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3127 commits

Author SHA1 Message Date
Lars-Dominik Braun 07f2e4993b
gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:54 +02:00
Lars-Dominik Braun e51a3f4a72
gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:54 +02:00
Lars-Dominik Braun fb1ffc53ba
gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:54 +02:00
Lars-Dominik Braun 7eb9fe4e53
gnu: ngless: Fix build.
Apply upstream patch to restore compatibility with current Stackage.

* gnu/packages/patches/ngless-unliftio.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bioinformatics.scm (ngless): Use it.
2021-10-08 09:13:53 +02:00
Xinglu Chen ed044023d7
gnu: idris: Fix build.
Backport some commits from upstream.

* gnu/packages/patches/idris-build-with-haskeline-0.8.patch:
* gnu/packages/patches/idris-build-with-megaparsec-9.patch: New patches
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/idris.scm (idris): Use them.

Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
2021-10-08 09:13:53 +02:00
Lars-Dominik Braun 2a1b6c0dbf
gnu: hedgewars: Fix build.
* gnu/packages/patches/hedgewars-network-bsd.patch: Import upstream patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/games.scm (hedgewars): Use it.
2021-10-08 09:13:53 +02:00
Lars-Dominik Braun a389190855
gnu: cabal-install: Build with GHC 8.10.
* gnu/packages/patches/cabal-install-base16-bytestring1.0.patch: New patch.
* gnu/packages/patches/cabal-install-ghc8.10.patch: Ditto.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/haskell-apps.scm (cabal-install) [source]: Use them.
2021-10-08 09:13:53 +02:00
Lars-Dominik Braun b97f549b14
gnu: Update Haskell ecosystem.
Bump packages’ versions to the lastest Stackage or Hackage
release. Since packages are interdependent, do so in a single commit.

525 packages have been updated.

These packages have been removed, because they fail to build, have no
newer version available and no dependencies:

corrode
ghc-easytest
ghc-edisonapi
ghc-edisoncore
ghc-pandoc-types
ghc-regex-tdfa-text

These have been removed, because they are no longer required:

ghc-happy-1.19.9
ghc-prettyprinter-1.6
ghc-protolude-0.3

ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc
does not use them any more.

Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
2021-10-08 09:13:52 +02:00
Julien Lepiller a3d528fa24
gnu: ocaml-cairo2: Update to 0.6.2.
* gnu/packages/ocaml.scm (ocaml-cairo2): Update to 0.6.2.
* gnu/packages/patches/ocaml-cairo2-caml_ba_array-fix.patch: Remove
file.
* gnu/local.scm (dist_patch_DATA): Remove it.
2021-10-08 04:34:07 +02:00
Greg Hogan 04c5d89482
gnu: ceph: Fix breaking change in snappy.
* gnu/packages/storage.scm (ceph)[source]: Add patch.
* gnu/packages/patches/ceph-fix-snappy-breaking-change.patch: New file.
* gnu/local.mk: Add it.

Signed-off-by: Marius Bakke <marius@gnu.org>
2021-10-08 00:00:21 +02:00
Ryan Sundberg via Guix-patches via 9aaf402a37
gnu: php: Patch failing test case.
Fixes a failing test case in PHP (Zend/tests/bug74093.phpt).  See
<https://github.com/php/php-src/pull/7555/files> for upstream status.

