 2.1.19. [arguments]: Add 'patch-test-paths' phase and remove 'set-gnupg-home' phase. Add '--enable-gnupg-builddir-envvar' to #:configure-flags. [source]: Add 'gnupg-2.1-fix-Y2038-test-failure.patch'. * gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + gnu/packages/gnupg.scm | 37 +++++++--- .../gnupg-2.1-fix-Y2038-test-failure.patch | 67 +++++++++++++++++++ 3 files changed, 97 insertions(+), 8 deletions(-) create mode 100644 gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5dec691d01..e3bf241c8e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -596,6 +596,7 @@ dist_patch_DATA = \ %D%/packages/patches/gmp-faulty-test.patch \ %D%/packages/patches/gnome-tweak-tool-search-paths.patch \ %D%/packages/patches/gnucash-price-quotes-perl.patch \ + %D%/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch \ %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \ %D%/packages/patches/gobject-introspection-cc.patch \ %D%/packages/patches/gobject-introspection-girepository.patch \ diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index befd29961c..4fc9f38521 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -217,14 +217,15 @@ compatible to GNU Pth.") (define-public gnupg (package (name "gnupg") - (version "2.1.18") + (version "2.1.19") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) + (patches (search-patches "gnupg-2.1-fix-Y2038-test-failure.patch")) (sha256 (base32 - "157rrv3ly9j2k0acz43nhiba5hfl6h7048jvj55wwqjmgsmnyk6h")))) + "1w4vccmb5l50lm4yrz9vkdj7whbfvzx543r55362kkj1aqgyvk26")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -243,7 +244,11 @@ compatible to GNU Pth.") ("sqlite" ,sqlite) ("zlib" ,zlib))) (arguments - `(#:configure-flags '("--enable-gpg2-is-gpg") + `(#:configure-flags '("--enable-gpg2-is-gpg" + ;; Otherwise, the test suite looks for the `gpg` + ;; executable in its installation directory in + ;; /gnu/store before it has been installed. + "--enable-gnupg-builddir-envvar") #:phases (modify-phases %standard-phases (add-before 'configure 'patch-paths @@ -259,11 +264,27 @@ compatible to GNU Pth.") (("/usr/bin/env gpgscm") (string-append (getcwd) "/tests/gpgscm/gpgscm"))) #t)) - ;; If this variable is undefined, /bin/pwd is invoked. - (add-before 'check 'set-gnupg-home - (lambda _ - (setenv "GNUPGHOME" (getcwd)) - #t))))) + (add-before 'build 'patch-test-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((coreutils (assoc-ref inputs "coreutils")) + (cat (string-append coreutils "/bin/cat")) + (pwd (string-append coreutils "/bin/pwd")) + (true (string-append coreutils "/bin/true")) + (false (string-append coreutils "/bin/false"))) + (substitute* '("tests/inittests" + "tests/pkits/inittests" + "tests/Makefile" + "tests/pkits/common.sh" + "tests/pkits/Makefile" + ) + (("/bin/pwd") pwd)) + (substitute* "common/t-exectool.c" + (("/bin/cat") cat)) + (substitute* "common/t-exectool.c" + (("/bin/true") true)) + (substitute* "common/t-exectool.c" + (("/bin/false") false)) + #t)))))) (home-page "https://gnupg.org/") (synopsis "GNU Privacy Guard") (description diff --git a/gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch b/gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch new file mode 100644 index 0000000000..b3a198c499 --- /dev/null +++ b/gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch @@ -0,0 +1,67 @@ +Fix a Y2038 test failure on systems where time_t is a signed 32-bit value: + +https://bugs.gnupg.org/gnupg/issue2988 + +Patch copied from upstream source repository: + +https://git.gnupg.org/cgi-bin/gitweb.cgi?p=gnupg.git;a=commit;h=de3838372ae3cdecbd83eea2c53c8e2656d93052 + +From de3838372ae3cdecbd83eea2c53c8e2656d93052 Mon Sep 17 00:00:00 2001 +From: Justus Winter +Date: Tue, 7 Mar 2017 12:18:59 +0100 +Subject: [PATCH] tests: Avoid overflowing signed 32 bit time_t. + +* tests/openpgp/quick-key-manipulation.scm: Use expiration times in +the year 2038 instead of 2105 to avoid overflowing 32 bit time_t. +time_t is used internally to parse the expiraton time from the iso +timestamp. + +GnuPG-bug-id: 2988 +Signed-off-by: Justus Winter +--- + tests/openpgp/quick-key-manipulation.scm | 15 +++++++++++---- + 1 file changed, 11 insertions(+), 4 deletions(-) + +diff --git a/tests/openpgp/quick-key-manipulation.scm b/tests/openpgp/quick-key-manipulation.scm +index 10f0bfe21..08ef62613 100755 +--- a/tests/openpgp/quick-key-manipulation.scm ++++ b/tests/openpgp/quick-key-manipulation.scm +@@ -125,8 +125,13 @@ + (default default never) + (rsa "sign auth encr" "seconds=600") ;; GPGME uses this + (rsa "auth,encr" "2") ;; "without a letter, days is assumed" +- (rsa "sign" "2105-01-01") ;; "last year GnuPG can represent is 2105" +- (rsa "sign" "21050101T115500") ;; "last year GnuPG can represent is 2105" ++ ;; Sadly, the timestamp is truncated by the use of time_t on ++ ;; systems where time_t is a signed 32 bit value. ++ (rsa "sign" "2038-01-01") ;; unix millennium ++ (rsa "sign" "20380101T115500") ;; unix millennium ++ ;; Once fixed, we can use later timestamps: ++ ;; (rsa "sign" "2105-01-01") ;; "last year GnuPG can represent is 2105" ++ ;; (rsa "sign" "21050101T115500") ;; "last year GnuPG can represent is 2105" + (rsa sign "2d") + (rsa1024 sign "2w") + (rsa2048 encr "2m") +@@ -157,7 +162,8 @@ + (lambda (subkey) + (assert (= 1 (:alg subkey))) + (assert (string-contains? (:cap subkey) "s")) +- (assert (time-matches? 4260207600 ;; 2105-01-01 ++ (assert (time-matches? 2145916800 ;; 2038-01-01 ++ ;; 4260207600 ;; 2105-01-01 + (string->number (:expire subkey)) + ;; This is off by 12h, but I guess it just + ;; choses the middle of the day. +@@ -165,7 +171,8 @@ + (lambda (subkey) + (assert (= 1 (:alg subkey))) + (assert (string-contains? (:cap subkey) "s")) +- (assert (time-matches? 4260254100 ;; UTC 2105-01-01 11:55:00 ++ (assert (time-matches? 2145959700 ;; UTC 2038-01-01 11:55:00 ++ ;; 4260254100 ;; UTC 2105-01-01 11:55:00 + (string->number (:expire subkey)) + (minutes->seconds 5)))) + (lambda (subkey) +-- +2.12.0 + From 3391e2a0783ee098b7f521ef54a469f025805293 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 7 Mar 2017 16:03:00 -0500 Subject: [PATCH 398/436] gnu: khal: Update to 0.9.3. * gnu/packages/calendar.scm (khal): Update to 0.9.3. [native-inputs]: Use python-pytest-2.9.2. --- gnu/packages/calendar.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index 7831870c55..1e9a93ca93 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -84,13 +84,13 @@ data units.") (define-public khal (package (name "khal") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (pypi-uri "khal" version)) (sha256 (base32 - "1ryh5c7408w8gpql5s9mkxkvz1ngnds3xm43p7r96ynx8prr9swp")))) + "1iva6cw2x3p2jzjj6bsyx7lc7yxin4fsd37j9c96j07x16p4imyl")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -112,7 +112,8 @@ data units.") "/share/zoneinfo/Zulu")) (zero? (system* "py.test" "tests"))))))) (native-inputs - `(("python-pytest" ,python-pytest) + ;; XXX Uses tmpdir_factory, introduced in pytest 2.8. + `(("python-pytest" ,python-pytest-2.9.2) ("python-pytest-cov" ,python-pytest-cov) ("python-setuptools-scm" ,python-setuptools-scm) ;; Required for tests From 9bb766e70d03164cb902122f3bbfbf46547f6cda Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 7 Mar 2017 15:58:26 +0100 Subject: [PATCH 399/436] gnu: pcre2: Update to 10.23. * gnu/packages/pcre.scm (pcre2): Update to 10.23. [source]: Remove patch. [arguments]: Add phase to substitute /bin/echo reference. * gnu/packages/patches/pcre2-CVE-2016-3191.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../patches/pcre2-CVE-2016-3191.patch | 179 ------------------ gnu/packages/pcre.scm | 15 +- 3 files changed, 11 insertions(+), 184 deletions(-) delete mode 100644 gnu/packages/patches/pcre2-CVE-2016-3191.patch diff --git a/gnu/local.mk b/gnu/local.mk index e3bf241c8e..ee40c1bd30 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -811,7 +811,6 @@ dist_patch_DATA = \ %D%/packages/patches/patchutils-xfail-gendiff-tests.patch \ %D%/packages/patches/patch-hurd-path-max.patch \ %D%/packages/patches/pcre-CVE-2016-3191.patch \ - %D%/packages/patches/pcre2-CVE-2016-3191.patch \ %D%/packages/patches/perl-autosplit-default-time.patch \ %D%/packages/patches/perl-deterministic-ordering.patch \ %D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \ diff --git a/gnu/packages/patches/pcre2-CVE-2016-3191.patch b/gnu/packages/patches/pcre2-CVE-2016-3191.patch deleted file mode 100644 index 80f9d3d4f1..0000000000 --- a/gnu/packages/patches/pcre2-CVE-2016-3191.patch +++ /dev/null @@ -1,179 +0,0 @@ -Fixes CVE-2016-3191 (remote execution of arbitrary code or denial of -service (stack-based buffer overflow) via a crafted regular expression). - -See . - -This is svn r489 at , omitting the -changes to 'testdata/testoutput8-16-4', which does not exist in the -source tarball. - -git-svn-id: svn://vcs.exim.org/pcre2/code/trunk@489 6239d852-aaf2-0410-a92c-79f79f948069 ---- - ChangeLog | 4 ++++ - src/pcre2_compile.c | 16 ++++++++++++++-- - testdata/testinput8 | 2 ++ - testdata/testoutput8-16-2 | 3 +++ - testdata/testoutput8-16-3 | 3 +++ - testdata/testoutput8-16-4 | 3 +++ - testdata/testoutput8-32-2 | 3 +++ - testdata/testoutput8-32-3 | 3 +++ - testdata/testoutput8-32-4 | 3 +++ - testdata/testoutput8-8-2 | 3 +++ - testdata/testoutput8-8-3 | 3 +++ - testdata/testoutput8-8-4 | 3 +++ - 12 files changed, 47 insertions(+), 2 deletions(-) - -diff --git a/ChangeLog b/ChangeLog -index 3ce0207..65e333e 100644 ---- a/ChangeLog -+++ b/ChangeLog -@@ -58,6 +58,10 @@ some head-scratching the next time this happens. - assertion, caused pcre2test to output a very large number of spaces when the - callout was taken, making the program appearing to loop. - -+12. A pattern that included (*ACCEPT) in the middle of a sufficiently deeply -+nested set of parentheses of sufficient size caused an overflow of the -+compiling workspace (which was diagnosed, but of course is not desirable). -+ - - Version 10.21 12-January-2016 - ----------------------------- -diff --git a/src/pcre2_compile.c b/src/pcre2_compile.c -index e33d620..887fbfd 100644 ---- a/src/pcre2_compile.c -+++ b/src/pcre2_compile.c -@@ -5901,10 +5901,22 @@ for (;; ptr++) - goto FAILED; - } - cb->had_accept = TRUE; -+ -+ /* In the first pass, just accumulate the length required; -+ otherwise hitting (*ACCEPT) inside many nested parentheses can -+ cause workspace overflow. */ -+ - for (oc = cb->open_caps; oc != NULL; oc = oc->next) - { -- *code++ = OP_CLOSE; -- PUT2INC(code, 0, oc->number); -+ if (lengthptr != NULL) -+ { -+ *lengthptr += CU2BYTES(1) + IMM2_SIZE; -+ } -+ else -+ { -+ *code++ = OP_CLOSE; -+ PUT2INC(code, 0, oc->number); -+ } - } - setverb = *code++ = - (cb->assert_depth > 0)? OP_ASSERT_ACCEPT : OP_ACCEPT; -diff --git a/testdata/testinput8 b/testdata/testinput8 -index ca3b1b9..7e2a1f0 100644 ---- a/testdata/testinput8 -+++ b/testdata/testinput8 -@@ -182,4 +182,6 @@ - - /((?1)(?2)(?3)(?4)(?5)(?6)(?7)(?8)(?9)(?9)(?8)(?7)(?6)(?5)(?4)(?3)(?2)(?1)(?0)){2,}()()()()()()()()()/debug - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+ - # End of testinput8 -diff --git a/testdata/testoutput8-16-2 b/testdata/testoutput8-16-2 -index 05669bb..a5e8dec 100644 ---- a/testdata/testoutput8-16-2 -+++ b/testdata/testoutput8-16-2 -@@ -1027,4 +1027,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 186 at offset 490: regular expression is too complicated -+ - # End of testinput8 -diff --git a/testdata/testoutput8-16-3 b/testdata/testoutput8-16-3 -index 31884e1..36133b3 100644 ---- a/testdata/testoutput8-16-3 -+++ b/testdata/testoutput8-16-3 -@@ -1023,4 +1023,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 114 at offset 509: missing closing parenthesis -+ - # End of testinput8 -diff --git a/testdata/testoutput8-32-2 b/testdata/testoutput8-32-2 -index babd0c7..99c4fad 100644 ---- a/testdata/testoutput8-32-2 -+++ b/testdata/testoutput8-32-2 -@@ -1023,4 +1023,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 114 at offset 509: missing closing parenthesis -+ - # End of testinput8 -diff --git a/testdata/testoutput8-32-3 b/testdata/testoutput8-32-3 -index babd0c7..99c4fad 100644 ---- a/testdata/testoutput8-32-3 -+++ b/testdata/testoutput8-32-3 -@@ -1023,4 +1023,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 114 at offset 509: missing closing parenthesis -+ - # End of testinput8 -diff --git a/testdata/testoutput8-32-4 b/testdata/testoutput8-32-4 -index babd0c7..99c4fad 100644 ---- a/testdata/testoutput8-32-4 -+++ b/testdata/testoutput8-32-4 -@@ -1023,4 +1023,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 114 at offset 509: missing closing parenthesis -+ - # End of testinput8 -diff --git a/testdata/testoutput8-8-2 b/testdata/testoutput8-8-2 -index 6a9aa0a..6dc1f42 100644 ---- a/testdata/testoutput8-8-2 -+++ b/testdata/testoutput8-8-2 -@@ -1026,4 +1026,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 114 at offset 509: missing closing parenthesis -+ - # End of testinput8 -diff --git a/testdata/testoutput8-8-3 b/testdata/testoutput8-8-3 -index 2fe1168..ae14946 100644 ---- a/testdata/testoutput8-8-3 -+++ b/testdata/testoutput8-8-3 -@@ -1024,4 +1024,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 114 at offset 509: missing closing parenthesis -+ - # End of testinput8 -diff --git a/testdata/testoutput8-8-4 b/testdata/testoutput8-8-4 -index 91993b2..6c79956 100644 ---- a/testdata/testoutput8-8-4 -+++ b/testdata/testoutput8-8-4 -@@ -1022,4 +1022,7 @@ Capturing subpattern count = 10 - May match empty string - Subject length lower bound = 0 - -+/([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00]([00](*ACCEPT)/ -+Failed: error 114 at offset 509: missing closing parenthesis -+ - # End of testinput8 --- -2.8.3 - diff --git a/gnu/packages/pcre.scm b/gnu/packages/pcre.scm index fe9157af12..8b92e47a4d 100644 --- a/gnu/packages/pcre.scm +++ b/gnu/packages/pcre.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2015 Ricardo Wurmus ;;; Copyright © 2016 Leo Famulari +;;; Copyright © 2017 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -73,16 +74,15 @@ POSIX regular expression API.") (define-public pcre2 (package (name "pcre2") - (version "10.21") + (version "10.23") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/pcre/pcre2/" version "/pcre2-" version ".tar.bz2")) - (patches (search-patches "pcre2-CVE-2016-3191.patch")) (sha256 (base32 - "1q6lrj9b08l1q39vxipb0fi88x6ybvkr6439h8bjb9r8jd81fsn6")))) + "0vn5g0mkkp99mmzpissa06hpyj6pk9s4mlwbjqrjvw3ihy8rpiyz")))) (build-system gnu-build-system) (inputs `(("bzip2" ,bzip2) ("readline" ,readline) @@ -95,7 +95,14 @@ POSIX regular expression API.") "--enable-unicode-properties" "--enable-pcre2-16" "--enable-pcre2-32" - "--enable-jit"))) + "--enable-jit") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda _ + (substitute* "RunGrepTest" + (("/bin/echo") (which "echo"))) + #t))))) (synopsis "Perl Compatible Regular Expressions") (description "The PCRE library is a set of functions that implement regular expression From faa65e2735d62254edb7cc897f91feae80e7c8d2 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 7 Mar 2017 13:35:39 +0100 Subject: [PATCH 400/436] gnu: kdevelop: Upgrade to 5.0.4. * gnu/packages/kde.scm (kdevelop, kdevplatform): Upgrade to 5.0.4. (kdevplatform)[source]: Use kde mirror instead of github. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index aef56bb202..03cfd0ee7b 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -39,7 +39,7 @@ (define-public kdevelop (package (name "kdevelop") - (version "5.0.3") + (version "5.0.4") (source (origin (method url-fetch) @@ -48,7 +48,7 @@ version ".tar.xz")) (sha256 (base32 - "00gn2c66pyd9qaa0zhn2lqam0zsg7fbyi13hk32wclxq73y8v98p")))) + "0max4g1i8xf5g7a8zm60qkr2j8w5bsqzxz914z43fj5ipnr4448r")))) (build-system cmake-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -148,15 +148,15 @@ for some KDevelop language plugins (Ruby, PHP, CSS...).") (define-public kdevplatform (package (name "kdevplatform") - (version "5.0.3") + (version "5.0.4") (source (origin (method url-fetch) - (uri (string-append "https://github.com/KDE/kdevplatform/archive/v" - version ".tar.gz")) + (uri (string-append "mirror://kde/stable/kdevelop" + "/" version "/src/kdevplatform-" + version ".tar.xz")) (sha256 (base32 - "1k40wg08iwyswnpbs4bfh4yq38pp0qi78shjh4pf7yfa2kbid30j")) - (file-name (string-append name "-" version ".tar.gz")))) + "0wfl5azblnpmc7hydfvm7450343m1v7cr2g9gw0qs1432gbzraq1")))) (build-system cmake-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) From 6c5b56f9fa01b7fe9034bac47b20e08a2fdb2629 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 7 Mar 2017 23:42:13 +0100 Subject: [PATCH 401/436] gnu: bash: Use the bootstrap Guile in 'url-fetch/reset-patch-level'. Fixes . Reported by Sirgazil, Ricardo Wurmus, Andy Wingo, and others. * guix/download.scm (in-band-download): Always use GUILE. This reverts 9f05908fb1e3707cae593d94688748294717a546. * gnu/packages/bash.scm (url-fetch/reset-patch-level): Remove #:guile. Pass %BOOTSTRAP-GUILE as #:guile to 'url-fetch'. Remove #:guile-for-build argument in 'gexp->derivation' call. --- gnu/packages/bash.scm | 9 ++++++--- guix/download.scm | 5 +---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm index c3b94391e1..388f5271c1 100644 --- a/gnu/packages/bash.scm +++ b/gnu/packages/bash.scm @@ -21,6 +21,7 @@ (define-module (gnu packages bash) #:use-module (guix licenses) #:use-module (gnu packages) + #:use-module (gnu packages bootstrap) #:use-module (gnu packages ncurses) #:use-module (gnu packages readline) #:use-module (gnu packages bison) @@ -243,14 +244,17 @@ without modification.") (define* (url-fetch/reset-patch-level url hash-algo hash #:optional name - #:key (system (%current-system)) guile) + #:key (system (%current-system))) "Fetch the Bash patch from URL and reset its 'PATCHLEVEL' definition so it can apply to a patch-level 0 Bash." + ;; Note: Forcefully use %BOOTSTRAP-GUILE here to work around bootstrapping + ;; issues when using a daemon that lacks the "download" built-in. See + ;; . (mlet* %store-monad ((name -> (or name (basename url))) (patch (url-fetch url hash-algo hash (string-append name ".orig") #:system system - #:guile guile))) + #:guile %bootstrap-guile))) (gexp->derivation name (with-imported-modules '((guix build utils)) #~(begin @@ -259,7 +263,6 @@ can apply to a patch-level 0 Bash." (substitute* #$output (("PATCHLEVEL [0-6]+") "PATCHLEVEL 0")))) - #:guile-for-build guile #:system system))) (define bash/fixed ;CVE-2017-5932 (RCE with completion) diff --git a/guix/download.scm b/guix/download.scm index 86f8598812..813f51f489 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -418,10 +418,7 @@ GnuTLS itself and its dependencies. See ." ;; hash of the expected result. #:verify-certificate? #f))))) - (mlet %store-monad ((guile (package->derivation - (or guile - (@@ (gnu packages bootstrap) %bootstrap-guile)) - system))) + (mlet %store-monad ((guile (package->derivation guile system))) (gexp->derivation file-name builder #:guile-for-build guile #:system system From 745c687be3fa6eeee97bd70141104156d8d8b811 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 9 Feb 2017 14:34:57 +0100 Subject: [PATCH 402/436] gnu: r: Fix syntax for INSTALL_OPTS. This is a follow-up to commit 4621acfd8272fa93d0530faa5f015b26a194b587. * gnu/packages/statistics.scm (r)[arguments]: Ensure that "--built-timestamp" appears on the same line as the other INSTALL_OPTS. --- gnu/packages/statistics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index bfa4cafe1e..db719f64dd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -131,8 +131,9 @@ be output in text, PostScript, PDF or HTML.") (add-after 'unpack 'build-recommended-packages-reproducibly (lambda _ (substitute* "src/library/Recommended/Makefile.in" - (("INSTALL_OPTS =.*" line) - (string-append line " --built-timestamp=1970-01-01"))) + (("INSTALL_OPTS =(.*)" line rest ) + (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01" + rest))) #t)) (add-before 'configure 'set-default-pager ;; Set default pager to "cat", because otherwise it is "false", From beaa026aa78a264e86668c0faa9af1f1f9b26b6b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 9 Feb 2017 15:40:02 +0100 Subject: [PATCH 403/436] gnu: r: Fix more reproducibility problems. * gnu/packages/statistics.scm (r)[arguments]: Patch locations in the build system that need special treatment for reproducibility. --- gnu/packages/statistics.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index db719f64dd..65e5c2e93b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -134,6 +134,16 @@ be output in text, PostScript, PDF or HTML.") (("INSTALL_OPTS =(.*)" line rest ) (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01" rest))) + ;; Ensure that gzipped files are reproducible + (substitute* '("src/library/grDevices/Makefile.in" + "doc/manual/Makefile.in") + (("R_GZIPCMD\\)" line) + (string-append line " -n"))) + ;; This library is installed using "install_package_description", + ;; so we need to pass the "builtStamp" argument. + (substitute* "src/library/tools/Makefile.in" + (("(install_package_description\\(.*\"')\\)\"" line prefix) + (string-append prefix ", builtStamp='1970-01-01')\""))) #t)) (add-before 'configure 'set-default-pager ;; Set default pager to "cat", because otherwise it is "false", From 3a38cf2dfdd8a03b4202ab8794fd2215b38ce680 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 8 Mar 2017 17:18:11 +0100 Subject: [PATCH 404/436] gnu: libinput: Update to 1.6.3. * gnu/packages/freedesktop.scm (libinput, libinput-minimal): Update to 1.6.3. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index f9007b1b36..4c15d4b2b0 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -88,14 +88,14 @@ freedesktop.org project.") (define-public libinput (package (name "libinput") - (version "1.6.0") + (version "1.6.3") (source (origin (method url-fetch) (uri (string-append "https://freedesktop.org/software/libinput/" name "-" version ".tar.xz")) (sha256 (base32 - "0cjq4mjqx8c7iiign330s34dvpw38rlv8byaxlx68p3kim8lylxp")))) + "18bx2fz04mf41nf3021pr9k3f741zvc6i8pzvypc6ycffac2gnkl")))) (build-system gnu-build-system) (native-inputs `(("cairo" ,cairo) From 9c974c93663b00a4cb1442d81c526a7bfcb8d4a1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 8 Mar 2017 17:37:51 +0100 Subject: [PATCH 405/436] gnu: iperf: Update to 3.1.7. * gnu/packages/networking.scm (iperf): Update to 3.1.7. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index fe9e6a5933..95253687cd 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1007,14 +1007,14 @@ that block port 22.") (define-public iperf (package (name "iperf") - (version "3.1.3") + (version "3.1.7") (source (origin (method url-fetch) (uri (string-append "http://downloads.es.net/pub/iperf" "/iperf-" version ".tar.gz")) (sha256 (base32 - "1gwmhm29zlp5grrpglmqj7vgx19s6xy33hk6hpbn8jnpn5lxpn30")))) + "0kvk8d0a3dcxc8fisyprbn01y8akxj4sx8ld5dh508p9dx077vx4")))) (build-system gnu-build-system) (synopsis "TCP, UDP and SCTP bandwidth measurement tool") (description From 1eaaea41e57ffd51cb548eeb4c5f708bb066c065 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Wed, 8 Mar 2017 13:53:08 +0100 Subject: [PATCH 406/436] gnu: python-matplotlib-documentation: Fix build. * gnu/packages/python.scm (python-matplotlib-documentation)[native-inputs]: Add python-mock and graphviz. [arguments]: Use separate build and install phases; correctly set latex paper size. Signed-off-by: Marius Bakke --- gnu/packages/python.scm | 61 +++++++++++++++++++++-------------------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1ce0cc47e3..70fd1557b4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3968,6 +3968,8 @@ toolkits.") ("python-sphinx" ,python-sphinx) ("python-numpydoc" ,python-numpydoc) ("python-ipython" ,python-ipython) + ("python-mock" ,python-mock) + ("graphviz" ,graphviz) ("texlive" ,texlive) ("texinfo" ,texinfo) ,@(package-native-inputs python-matplotlib))) @@ -3975,42 +3977,41 @@ toolkits.") `(#:tests? #f ; we're only generating documentation #:phases (modify-phases %standard-phases - (delete 'build) + (replace 'build + (lambda _ + (chdir "doc") + ;; Produce pdf in 'A4' format. + (substitute* "conf.py" + (("latex_paper_size = 'letter'") "") + ;; latex_paper_size is deprecated -> set paper size using + ;; latex_elements + (("latex_elements\\['pointsize'\\] = '11pt'" match) + ;; insert at a point where latex_elements{} is defined: + (string-append match "\nlatex_elements['papersize'] = 'a4paper'"))) + (zero? (system* "python" "make.py" "html" "latex" "texinfo")))) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((data (string-append (assoc-ref outputs "out") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) + (doc (string-append data "/doc/python-matplotlib-" ,version)) (info (string-append data "/info")) (html (string-append doc "/html"))) - ;; Make installed package available for building the - ;; documentation - (with-directory-excursion "doc" - ;; Produce pdf in 'A4' format. - (substitute* (find-files "." "conf\\.py") - (("latex_paper_size = 'letter'") - "latex_paper_size = 'a4'")) - (mkdir-p html) - (mkdir-p info) - ;; The doc recommends to run the 'html' target twice. - (system* "python" "make.py" "html") - (system* "python" "make.py" "html") - (copy-recursively "build/html" html) - (system* "python" "make.py" "latex") - (system* "python" "make.py" "texinfo") + (mkdir-p html) + (mkdir-p info) + (copy-recursively "build/html" html) + (symlink (string-append html "/_images") + (string-append info "/matplotlib-figures")) + (with-directory-excursion "build/texinfo" + (substitute* "matplotlib.texi" + (("@image\\{([^,]*)" all file) + (string-append "@image{matplotlib-figures/" file))) (symlink (string-append html "/_images") - (string-append info "/matplotlib-figures")) - (with-directory-excursion "build/texinfo" - (substitute* "matplotlib.texi" - (("@image\\{([^,]*)" all file) - (string-append "@image{matplotlib-figures/" file))) - (symlink (string-append html "/_images") - "./matplotlib-figures") - (system* "makeinfo" "--no-split" - "-o" "matplotlib.info" "matplotlib.texi")) - (copy-file "build/texinfo/matplotlib.info" - (string-append info "/matplotlib.info")) - (copy-file "build/latex/Matplotlib.pdf" - (string-append doc "/Matplotlib.pdf")))) + "./matplotlib-figures") + (system* "makeinfo" "--no-split" + "-o" "matplotlib.info" "matplotlib.texi")) + (copy-file "build/texinfo/matplotlib.info" + (string-append info "/matplotlib.info")) + (copy-file "build/latex/Matplotlib.pdf" + (string-append doc "/Matplotlib.pdf"))) #t))))) (home-page (package-home-page python-matplotlib)) (synopsis "Documentation for the python-matplotlib package") From ce7911ddae5d30ba73c8c9552b7d4e71268e5db3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 17:21:07 +0100 Subject: [PATCH 407/436] gnu: Add python-faker. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: Adjust paths. Also rename to ... * gnu/packages/patches/python-faker-fix-build-32bit.patch: ... this. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/python.scm (python-faker, python2-faker): New variables. (python-fake-factory)[properties]: Superseded by PYTHON-FAKER. (python2-fake-factory)[properties]: Superseded by PYTHON2-FAKER. (python-orator, python2-orator)[propagated-inputs]: Replace PYTHON-FAKE-FACTORY with PYTHON-FAKER. --- gnu/local.mk | 2 +- ...tch => python-faker-fix-build-32bit.patch} | 6 +- gnu/packages/python.scm | 55 ++++++++++++++++++- 3 files changed, 57 insertions(+), 6 deletions(-) rename gnu/packages/patches/{python-fake-factory-fix-build-32bit.patch => python-faker-fix-build-32bit.patch} (94%) diff --git a/gnu/local.mk b/gnu/local.mk index ee40c1bd30..819fb4fcd3 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -862,7 +862,7 @@ dist_patch_DATA = \ %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \ %D%/packages/patches/python-statsmodels-fix-tests.patch \ %D%/packages/patches/python-configobj-setuptools.patch \ - %D%/packages/patches/python-fake-factory-fix-build-32bit.patch \ + %D%/packages/patches/python-faker-fix-build-32bit.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ %D%/packages/patches/python-pygit2-disable-network-tests.patch \ diff --git a/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch b/gnu/packages/patches/python-faker-fix-build-32bit.patch similarity index 94% rename from gnu/packages/patches/python-fake-factory-fix-build-32bit.patch rename to gnu/packages/patches/python-faker-fix-build-32bit.patch index cb60896fad..466b289012 100644 --- a/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch +++ b/gnu/packages/patches/python-faker-fix-build-32bit.patch @@ -2,10 +2,10 @@ These tests fail on 32-bit due to an overflow. Upstream bug URL: https://github.com/joke2k/faker/issues/408 -diff --git a/faker/tests/__init__.py b/faker/tests/__init__.py +diff --git a/tests/__init__.py b/tests/__init__.py index 6026772..58b6b83 100644 ---- a/faker/tests/__init__.py -+++ b/faker/tests/__init__.py +--- a/tests/__init__.py ++++ b/tests/__init__.py @@ -384,7 +384,6 @@ class FactoryTestCase(unittest.TestCase): provider = Provider # test century diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 70fd1557b4..76e6ead644 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11434,6 +11434,55 @@ parsing UK postcodes.") (define-public python2-ukpostcodeparser (package-with-python2 python-ukpostcodeparser)) +(define-public python-faker + (package + (name "python-faker") + (version "0.7.9") + (source (origin + (method url-fetch) + (uri (pypi-uri "Faker" version)) + (sha256 + (base32 + "1fh2p2yz0fsdr4fqwxgddwbvfb6qn6vp8yx0qwqzra27yq5d1wsm")) + (patches + (search-patches "python-faker-fix-build-32bit.patch")) + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file (find-files "." "\\.pyc$")) + #t)))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (zero? (system* "python" "-m" "unittest" "-v" "tests"))))))) + (native-inputs + `(;; For testing + ("python-email-validator" ,python-email-validator) + ("python-mock" ,python-mock) + ("python-ukpostcodeparser" ,python-ukpostcodeparser))) + (propagated-inputs + `(("python-dateutil" ,python-dateutil) + ("python-six" ,python-six))) + (home-page "https://github.com/joke2k/faker") + (synopsis "Python package that generates fake data") + (description + "Faker is a Python package that generates fake data such as names, +addresses, and phone numbers.") + (license license:expat) + (properties `((python2-variant . ,(delay python2-faker)))))) + +(define-public python2-faker + (let ((base (package-with-python2 (strip-python2-variant + python-faker)))) + (package + (inherit base) + (propagated-inputs + `(("python2-ipaddress" ,python2-ipaddress) + ,@(package-propagated-inputs base)))))) + (define-public python-fake-factory (package (name "python-fake-factory") @@ -11468,13 +11517,15 @@ parsing UK postcodes.") "Faker is a Python package that generates fake data such as names, addresses, and phone numbers.") (license license:expat) - (properties `((python2-variant . ,(delay python2-fake-factory)))))) + (properties `((python2-variant . ,(delay python2-fake-factory)) + (superseded . ,python-faker))))) (define-public python2-fake-factory (let ((base (package-with-python2 (strip-python2-variant python-fake-factory)))) (package (inherit base) + (properties `((superseded . ,python2-faker))) (propagated-inputs `(("python2-ipaddress" ,python2-ipaddress) ,@(package-propagated-inputs base)))))) @@ -11541,7 +11592,7 @@ mocks, stubs and fakes.") `(("python-arrow" ,python-arrow) ("python-blinker" ,python-blinker) ("python-cleo" ,python-cleo) - ("python-fake-factory" ,python-fake-factory) + ("python-faker" ,python-faker) ("python-inflection" ,python-inflection) ("python-lazy-object-proxy" ,python-lazy-object-proxy) ("python-pyaml" ,python-pyaml) From b03ee02f0d111bf75f8a87c9948c372974dcb243 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 8 Mar 2017 17:54:48 +0100 Subject: [PATCH 408/436] gnu: python-pandas: Fix build on 32-bit. * gnu/packages/patches/python-pandas-skip-failing-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-pandas, python2-pandas): Use it. --- gnu/local.mk | 1 + .../python-pandas-skip-failing-tests.patch | 59 +++++++++++++++++++ gnu/packages/python.scm | 4 +- 3 files changed, 63 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-pandas-skip-failing-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 819fb4fcd3..4297cbb965 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -863,6 +863,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-statsmodels-fix-tests.patch \ %D%/packages/patches/python-configobj-setuptools.patch \ %D%/packages/patches/python-faker-fix-build-32bit.patch \ + %D%/packages/patches/python-pandas-skip-failing-tests.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ %D%/packages/patches/python-pygit2-disable-network-tests.patch \ diff --git a/gnu/packages/patches/python-pandas-skip-failing-tests.patch b/gnu/packages/patches/python-pandas-skip-failing-tests.patch new file mode 100644 index 0000000000..31fc912d00 --- /dev/null +++ b/gnu/packages/patches/python-pandas-skip-failing-tests.patch @@ -0,0 +1,59 @@ +These tests fail on 32bit architectures. + +Upstream bug URL: https://github.com/pandas-dev/pandas/issues/14866 + +--- a/pandas/tests/test_base.py 2017-03-08 17:49:44.422282717 +0100 ++++ b/pandas/tests/test_base.py 2017-03-08 17:50:59.476701799 +0100 +@@ -363,30 +363,6 @@ + self.assertFalse(result.iat[0]) + self.assertFalse(result.iat[1]) + +- def test_ndarray_compat_properties(self): +- +- for o in self.objs: +- +- # check that we work +- for p in ['shape', 'dtype', 'flags', 'T', 'strides', 'itemsize', +- 'nbytes']: +- self.assertIsNotNone(getattr(o, p, None)) +- self.assertTrue(hasattr(o, 'base')) +- +- # if we have a datetimelike dtype then needs a view to work +- # but the user is responsible for that +- try: +- self.assertIsNotNone(o.data) +- except ValueError: +- pass +- +- self.assertRaises(ValueError, o.item) # len > 1 +- self.assertEqual(o.ndim, 1) +- self.assertEqual(o.size, len(o)) +- +- self.assertEqual(Index([1]).item(), 1) +- self.assertEqual(Series([1]).item(), 1) +- + def test_ops(self): + for op in ['max', 'min']: + for o in self.objs: +--- a/pandas/tools/tests/test_tile.py 2017-03-08 17:47:39.762261841 +0100 ++++ b/pandas/tools/tests/test_tile.py 2017-03-08 17:48:26.831780495 +0100 +@@ -271,19 +271,6 @@ + np.array([0, 0, 1, 1], dtype=np.int8)) + tm.assert_numpy_array_equal(bins, np.array([0, 1.5, 3])) + +- def test_single_bin(self): +- # issue 14652 +- expected = Series([0, 0]) +- +- s = Series([9., 9.]) +- result = cut(s, 1, labels=False) +- tm.assert_series_equal(result, expected) +- +- s = Series([-9., -9.]) +- result = cut(s, 1, labels=False) +- tm.assert_series_equal(result, expected) +- +- + def curpath(): + pth, _ = os.path.split(os.path.abspath(__file__)) + return pth diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 76e6ead644..15c8a8eff4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1171,7 +1171,9 @@ datetime module, available in Python 2.3+.") (method url-fetch) (uri (pypi-uri "pandas" version)) (sha256 - (base32 "0540cnbwy2hc4hv2sxfs8i47xi91qzvzxfn80dl785ibiicly3vg")))) + (base32 "0540cnbwy2hc4hv2sxfs8i47xi91qzvzxfn80dl785ibiicly3vg")) + (patches + (search-patches "python-pandas-skip-failing-tests.patch")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy) From 6f5d28f9d05aaa9743b3aac6bceb2c6323122d2d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 22 Feb 2017 09:03:25 -0800 Subject: [PATCH 409/436] gnu: inetutils: Enable tests. * gnu/packages/admin.scm (inetutils)[arguments]: Remove '#:tests? #f' and #:configure-flags. [native-inputs]: Add net-tools. Signed-off-by: Leo Famulari --- gnu/packages/admin.scm | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index d2001d4e2c..a7f97f6893 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -253,13 +253,9 @@ re-executing them as necessary.") (base32 "05n65k4ixl85dc6rxc51b1b732gnmm8xnqi424dy9f1nz7ppb3xy")))) (build-system gnu-build-system) - (arguments `(#:configure-flags '("--localstatedir=/var") - - ;; FIXME: `tftp.sh' relies on `netstat' from utils-linux, - ;; which is currently missing. - #:tests? #f)) (inputs `(("ncurses" ,ncurses) - ("readline" ,readline))) ; for 'ftp' + ("readline" ,readline))) ;for 'ftp' + (native-inputs `(("netstat" ,net-tools))) ;for tests (home-page "http://www.gnu.org/software/inetutils/") (synopsis "Basic networking utilities") (description From 6aa9d63c92bd0c33dd331d2a9d224cfef1b78331 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 10:41:34 +0100 Subject: [PATCH 410/436] guix archive: Allow compilation with Guile 2.2. * guix/scripts/archive.scm (export-from-store): Avoid shadowing the top-level '_'. --- guix/scripts/archive.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/scripts/archive.scm b/guix/scripts/archive.scm index 9e49c53635..cad279fb50 100644 --- a/guix/scripts/archive.scm +++ b/guix/scripts/archive.scm @@ -268,7 +268,7 @@ resulting archive to the standard output port." (let ((system (assoc-ref opts 'system))) (format #t "~a\n" (build-docker-image file #:system system)))) - (_ + (x ;; TODO: Remove this restriction. (leave (_ "only a single item can be exported to Docker~%"))))) (format From beb1e8067d163b9d681b613c56e13e4da304582e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 10:54:50 +0100 Subject: [PATCH 411/436] gnu: Remove unneeded imports. * gnu/packages/backup.scm: Remove unneeded (guix build utils) import. * gnu/packages/finance.scm: Likewise. --- gnu/packages/backup.scm | 1 - gnu/packages/finance.scm | 1 - 2 files changed, 2 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 986ffef08f..d557bf3f01 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -24,7 +24,6 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) #:use-module (guix utils) - #:use-module (guix build utils) #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (gnu packages) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index ee90c38eb7..234e40c281 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -24,7 +24,6 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix build utils) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system python) From 5d1ee4d7bc8fa3953c498057da3220029ba7c69d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 13:23:57 +0100 Subject: [PATCH 412/436] services: prosody: Make sure 'id' is available at expansion time. * gnu/services/messaging.scm (id): Use 'define-syntax-rule' instead of 'define' to make sure 'id' is available at expansion time. --- gnu/services/messaging.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/services/messaging.scm b/gnu/services/messaging.scm index 9f59d6eac6..cd740c7bc0 100644 --- a/gnu/services/messaging.scm +++ b/gnu/services/messaging.scm @@ -49,8 +49,9 @@ ;;; ;;; Code: -(define (id ctx . parts) - (datum->syntax ctx (apply symbol-append (map syntax->datum parts)))) +(define-syntax-rule (id ctx parts ...) + "Assemble PARTS into a raw (unhygienic) identifier." + (datum->syntax ctx (symbol-append (syntax->datum parts) ...))) (define-syntax define-maybe (lambda (x) From 10999889042cff74b98515507d822f2096e91e8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 14:04:52 +0100 Subject: [PATCH 413/436] services: prosody: Use 'id' to introduce unhygienic top-level identifiers. * gnu/services/messaging.scm (define-all-configurations): Use 'id' to introduce raw/literal/unhygienic top-level identifiers. Fixes compilation with Guile 2.2. --- gnu/services/messaging.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/services/messaging.scm b/gnu/services/messaging.scm index cd740c7bc0..34723dc11c 100644 --- a/gnu/services/messaging.scm +++ b/gnu/services/messaging.scm @@ -95,21 +95,21 @@ "" doc)) #'(doc ...) #'(target ...)))) #`(begin - (define common-fields + (define #,(id #'stem #'common-fields) '(#,@(filter-map (make-pred #f) #'(field ...) #'(target ...)))) - (define-configuration prosody-configuration + (define-configuration #,(id #'stem #'prosody-configuration) #,@(filter-map (make-pred 'global) #'((field (field-type def) doc) ...) #'(target ...))) - (define-configuration virtualhost-configuration + (define-configuration #,(id #'stem #'virtualhost-configuration) #,@(filter-map (make-pred 'virtualhost) #'((field (new-field-type new-def) new-doc) ...) #'(target ...))) - (define-configuration int-component-configuration + (define-configuration #,(id #'stem #'int-component-configuration) #,@(filter-map (make-pred 'int-component) #'((field (new-field-type new-def) new-doc) ...) #'(target ...))) - (define-configuration ext-component-configuration + (define-configuration #,(id #'stem #'ext-component-configuration) #,@(filter-map (make-pred 'ext-component) #'((field (new-field-type new-def) new-doc) ...) #'(target ...))))))))) From 19c1ac8d88b0925863623530ee65ac40861c2d8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 14:45:55 +0100 Subject: [PATCH 414/436] build: Unset 'NIX_BUILD_HOOK' when offloading support is missing. * build-aux/pre-inst-env.in: Export 'NIX_BUILD_HOOK' only when nix/scripts/offload is executable; unset it otherwise. --- build-aux/pre-inst-env.in | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/build-aux/pre-inst-env.in b/build-aux/pre-inst-env.in index fe56da6944..dca2699687 100644 --- a/build-aux/pre-inst-env.in +++ b/build-aux/pre-inst-env.in @@ -1,7 +1,7 @@ #!/bin/sh # GNU Guix --- Functional package management for GNU -# Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès +# Copyright © 2012, 2013, 2014, 2015, 2017 Ludovic Courtès # # This file is part of GNU Guix. # @@ -45,11 +45,18 @@ export PATH NIX_ROOT_FINDER="$abs_top_builddir/nix/scripts/list-runtime-roots" NIX_SUBSTITUTERS="$abs_top_builddir/nix/scripts/substitute" -NIX_BUILD_HOOK="$abs_top_builddir/nix/scripts/offload" NIX_LIBEXEC_DIR="@abs_top_builddir@/nix/scripts" # for 'guix-authenticate' -export NIX_ROOT_FINDER NIX_SUBSTITUTERS \ - NIX_BUILD_HOOK NIX_LIBEXEC_DIR +export NIX_ROOT_FINDER NIX_SUBSTITUTERS NIX_LIBEXEC_DIR + +NIX_BUILD_HOOK="$abs_top_builddir/nix/scripts/offload" +if [ -x "$NIX_BUILD_HOOK" ] +then + export NIX_BUILD_HOOK +else + # No offloading support. + unset NIX_BUILD_HOOK +fi # The 'guix-register' program. GUIX_REGISTER="$abs_top_builddir/guix-register" From 6f38960055e496193a49d690d7f1b5516b2b8625 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 15:04:18 +0100 Subject: [PATCH 415/436] hash: Close or flush sha256 output ports before calling their 'get' procedure. Slightly different buffering of custom binary output ports in Guile 2.1.7 would lead tests missing 'close-port' or 'force-output' to fail. * tests/hash.scm ("open-sha256-port, hello"): Add call to 'force-output' before call to 'get'. * tests/nar.scm ("write-file puts file in C locale collation order"): Call 'close-port' before calling 'get-hash'. --- tests/hash.scm | 3 ++- tests/nar.scm | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/hash.scm b/tests/hash.scm index 8039549971..86501dca2d 100644 --- a/tests/hash.scm +++ b/tests/hash.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014 Ludovic Courtès +;;; Copyright © 2013, 2014, 2017 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,6 +67,7 @@ In Guile <= 2.0.9, CBIPs were always fully buffered, so the (let-values (((port get) (open-sha256-port))) (put-bytevector port (string->utf8 "hello world")) + (force-output port) (get))) (test-assert "port-sha256" diff --git a/tests/nar.scm b/tests/nar.scm index 4f4b304b1d..28ead8b783 100644 --- a/tests/nar.scm +++ b/tests/nar.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -186,6 +186,7 @@ (lambda () (let-values (((port get-hash) (open-sha256-port))) (write-file input port) + (close-port port) (get-hash))) (lambda () (rm-rf input))))) From dd420bf3430eb644b93ca224da4c0a3f5db7a42f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 15:22:07 +0100 Subject: [PATCH 416/436] tests: Avoid zero-expression 'begin' form. * tests/cran.scm ("description->package"): Add body after the expected pattern in 'match'. --- tests/cran.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/cran.scm b/tests/cran.scm index f92934c468..c162d45d8a 100644 --- a/tests/cran.scm +++ b/tests/cran.scm @@ -126,7 +126,8 @@ Date/Publication: 2015-07-14 14:15:16 "This is a long description spanning multiple lines: \ and it could confuse the parser that there is a colon : on the \ lines. And: this line continues the description.") - ('license 'gpl3+))) + ('license 'gpl3+)) + #t) (x (begin (format #t "~s\n" x) From 77aa0887e1d125a612ac7156a8e54902af387f45 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 17:46:31 +0100 Subject: [PATCH 417/436] gnu: guile-reader: Update to 0.6.2. * gnu/packages/guile.scm (guile-reader): Update to 0.6.2. [arguments]: Remove. --- gnu/packages/guile.scm | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 4440c6c602..4ed083cf09 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -443,22 +443,18 @@ more.") (define-public guile-reader (package (name "guile-reader") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/guile-reader/guile-reader-" version ".tar.gz")) (sha256 (base32 - "020wz5w8z6g79nbqifg2n496wxwkcjzh8xizpv6mz0hczpl155ma")))) + "0592s2s8ampqmqwilc4fvcild6rb9gy79di6vxv5kcdmv23abkgx")))) (build-system gnu-build-system) (native-inputs `(("pkgconfig" ,pkg-config) ("gperf" ,gperf))) (inputs `(("guile" ,guile-2.0))) - (arguments `(#:configure-flags - (let ((out (assoc-ref %outputs "out"))) - (list (string-append "--with-guilemoduledir=" - out "/share/guile/site/2.0"))))) (synopsis "Framework for building readers for GNU Guile") (description "Guile-Reader is a simple framework for building readers for GNU Guile. From 517fce63273649ca5e0263088aab46f9e25c986d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 17:48:27 +0100 Subject: [PATCH 418/436] gnu: Add guile2.2-reader. * gnu/packages/guile.scm (guile2.2-reader): New variable. --- gnu/packages/guile.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 4ed083cf09..52a0beb1cd 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -471,6 +471,9 @@ many readers as needed).") (home-page "http://www.nongnu.org/guile-reader/") (license license:gpl3+))) +(define-public guile2.2-reader + (package-for-guile-2.2 guile-reader)) + (define-public guile-ncurses (package (name "guile-ncurses") From 64f34aefe722646ffdf6a6c8cb15de15a13fb7ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 21:30:26 +0100 Subject: [PATCH 419/436] gnu: Add guile2.2-haunt. * gnu/packages/guile.scm (guile2.2-haunt): New variable. --- gnu/packages/guile.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 52a0beb1cd..a9fd471cd9 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1063,6 +1063,10 @@ interface for reading articles in any format.") (home-page "http://haunt.dthompson.us") (license license:gpl3+))) +(define-public guile2.2-haunt + (package-for-guile-2.2 + (package (inherit haunt) (name "guile2.2-haunt")))) + (define-public guile-config (package (name "guile-config") From 3f6d5b8a691fee5574efd3e13f88201ea5c3b416 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 21:30:55 +0100 Subject: [PATCH 420/436] download: Update the Savannah mirror list. * guix/download.scm (%mirrors) : Remove centervenus.com, which seems to be broken. Add download-mirror.sv.gnu.org as a last resort. --- guix/download.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/guix/download.scm b/guix/download.scm index 813f51f489..dda18ff04d 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -103,8 +103,8 @@ "http://mirror.csclub.uwaterloo.ca/nongnu/" "http://nongnu.askapache.com/" "http://savannah.c3sl.ufpr.br/" - "http://www.centervenus.com/mirrors/nongnu/" - "http://download.savannah.gnu.org/releases-noredirect/") + "http://download.savannah.gnu.org/releases-noredirect/" + "http://download-mirror.savannah.gnu.org/releases/") (sourceforge ; https://sourceforge.net/p/forge/documentation/Mirrors/ "http://downloads.sourceforge.net/project/" "http://ufpr.dl.sourceforge.net/project/" From 30906825cb99122f6b068a1d9223937757d75ce5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 21:36:54 +0100 Subject: [PATCH 421/436] ui: Avoid '_' as a pattern variable in 'match'. * guix/ui.scm (fill-paragraph): Don't use '_' as a pattern variable since that is shadowed by the top-level '_' binding on Guile 2.2. (show-manifest-transaction): Likewise. --- guix/ui.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/guix/ui.scm b/guix/ui.scm index 6247944068..5ae082fc0a 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -687,7 +687,7 @@ replacement if PORT is not Unicode-capable." "The following packages will be removed:~%~{~a~%~}~%" len) remove)))) - (_ #f)) + (x #f)) (match downgrade (((($ name old-version) . ($ _ new-version output item)) ..1) @@ -705,7 +705,7 @@ replacement if PORT is not Unicode-capable." "The following packages will be downgraded:~%~{~a~%~}~%" len) downgrade)))) - (_ #f)) + (x #f)) (match upgrade (((($ name old-version) . ($ _ new-version output item)) ..1) @@ -723,7 +723,7 @@ replacement if PORT is not Unicode-capable." "The following packages will be upgraded:~%~{~a~%~}~%" len) upgrade)))) - (_ #f)) + (x #f)) (match install ((($ name version output item _) ..1) (let ((len (length name)) @@ -739,7 +739,7 @@ replacement if PORT is not Unicode-capable." "The following packages will be installed:~%~{~a~%~}~%" len) install)))) - (_ #f)))) + (x #f)))) (define-syntax with-error-handling (syntax-rules () @@ -820,7 +820,7 @@ converted to a space; sequences of more than one line break are preserved." (match (string-fold maybe-break `(,column 0 ()) str) - ((_ _ chars) + ((column newlines chars) (list->string (reverse chars))))) @@ -1024,7 +1024,7 @@ DURATION-RELATION with the current time." (valid-generations (iota n 1))) ((lst ..1) (valid-generations lst)) - (_ #f))) + (x #f))) (define (filter-by-duration duration) (define (time-at-midnight time) From 1062063a65036f32a061c54866d33ffe079ec44e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 22:21:31 +0100 Subject: [PATCH 422/436] ui: Don't use '%default-port-encoding' to set the encoding of string ports. * guix/ui.scm (right-arrow): Call 'set-port-encoding!' to set PORT's encoding; remove use of 'with-fluids'. This is for compatibility with Guile 2.2 where the encoding of string ports is not influenced by %DEFAULT-PORT-ENCODING. * tests/ui.scm ("show-manifest-transaction"): Likewise. --- guix/ui.scm | 21 +++++++++++---------- tests/ui.scm | 11 +++++++---- 2 files changed, 18 insertions(+), 14 deletions(-) diff --git a/guix/ui.scm b/guix/ui.scm index 5ae082fc0a..3a0a6501d1 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -635,16 +635,17 @@ report what is prerequisites are available for download." (define (right-arrow port) "Return either a string containing the 'RIGHT ARROW' character, or an ASCII replacement if PORT is not Unicode-capable." - (with-fluids ((%default-port-encoding (port-encoding port))) - (let ((arrow "→")) - (catch 'encoding-error - (lambda () - (call-with-output-string - (lambda (port) - (set-port-conversion-strategy! port 'error) - (display arrow port)))) - (lambda (key . args) - "->"))))) + (let ((encoding (port-encoding port)) + (arrow "→")) + (catch 'encoding-error + (lambda () + (call-with-output-string + (lambda (port) + (set-port-encoding! port encoding) + (set-port-conversion-strategy! port 'error) + (display arrow port)))) + (lambda (key . args) + "->")))) (define* (show-manifest-transaction store manifest transaction #:key dry-run?) diff --git a/tests/ui.scm b/tests/ui.scm index 058207e8b9..cfe417d497 100644 --- a/tests/ui.scm +++ b/tests/ui.scm @@ -248,9 +248,12 @@ Second line" 24)) (lambda () (show-manifest-transaction store m t))))) (string-match "guile\t1.8.8 -> 2.0.9" - (with-fluids ((%default-port-encoding "ISO-8859-1")) - (with-error-to-string - (lambda () - (show-manifest-transaction store m t))))))))) + (with-error-to-string + (lambda () + ;; In Guile 2.2, %DEFAULT-PORT-ENCODING doesn't + ;; influence the encoding of string ports. + (set-port-encoding! (current-error-port) + "ISO-8859-1") + (show-manifest-transaction store m t)))))))) (test-end "ui") From ac9c1dc7bdf1a016fcd1989993999e4a32d0c885 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 23:10:09 +0100 Subject: [PATCH 423/436] list-runtime-roots: Bufferize the lsof pipe. * nix/scripts/list-runtime-roots.in (lsof-roots): Add 'setvbuf' call for PIPE. --- nix/scripts/list-runtime-roots.in | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/nix/scripts/list-runtime-roots.in b/nix/scripts/list-runtime-roots.in index 993eb169c1..a6938087b5 100644 --- a/nix/scripts/list-runtime-roots.in +++ b/nix/scripts/list-runtime-roots.in @@ -1,7 +1,7 @@ #!@GUILE@ -ds !# ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2017 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -133,6 +133,9 @@ or the empty list." (define %file-rx (make-regexp "^n/(.*)$")) + ;; We're going to read it all. + (setvbuf pipe _IOFBF 16384) + (let loop ((line (read-line pipe)) (roots '())) (cond ((eof-object? line) From d75e8f36a80be8155f40678e30d8384c205cf96f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 23:12:09 +0100 Subject: [PATCH 424/436] packages: Use PACKAGE@VERSION syntax when reporting ambiguities. * gnu/packages.scm (%find-package): Upon ambiguity, use the PACKAGE@VERSION syntax instead of 'package-full-name'. --- gnu/packages.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages.scm b/gnu/packages.scm index 10ca3bb314..92bab7228a 100644 --- a/gnu/packages.scm +++ b/gnu/packages.scm @@ -311,8 +311,8 @@ return its return value." ((pkg . pkg*) (unless (null? pkg*) (warning (_ "ambiguous package specification `~a'~%") spec) - (warning (_ "choosing ~a from ~a~%") - (package-full-name pkg) + (warning (_ "choosing ~a@~a from ~a~%") + (package-name pkg) (package-version pkg) (location->string (package-location pkg)))) (when fallback? (warning (_ "deprecated NAME-VERSION syntax; \ From 7447aa36e16fb77f75df4d3369db9c942615632e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 8 Mar 2017 23:39:03 +0100 Subject: [PATCH 425/436] utils: Make sure to use the right 'bytevector->string'. In Guile 2.2, (rnrs io ports) exports 'bytevector->string', which conflicts with that of (ice-9 iconv). * guix/utils.scm: Hide 'bytevector->string' from (rnrs io ports). --- guix/utils.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/utils.scm b/guix/utils.scm index 72dc0687a4..2d59cccf3c 100644 --- a/guix/utils.scm +++ b/guix/utils.scm @@ -31,7 +31,7 @@ #:use-module (srfi srfi-60) #:use-module (rnrs bytevectors) #:use-module (ice-9 binary-ports) - #:autoload (rnrs io ports) (make-custom-binary-input-port) + #:use-module ((rnrs io ports) #:hide (bytevector->string)) #:use-module ((rnrs bytevectors) #:select (bytevector-u8-set!)) #:use-module (guix memoization) #:use-module ((guix build utils) #:select (dump-port)) From c49840f8d44859fd5ee537d329209d8fac5dcd7d Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 8 Mar 2017 23:49:24 +0100 Subject: [PATCH 426/436] gnu: Add lensfun. * gnu/packages/photo.scm (lensfun): New variable. --- gnu/packages/photo.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index ce71d2a441..c782ecf47f 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2015 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2017 Roel Janssen ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,6 +34,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) + #:use-module (gnu packages glib) #:use-module (gnu packages graphics) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) @@ -263,3 +265,38 @@ overlapping images, as well as some command line tools.") multi-resolution spline. Enfuse merges different exposures of the same scene to produce an image that looks much like a tone-mapped image.") (license license:gpl2+))) + +(define-public lensfun + (package + (name "lensfun") + (version "0.3.2") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/lensfun/" + version "/lensfun-" version ".tar.gz")) + (sha256 + (base32 + "0cfk8jjhs9nbfjfdy98plrj9ayi59aph0nx6ppslgjhlcvacm2xf")))) + (build-system cmake-build-system) + (arguments `(#:tests? #f)) ; There are no tests to run. + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("glib" ,glib))) + (home-page "https://sourceforge.net/projects/lensfun/") + (synopsis "Library to correct optical lens defects with a lens database") + (description "Digital photographs are not ideal. Of course, the better is +your camera, the better the results will be, but in any case if you look +carefully at shots taken even by the most expensive cameras equipped with the +most expensive lenses you will see various artifacts. It is very hard to make +ideal cameras, because there are a lot of factors that affect the final image +quality, and at some point camera and lens designers have to trade one factor +for another to achieve the optimal image quality, within the given design +restrictions and budget. But we all want ideal shots, don't we? So that's +what's Lensfun is all about: rectifying the defects introduced by your +photographic equipment.") + ;; The libraries are licensed under the LGPL3, the programs are + ;; licensed GPL3, and the database is license CC-BY-SA 3.0. See the + ;; README.md file for this clarification. + (license (list license:lgpl3 license:gpl3 license:cc-by-sa3.0)))) From f7db12022ca4a688875b85004402f8012a27d820 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 9 Mar 2017 06:37:17 +0100 Subject: [PATCH 427/436] gnu: r: Update to 3.3.3. * gnu/packages/statistics.scm (r): Update to 3.3.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 65e5c2e93b..c46036368a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -102,7 +102,7 @@ be output in text, PostScript, PDF or HTML.") (define-public r (package (name "r") - (version "3.3.2") + (version "3.3.3") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -110,7 +110,7 @@ be output in text, PostScript, PDF or HTML.") version ".tar.gz")) (sha256 (base32 - "0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j")))) + "0v7wpj89b0i3ad3fi1wak5c93hywmbxv8sdnixhq8l17782nidss")))) (build-system gnu-build-system) (arguments `(#:make-flags From f2ac9379249b394571691f26298e338cbda49582 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 9 Mar 2017 06:37:40 +0100 Subject: [PATCH 428/436] gnu: r: Remove obsolete configure flags. * gnu/packages/statistics.scm (r)[arguments]: Remove obsolete configure flags. --- gnu/packages/statistics.scm | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c46036368a..e02c342c6f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -170,11 +170,7 @@ be output in text, PostScript, PDF or HTML.") "--with-ICU" "--enable-R-shlib" "--enable-BLAS-shlib" - "--with-system-zlib" - "--with-system-bzlib" - "--with-system-pcre" - "--with-system-tre" - "--with-system-xz"))) + "--with-system-tre"))) ;; R has some support for Java. When the JDK is available at configure ;; time environment variables pointing to the JDK will be recorded under ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R From 3104475148af4f355f9ed5728582e79fea8b2c96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 9 Mar 2017 09:48:33 +0100 Subject: [PATCH 429/436] utils: Use an idiom compatible with both 2.0 and 2.2. Fixes a regression introduced in 7447aa36e16fb77f75df4d3369db9c942615632e. Reported by Ricardo Wurmus. * guix/utils.scm: Revert 7447aa36e16fb77f75df4d3369db9c942615632e. Use #:prefix for (ice-9 iconv) to support both 2.0 and 2.2. --- guix/utils.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/guix/utils.scm b/guix/utils.scm index 2d59cccf3c..b72e3f233f 100644 --- a/guix/utils.scm +++ b/guix/utils.scm @@ -31,7 +31,7 @@ #:use-module (srfi srfi-60) #:use-module (rnrs bytevectors) #:use-module (ice-9 binary-ports) - #:use-module ((rnrs io ports) #:hide (bytevector->string)) + #:autoload (rnrs io ports) (make-custom-binary-input-port) #:use-module ((rnrs bytevectors) #:select (bytevector-u8-set!)) #:use-module (guix memoization) #:use-module ((guix build utils) #:select (dump-port)) @@ -43,7 +43,7 @@ #:use-module (ice-9 regex) #:use-module (ice-9 match) #:use-module (ice-9 format) - #:use-module ((ice-9 iconv) #:select (bytevector->string)) + #:use-module ((ice-9 iconv) #:prefix iconv:) #:use-module (system foreign) #:re-export (memoize) ; for backwards compatibility #:export (bytevector->base16-string @@ -326,7 +326,7 @@ This procedure returns #t on success." (seek in 0 SEEK_SET) ; read from the beginning of the file. (let* ((pre-bv (get-bytevector-n in start)) ;; The expression in string form. - (str (bytevector->string + (str (iconv:bytevector->string (get-bytevector-n in (- end start)) (port-encoding in))) (post-bv (get-bytevector-all in)) From c9b631aef4976e77df4440bae51549ad6b0c44e9 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 9 Mar 2017 00:40:01 -0500 Subject: [PATCH 430/436] gnu: icecat: Update to 45.7.0-gnu1. * gnu/packages/gnuzilla.scm (icecat): Update to 45.7.0-gnu1. Remove patches included in 45.7.0. --- gnu/packages/gnuzilla.scm | 63 ++------------------------------------- 1 file changed, 3 insertions(+), 60 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index c4543aa7d9..5ec90e500f 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -303,7 +303,7 @@ standards.") (define-public icecat (package (name "icecat") - (version "45.5.1-gnu1") + (version "45.7.0-gnu1") (source (origin (method url-fetch) @@ -312,68 +312,11 @@ standards.") "/" name "-" version ".tar.bz2")) (sha256 (base32 - "1sbfgsibmb8wfmb2g40gmqwq3nikmrgzksf51ydrz7gnafyfaqw1")) + "1mn73liylqzxk441f28wk326yglqs8zcwqs4zz51s8i2id2jsnv3")) (patches (list (search-patch "icecat-avoid-bundled-libraries.patch") - (search-patch "icecat-binutils.patch") - (mozilla-patch "icecat-CVE-2016-9897.patch" "2e5438a92617" "0pyjbzyy04759ldpcar8q8cccv67j1jkxsg46rkq7a3rbhmwmw4p") - (mozilla-patch "icecat-CVE-2016-9899.patch" "7391f60fb790" "1hydggpmmm2cs9lb15micnkxn4wl4cda9g74hkn3zmks805vjz3h") - (mozilla-patch "icecat-CVE-2016-9893-pt1.patch" "744e01001e6e" "0z2fq765kap3ll9as5rvjpnbj3pw26074alw7df0zi215qz47nxr") - (mozilla-patch "icecat-CVE-2016-9904-pt1.patch" "8ae673f34a5b" "1rlbihckl9afa0y91lqs7gpnv6a7zxzrmxjv95y3yrl03kibqp76") - (mozilla-patch "icecat-CVE-2016-9904-pt2.patch" "409c23c144fe" "05kgs16y8s5pxmg2dxp93247zagnj6zgj3209qpm5hz3an7gr13h") - (mozilla-patch "icecat-CVE-2016-9900.patch" "994d9bd0e28d" "007wifyx3b2ln4fwv1i8n24yz5ngjf4mkzd7sqr5bpd3q88ff293") - (mozilla-patch "icecat-CVE-2016-9893-pt2.patch" "0fc43af8982e" "0pc8q9knzq2knj723mwkay1lnzbzysb07ygxnc16mcb6f7vl2mw8") - (mozilla-patch "icecat-CVE-2016-9893-pt3.patch" "19f9a4643d77" "0w5yxj1l0hvs66q9agjp4m5sfby7fj05lx33gaqf899bw4hn4vcf") - (mozilla-patch "icecat-CVE-2016-9893-pt4.patch" "c58442c414f5" "1z1w1v8xagkhrwgp51ij1k2gx0ripslia09vm78812n7gcwddaas") - (mozilla-patch "icecat-CVE-2016-9898.patch" "5054047b7328" "0xlw8irymfp3bcaa5jpf7clf7bq6qxp3i8zapp8jya8lzr1nf868") - (mozilla-patch "icecat-bug-881832-pt1.patch" "1123263318a3" "1qkxwva3zrcs1zhga8ncmndq03988dx75i896g53gbvpskj06915") - (mozilla-patch "icecat-bug-881832-pt2.patch" "dc87c0a39adf" "01rapf14f3r2wk0cjd16dn1rll4ipgs33cnjmjck48nvk67ikz6h") - (mozilla-patch "icecat-bug-881832-pt3.patch" "f20e5f488368" "15ql9ywifb3gm2g1057k63f821dbs3wqsh3zhndprzf3dn6aha4i") - (mozilla-patch "icecat-bug-881832-pt4.patch" "7950c4d5bd7c" "0jhkg5hq5yfy7rh21k1mpbsbr81ql85aazym30zy3n2cf28xxhd7") - (mozilla-patch "icecat-bug-881832-pt5.patch" "972734ec21b6" "073i4v1f1ydy49i57pvzscz95sjr5bbk9s5sajxvmmcsmwhpjdfy") - (mozilla-patch "icecat-CVE-2016-9905-pt1.patch" "aebd3687e05e" "1qz6hdgflcrqyg7fv66cbg23v4b7q5bc2yxzrgjxs4j1d7jy1s0s") - (mozilla-patch "icecat-CVE-2016-9905-pt2.patch" "63d8e5cd27cb" "11fsgyngy7v59ma30xdbmycwf4izwikzvaljngm3ks4534inpl4a") - (mozilla-patch "icecat-bug-1279202.patch" "e560997291af" "1hn35slasfcj3ryka4fsarx4l9r99z0iwj67fmbv6zxz4z133kks") - (mozilla-patch "icecat-CVE-2016-9902.patch" "21c615b65048" "0ibgsxa36x9ajn2jqbhxxvrfvj6x6iyspsmzzn4brdz11n93skhr") - (mozilla-patch "icecat-CVE-2016-9901.patch" "c15e5afc0430" "17gj32agqs94548z8lvz0l6zz3kbwajn8as0y4iw5nb6jsll4c66") - (mozilla-patch "icecat-CVE-2016-9893-pt5.patch" "46163fb1cb34" "1yikayczfgfla3aka0159apq3149d52sgvlca0sivx4myd0lvjm7") - (mozilla-patch "icecat-CVE-2016-9893-pt6.patch" "cde2a37100f5" "100abggnhwyw84almxrkxqfpyfkd4pqkcrh5y9g4d3jd2h16asvl") - (mozilla-patch "icecat-CVE-2016-9893-pt7.patch" "9b78ab1e6d07" "19ib6bp96xk000ll40b8qxvizkncyzclz2rsb9w5fa42qs9978ff") - (mozilla-patch "icecat-CVE-2016-9893-pt8.patch" "78ebf9c9dfb0" "1shgr4rk6r2zxr1qqk1j3qnnqzqxnbi093qhlrfh8q5q1ivqf6k1") - (mozilla-patch "icecat-CVE-2016-9893-pt9.patch" "a46a9f16823c" "0dwkyz3kcqnfcbhbfh2lss7s0yh87rgzb871qxx3x4ynyqph9mnz") - (mozilla-patch "icecat-CVE-2017-5376.patch" "6bc7cc7a33a6" "1wggcqv84n8mp7xps7hy4rwy61fkh45imfqzc0b46s3w5hyhypn2") - (mozilla-patch "icecat-CVE-2016-9893-pt10.patch" "778f65148b40" "0j2a153sk0654vv2lnxjib4lwml3mlqn6vs46c2pp82iba8nyfrm") - (mozilla-patch "icecat-CVE-2016-9895.patch" "94bd2b43c766" "10h0qpr6m9cqyqxxnkbb6mzb3cagavzlynkxgd7a4izyq1bv28rk") - (mozilla-patch "icecat-CVE-2016-9893-pt11.patch" "893de7431d51" "11gyik8mwipl6ipypkvdq519pw7ccbg0g0bnvxb7271n44cqqcq5") - (mozilla-patch "icecat-CVE-2017-5383-pt1.patch" "b21dee058b2c" "005khpimffqzas7slajid4dd2c15nyk7rjk6fsps87bgnx0gx0s4") - (mozilla-patch "icecat-bug-1258410-pt1.patch" "cd23c5d74be8" "1myzkpzg6pmjacjz8az06m9kz84in1mwsiaw5sgx47pm02598wm5") - (mozilla-patch "icecat-bug-1258410-pt2.patch" "b83594617d15" "171cqflc9jh47az96im1whwhyq4ayicspqsczsmn2x5ll9lqw5fq") - (mozilla-patch "icecat-CVE-2017-5380.patch" "d6c6f5e4e641" "10x9f46ylm2q3i669hj1csd6agdm8w7xa0iln691z8ayg2hcrxdz") - (mozilla-patch "icecat-CVE-2017-5373-pt1.patch" "122f5fbfc563" "05pp2f4pg4j8a8pdgjhfrc8g2chhkhsarn9n8sbyag0fy3ig1cvd") - (mozilla-patch "icecat-CVE-2017-5390.patch" "297c675ddadc" "1jc1b5i69vq1fvz3qfnnv52c9cj17bjbmfyzmqlw5ywna0wfvabz") - (mozilla-patch "icecat-CVE-2017-5373-pt2.patch" "3cff736e3bb6" "1nxqwnl9zksvkfkmis7zica4xrhwfndjyy2sxc1dvrh9rshk1swq") - (mozilla-patch "icecat-CVE-2017-5373-pt3.patch" "2732280adabc" "0zrpq3aybaw2yy38vs6883a4nw01x4kxn3lfqn9yhcgjvngmmyia") - (mozilla-patch "icecat-CVE-2017-5373-pt4.patch" "81c9fdbd96e8" "0scv1zyi4vbsjdsyj4w70n5jd50baq0dzw3qpxqf1n69nfb9k214") - (mozilla-patch "icecat-CVE-2017-5373-pt5.patch" "a386ca6a3013" "1m1scz2pxzmg9wya8is5dcr3mgvkx3g1xlykgigmw2mqs5zcdg9s") - (mozilla-patch "icecat-CVE-2017-5373-pt6.patch" "0521b0e4707c" "1mv057p4hcvapibpbd9apryag19aiqdzafc6df2angl97m4mcbjx") - (mozilla-patch "icecat-bug-1290037.patch" "bf0dd9ae6807" "02iw5ngsvvij95arnn69a744d6si27g1x41ixg16l51dbn900b3r") - (mozilla-patch "icecat-bug-1322666.patch" "576f03e362c5" "0m88xs0jwhzx2lg12cvimxjknp7rpsvvhxxblhiqqjwnqip0pyc0") - (mozilla-patch "icecat-bug-1304266.patch" "4d82e7314a72" "1rrrw4rw0xv7c2myiypcqh1fk47rk3fvic79zh6m04bl3knclr1r") - (mozilla-patch "icecat-CVE-2017-5373-pt7.patch" "0617dd4b444d" "1ipags2cl2p521pm0qx110h5di2mgif6h1r3g8l9b0rc5m9b1y2j") - (mozilla-patch "icecat-CVE-2017-5375.patch" "ead08c2a6c57" "1nnnwdr7411xpz6n9j869g6sz447cq6xsmds9cw6d24iprcinp5m") - (mozilla-patch "icecat-CVE-2017-5378-pt1.patch" "c5e67d41bdd0" "05kwn5zv381lsiw9vbzm8fh6s1lddx47l8f4pwg487h9dj7vbdfq") - (mozilla-patch "icecat-CVE-2017-5373-pt8.patch" "2ce94f2ea797" "1yrnjqpafjns68z99s1m6jins3agid7c1z3v9qgk5xzfcddl31pn") - (mozilla-patch "icecat-CVE-2017-5373-pt9.patch" "e4ac8a66d3db" "1ggbh6nk005plm7kvp7qznbnlpidqkipxc5hlaqbjc3m0z9mypzl") - (mozilla-patch "icecat-CVE-2017-5386.patch" "8c171b75a0c6" "1cplkgwkhqvb62q7s8cya2drjdswnlicv5d9a60fxvnp6m7a3z02") - (mozilla-patch "icecat-CVE-2017-5383-pt2.patch" "79a31d8153bf" "0dzwk2hc741c0jr8xya4y8q59lk8mcgnvfdrdk0vzq1gby16b9zi") - (mozilla-patch "icecat-CVE-2017-5378-pt2.patch" "747085a1cd93" "0rpc8hl0jka4akdjnlwya4x9v4pqa1r5vc4pkmxsgvqpp2vkq4m2") - (mozilla-patch "icecat-bug-1331606.patch" "f0329536734b" "1br5shyfwp009y623wgjq60vhcp5k5zpzkgy4r3s5yrm5xyfcprf") - (mozilla-patch "icecat-bug-1328642.patch" "237c1ca6e035" "0808g5j17var6wv6ivj08i43fwkga9abmmgmz5w3hb8mhajkjw58") - (mozilla-patch "icecat-CVE-2017-5396.patch" "910ad552cbf5" "1qss3gc6n4myzwvwanc09xvyiq3hwhixn2xvpbk9xkfz2apdlfa6") - (mozilla-patch "icecat-bug-1312827.patch" "5c894801eb1e" "03xyjwx9rfx5w7q6wq9if83fcfgrlvvbyxpsawzxxgybnizyy7g8") - (mozilla-patch "icecat-bug-1191841.patch" "83ee87b301bd" "1kd9z4py372a2f1jg7jwvwri43vipf0k7lcvsg7b0cqr5p70zwcg") - (mozilla-patch "icecat-bug-1234317.patch" "eb6f18dbfe8d" "1dh3263fvg3dxav09g6fn41ax4q1jmwp5fk6pl6shn16mrfha1qq"))) + (search-patch "icecat-binutils.patch"))) (modules '((guix build utils))) (snippet '(begin From 1fa8a51ecc438581bfa77c11a5ca0eeb78b3b917 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 9 Mar 2017 03:34:16 -0500 Subject: [PATCH 431/436] gnu: icecat: Add fixes from upstream Firefox ESR 45.8.0. Includes fixes for CVE-2017-5398, CVE-2017-5400, CVE-2017-5401, CVE-2017-5402, CVE-2017-5404, CVE-2017-5405, CVE-2017-5407, CVE-2017-5408, CVE-2017-5409, and CVE-2017-5410. * gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr45 repository. --- gnu/packages/gnuzilla.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 5ec90e500f..e6e24f6650 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -316,7 +316,39 @@ standards.") (patches (list (search-patch "icecat-avoid-bundled-libraries.patch") - (search-patch "icecat-binutils.patch"))) + (search-patch "icecat-binutils.patch") + (mozilla-patch "icecat-CVE-2017-5398-pt01.patch" "1a39a54b5fea" "0k3sbf2w2yng2rpv6wl9zrm5cbsgq3pslr19xwrk8sk753as79fp") + (mozilla-patch "icecat-CVE-2017-5402.patch" "9828c3bb7b73" "0zgks0v9sqhwwkmry4daswvjwk6aqln6abx0iac1vwqqpg6swff6") + (mozilla-patch "icecat-CVE-2017-5398-pt02.patch" "fa3268a1147e" "1jyd1hvp42pz5l15agmb1jhw74b38x8xnj9ih5v4pskv41bgmyg5") + (mozilla-patch "icecat-CVE-2017-5400.patch" "347c10e4d6d1" "1w6yrm97l477q4ripbj0nimc87p4jscabvihpncxqbq9xzc4km7p") + (mozilla-patch "icecat-CVE-2017-5410.patch" "fe4a2cda54ad" "0spcs93hpz13d8670jgvww80f0ynrbhwbh62fkv27lpr6wmqwqh1") + (mozilla-patch "icecat-CVE-2017-5401.patch" "c38f8546be5f" "1sa22w9kzgynsn4c6zh4d66byskk5kffzbvlzrhyzvqjddypf9p8") + (mozilla-patch "icecat-CVE-2017-5398-pt03.patch" "41c80ecafa99" "0r33arr5wcgl00zgncasiyl65bmm6jy45clxnbb75nzjmsd1zx1s") + (mozilla-patch "icecat-CVE-2017-5405.patch" "381552c888b4" "1sjhh390cx1jqx74lxk6qd8f8ccppqgagqfhc9pnbm2m67hxvkj9") + (mozilla-patch "icecat-CVE-2017-5407.patch" "4ba337cdb998" "0vyknizid2z9nvl31m08c7fknizhv8dh8m54apm39k8lx77vf70p") + (mozilla-patch "icecat-CVE-2017-5398-pt04.patch" "886650fac531" "18fsr5dmav96ja0dah7mj34n8mjpckp0bbc32zjyaj5qx0m4h5cw") + (mozilla-patch "icecat-CVE-2017-5409.patch" "0a22becb23cd" "19fshrq4qkj5s0mjrads6by84gy7rsq3k57gha6sw6rvx8chjaz6") + (mozilla-patch "icecat-CVE-2017-5398-pt05.patch" "a0ead6ef09eb" "1hpsq81hhhq2a2dcq2dfndiwx93vvp5rfq0cgv6kwk2bsrq77wqq") + (mozilla-patch "icecat-CVE-2017-5398-pt06.patch" "d3fede027d06" "1aw02p367cm0ayijdiiawlb7qhab6jwqwkakj317yd1cjnmkalwr") + (mozilla-patch "icecat-CVE-2017-5398-pt07.patch" "ffca0f060bb4" "0qwisfp7idjj5nc1vp1afrf5lj66l2gp7rllkjmrqpz6cyfc708v") + (mozilla-patch "icecat-CVE-2017-5398-pt08.patch" "4aa65b44dcb9" "07j6dz2b7hp1bkfvkxwgpn2wc3hqrgjgwpaz96fcpz8yadg2fssw") + (mozilla-patch "icecat-bug-1318914.patch" "30e2382d800f" "0w8zky5i7zc5q943x37rdvi4wbcing0q7w9fcgvnnh5li2sbrsy8") + (mozilla-patch "icecat-CVE-2017-5408.patch" "403d2300adc2" "06r4j48rc1fd9gvmvqy68mlqah5xfxpkvwmxk0gnqc364kpq9slk") + (mozilla-patch "icecat-CVE-2017-5398-pt09.patch" "546ab5e99568" "05rdb9bm3n4lj0zq5a95xnwsb0vzirb9mbc2wf9xbi4xlamsgvvw") + (mozilla-patch "icecat-bug-1311380.patch" "ef6eeb7f8846" "1w19is5blbrwf3wlmy6wzgabih8sxp2kmkffqcj2g4jypfwyqn73") + (mozilla-patch "icecat-CVE-2017-5398-pt10.patch" "eec69810d80e" "1r20abhw7b38igsrdpkhcfwx9i9gmcxikv4y3sjr4wkbp684f7av") + (mozilla-patch "icecat-CVE-2017-5398-pt11.patch" "fec35ce6e68b" "1imdfrs8dxz44rhsmvydh29w5j64cij6g5ggrmhvz3386xvlil2v") + (mozilla-patch "icecat-CVE-2017-5398-pt12.patch" "725e2a217722" "06gfhi2ich279rjnxi15fb4igimsxnv5w6bx4g91js8wbvp2r3v0") + (mozilla-patch "icecat-CVE-2017-5398-pt13.patch" "d905a2e3a4d9" "1ibxi2s0czj47b739zmmjzbln8lpn27hdg4b17w58vhbhzkq31cx") + (mozilla-patch "icecat-CVE-2017-5398-pt14.patch" "0032560ae945" "0md3p5cix6nzbj5m199awc9gk52pygy5s9lx3a38vh3xvd92lsbj") + (mozilla-patch "icecat-CVE-2017-5398-pt15.patch" "91dda1e79ad8" "0b5h8fhagczfqkdgby982w6qgkw9y11zxxpdbn89rwmjpyp9nghx") + (mozilla-patch "icecat-CVE-2017-5404.patch" "556dd9e4a9e3" "0mbdx4xn1xs67n47ys9m42lc5ny96rz21ala848yajpdlxsz680g") + (mozilla-patch "icecat-bug-1341137-pt1.patch" "e86e0423dad1" "0dk1v7lcs61nx76qxcibha3ygqri15ldcvwwsrsayff9fq6k0v4y") + (mozilla-patch "icecat-bug-1341137-pt2.patch" "9aebee8b8cb9" "0m7p5iprhhwdv89aqqg7fla5szw6v7x2sll4ns0zg60pk4vm6izq") + (mozilla-patch "icecat-bug-1341137-pt3.patch" "69f3d44bdb48" "1ad7rw6nmg3c49ylqxlqqkb6cm2f0ygfzrigs6b60a2zkjqhbl0h") + (mozilla-patch "icecat-bug-1341137-pt4.patch" "22546e2cee64" "0gbwxa3p7qkq53hwnvxcqhx8h34qmnjdxy0h3ajik4mw76vrna9s") + (mozilla-patch "icecat-bug-1341137-pt5.patch" "e5083d8a855a" "1247vbpqzf007nigbxxqd6nwgr1dxd4p8cd0dr45afqh19vhlapj") + (mozilla-patch "icecat-bug-1339122.patch" "b0d156c7445e" "026jp5bb565yvhkmmicgygcn1lmak85p0466yl1vnjlx1rc8n724"))) (modules '((guix build utils))) (snippet '(begin From 483188b76efcda27865a9d5082c99d91b9bde35b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 9 Mar 2017 02:05:07 -0500 Subject: [PATCH 432/436] gnu: inetutils: Set the $localstatedir. This is a followup to commit 6f5d28f9d05aaa9743b3aac6bceb2c6323122d2d. * gnu/packages/admin.scm (inetutils)[arguments]: Pass '--localstatedir=/var' to #:configure-flags. --- gnu/packages/admin.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index a7f97f6893..e7364f6e53 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -253,6 +253,8 @@ re-executing them as necessary.") (base32 "05n65k4ixl85dc6rxc51b1b732gnmm8xnqi424dy9f1nz7ppb3xy")))) (build-system gnu-build-system) + (arguments + '(#:configure-flags '("--localstatedir=/var"))) (inputs `(("ncurses" ,ncurses) ("readline" ,readline))) ;for 'ftp' (native-inputs `(("netstat" ,net-tools))) ;for tests From 7b1866d7835423554308f54e7736734731cfc0cb Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 9 Mar 2017 06:08:18 -0500 Subject: [PATCH 433/436] gnu: python-fake-factory: Add back missing patch file. This reverts the removal of "python-fake-factory-fix-build-32bit.patch" by commit ce7911ddae5d30ba73c8c9552b7d4e71268e5db3. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + .../python-fake-factory-fix-build-32bit.patch | 36 +++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 gnu/packages/patches/python-fake-factory-fix-build-32bit.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4297cbb965..cbd61e0972 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -862,6 +862,7 @@ dist_patch_DATA = \ %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \ %D%/packages/patches/python-statsmodels-fix-tests.patch \ %D%/packages/patches/python-configobj-setuptools.patch \ + %D%/packages/patches/python-fake-factory-fix-build-32bit.patch \ %D%/packages/patches/python-faker-fix-build-32bit.patch \ %D%/packages/patches/python-pandas-skip-failing-tests.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ diff --git a/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch b/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch new file mode 100644 index 0000000000..cb60896fad --- /dev/null +++ b/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch @@ -0,0 +1,36 @@ +These tests fail on 32-bit due to an overflow. + +Upstream bug URL: https://github.com/joke2k/faker/issues/408 + +diff --git a/faker/tests/__init__.py b/faker/tests/__init__.py +index 6026772..58b6b83 100644 +--- a/faker/tests/__init__.py ++++ b/faker/tests/__init__.py +@@ -384,7 +384,6 @@ class FactoryTestCase(unittest.TestCase): + provider = Provider + # test century + self.assertTrue(self._datetime_to_time(provider.date_time_this_century(after_now=False)) <= self._datetime_to_time(datetime.datetime.now())) +- self.assertTrue(self._datetime_to_time(provider.date_time_this_century(before_now=False, after_now=True)) >= self._datetime_to_time(datetime.datetime.now())) + # test decade + self.assertTrue(self._datetime_to_time(provider.date_time_this_decade(after_now=False)) <= self._datetime_to_time(datetime.datetime.now())) + self.assertTrue(self._datetime_to_time(provider.date_time_this_decade(before_now=False, after_now=True)) >= self._datetime_to_time(datetime.datetime.now())) +@@ -413,8 +412,6 @@ class FactoryTestCase(unittest.TestCase): + + # ensure all methods provide timezone aware datetimes + with self.assertRaises(TypeError): +- provider.date_time_this_century(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now() +- with self.assertRaises(TypeError): + provider.date_time_this_decade(after_now=False, tzinfo=utc) <= datetime.datetime.now() + with self.assertRaises(TypeError): + provider.date_time_this_year(after_now=False, tzinfo=utc) <= datetime.datetime.now() +@@ -423,7 +420,6 @@ class FactoryTestCase(unittest.TestCase): + + # test century + self.assertTrue(provider.date_time_this_century(after_now=False, tzinfo=utc) <= datetime.datetime.now(utc)) +- self.assertTrue(provider.date_time_this_century(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now(utc)) + # test decade + self.assertTrue(provider.date_time_this_decade(after_now=False, tzinfo=utc) <= datetime.datetime.now(utc)) + self.assertTrue(provider.date_time_this_decade(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now(utc)) +-- +2.11.1 + From 0da4f3659aadeb3f72b405a19dd6c69ccff7c30e Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Wed, 8 Mar 2017 18:04:58 +0100 Subject: [PATCH 434/436] gnu: Add rsnapshot. * gnu/packages/backup.scm (rsnapshot): New variable. --- gnu/packages/backup.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index d557bf3f01..8eaab8a871 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2014 Ian Denhardt ;;; Copyright © 2015, 2016 Leo Famulari ;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017 Thomas Danckaert ;;; ;;; This file is part of GNU Guix. ;;; @@ -42,6 +43,7 @@ #:use-module (gnu packages mcrypt) #:use-module (gnu packages nettle) #:use-module (gnu packages pcre) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages rsync) @@ -372,6 +374,42 @@ to a remote location, and only the differences will be transmitted. Finally, rdiff-backup is easy to use and settings have sensible defaults.") (license license:gpl2+))) +(define-public rsnapshot + (package + (name "rsnapshot") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/rsnapshot/rsnapshot/releases/download/" + version "/rsnapshot-" version ".tar.gz")) + (sha256 + (base32 + "05jfy99a0xs6lvsjfp3wz21z0myqhmwl2grn3jr9clijbg282ah4")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (substitute* '("t/cmd-post_pre-exec/conf/pre-true-post-true.conf" + "t/backup_exec/conf/backup_exec_fail.conf" + "t/backup_exec/conf/backup_exec.conf") + (("/bin/true") (which "true")) + (("/bin/false") (which "false"))) + (zero? (system* "make" "test"))))))) + (inputs + `(("perl" ,perl) + ("rsync" ,rsync))) + (home-page "http://rsnapshot.org") + (synopsis "Deduplicating snapshot backup utility based on rsync") + (description "rsnapshot is a filesystem snapshot utility based on rsync. +rsnapshot makes it easy to make periodic snapshots of local machines, and +remote machines over SSH. To reduce the disk space required for each backup, +rsnapshot uses hard links to deduplicate identical files.") + (license license:gpl2+))) + (define-public libchop (package (name "libchop") From 64fc9f65f10b7ec584e6246914be322207162c0e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 9 Mar 2017 12:37:21 +0100 Subject: [PATCH 435/436] gexp: Expose functions to allow creating derivation builders. * guix/gexp.scm: Add load-path-expression and gexp-modules to the public interface of the module. See . --- guix/gexp.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/guix/gexp.scm b/guix/gexp.scm index 1f7fbef0a0..d11ed177fe 100644 --- a/guix/gexp.scm +++ b/guix/gexp.scm @@ -68,6 +68,9 @@ file-append-base file-append-suffix + load-path-expression + gexp-modules + gexp->derivation gexp->file gexp->script From 9ec2a4d3fec44f08a55df9f5f3d1a04b83e7fcf6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 9 Mar 2017 16:26:14 +0100 Subject: [PATCH 436/436] hydra: Really disable 32-to-64-bit cross-builds. Fixes . Reported by Efraim Flashner . * build-aux/hydra/gnu-system.scm (hydra-jobs)[cross-jobs](from-32-to-64?): Check whether TARGET contains "64" rather than checking whether TARGET ends in "64", which is rarely the case. (same?): Add special case for armhf-linux. --- build-aux/hydra/gnu-system.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/build-aux/hydra/gnu-system.scm b/build-aux/hydra/gnu-system.scm index a9df44a64d..04a9d0508a 100644 --- a/build-aux/hydra/gnu-system.scm +++ b/build-aux/hydra/gnu-system.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -257,14 +257,17 @@ valid." ;; prevents known-to-fail cross-builds from i686-linux or armhf-linux to ;; mips64el-linux-gnuabi64. (and (or (string-prefix? "i686-" system) + (string-prefix? "i586-" system) (string-prefix? "armhf-" system)) - (string-suffix? "64" target))) + (string-contains target "64"))) ;x86_64, mips64el, aarch64, etc. (define (same? target) ;; Return true if SYSTEM and TARGET are the same thing. This is so we ;; don't try to cross-compile to 'mips64el-linux-gnu' from ;; 'mips64el-linux'. - (string-contains target system)) + (or (string-contains target system) + (and (string-prefix? "armhf" system) ;armhf-linux + (string-prefix? "arm" target)))) ;arm-linux-gnueabihf (define (pointless? target) ;; Return #t if it makes no sense to cross-build to TARGET from SYSTEM.