* gnu/packages/php.scm (php)[source]: Add patch.
* gnu/packages/patches/php-bug-74093-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2021-10-05 13:45:29 +02:00
Tobias Geerinckx-Rice 9f55a39cf1
gnu: diffoscope: Update to 186.
* gnu/packages/diffoscope.scm (diffoscope): Update to 186.
[source]: Add patch.
[arguments]: Add a new 'fix-failing-tests phase.
Don't explicitly return #t from phases.
* gnu/packages/patches/diffoscope-fix-test_item3_deflate_llvm_bitcode.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2021-10-04 21:21:11 +02:00
Tobias Geerinckx-Rice 4d5f7986d6
gnu: libcacard: Update to 2.8.1.
* gnu/packages/spice.scm (libcacard): Update to 2.8.1.
[source]: Remove patch.
* gnu/packages/patches/libcacard-unknown-variable.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-10-04 13:31:36 +02:00
Tobias Geerinckx-Rice 413f8f3fa5
gnu: hexchat: Update to 2.16.0.
* gnu/packages/messaging.scm (hexchat): Update to 2.16.0.
[source]: Remove patch.
[inputs]: Remove libnotify and libproxy.  Upgrade python-2 to python@3.
Add python-cffi and bash-minimal.
[arguments]: Don't explicitly return #t from phases.
Add a new 'wrap-program phase.
2021-10-03 21:49:54 +02:00
Tobias Geerinckx-Rice 9b9c74eaa7
gnu: ccache: Update to 4.4.2.
* gnu/packages/ccache.scm (ccache): Update to 4.4.2.
[source]: Remove patch.
[arguments]: Substitute nonexistent compgen.
* gnu/packages/patches/ccache-fix-basedir-test.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-10-03 19:23:49 +02:00
Guillaume Le Vaillant 1623e6023b
gnu: sbcl-burgled-batteries3: Fix compiling with sbcl >= 2.1.6.
* gnu/packages/patches/sbcl-burgled-batteries3-fix-signals.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/lisp-xyz.scm (sbcl-burgled-batteries3)[source]: Use it.
2021-09-28 11:37:02 +02:00
Guillaume Le Vaillant dce9b98d55
gnu: sbcl-png: Fix compiling with sbcl >= 2.1.6.
* gnu/packages/patches/sbcl-png-fix-sbcl-compatibility.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/lisp-xyz.scm (sbcl-png)[source]: Use it.
2021-09-28 10:46:40 +02:00
Tobias Geerinckx-Rice 85d757b53d
gnu: ccache: Update to 4.4.1.
* gnu/packages/ccache.scm (ccache): Update to 4.4.1.
[source]: Add patch.
[arguments]: Remove explicit #t return values from phases.
* gnu/packages/patches/ccache-fix-basedir-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2021-09-28 02:15:35 +02:00
Oleg Pykhalov 6ae4644984
Merge branch 'wip-guix-home' 2021-09-27 17:27:12 +03:00
Maxim Cournoyer 8153a402ae
gnu: Add patool.
* gnu/packages/patool.scm: New module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register it.
2021-09-26 20:42:34 -04:00
Vinicius Monego 6e5e60a20c
gnu: Add xgboost.
* gnu/packages/machine-learning.scm (xgboost): New variable.
* gnu/packages/patches/xgboost-use-system-dmlc-core.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>
2021-09-25 16:06:28 -04:00
Ludovic Courtès 8df301d467
gnu: Add NNPACK.
* gnu/packages/machine-learning.scm (nnpack): New variable.
* gnu/packages/patches/nnpack-system-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2021-09-24 13:48:49 +02:00
Marius Bakke 6a805f22a3
gnu: ungoogled-chromium: Update to 93.0.4577.82-0.3f62dbc.
* gnu/packages/patches/ungoogled-chromium-ffmpeg-compat.patch,
gnu/packages/patches/ungoogled-chromium-system-nspr.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for version
93.
(%chromium-version): Set to 93.0.4577.82.
(%ungoogled-revision): Set to 93.0.4577.82-1-2-g3f62dbc.
(%debian-patches): Remove 'system/nspr.patch'.
(%ungoogled-origin): Update source hash.
(%guix-patches): Add 'ungoogled-chromium-ffmpeg-compat.patch' and
'ungoogled-chromium-system-nspr.patch'.
(ungoogled-chromium-snippet): Remove PYTHON-2 usage.  Don't unbundle
'snappy'.
(libvpx/chromium): Remove variable.
(ungoogled-chromium)[source]: Update hash.
[arguments]: Add "is_cfi=false", "use_thin_lto=false", and
"blink_enable_generated_code_formatting=false".
[native-inputs]: Change CLANG-11 to CLANG-12.  Change NODE to NODE-LTS.  Add
PYTHON-BEAUTIFULSOUP4 and PYTHON-HTML5LIB.  Remove PYTHON-2.
[inputs]: Change LIBVPX/CHROMIUM to LIBVPX.
2021-09-23 12:05:53 +02:00
Marius Bakke 855e34d44f
gnu: LLVM, Clang: Update to 12.0.1.
* gnu/packages/patches/clang-12-tools-extra-directory.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/llvm.scm (llvm-12, clang-runtime-12): Update to 12.0.1.
(clang-12): Likewise.  Remove obsolete patch.
2021-09-23 12:05:53 +02:00
Leo Famulari 1e3262d74f
gnu: ntfs-3g: Update to 2021.8.22 [security fixes].
The upstream security advisory is named NTFS3G-SA-2021-0001.

Fixes CVE-2021-33285, CVE-2021-35269, CVE-2021-35268, CVE-2021-33289,
CVE-2021-33286, CVE-2021-35266, CVE-2021-33287, CVE-2021-35267, CVE-2021-39251,
CVE-2021-39252, CVE-2021-39253, CVE-2021-39254, CVE-2021-39255, CVE-2021-39256,
CVE-2021-39257, CVE-2021-39258, CVE-2021-39259, CVE-2021-39260, CVE-2021-39261,
CVE-2021-39262, CVE-2021-39263.

For more information:

https://seclists.org/oss-sec/2021/q3/139

* gnu/packages/linux.scm (ntfs-3g): Update to 2021.8.22.
[source]: Remove obsolete patch.
* gnu/packages/patches/ntfs-3g-CVE-2019-9755.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-09-21 13:28:02 -04:00
Xinglu Chen 94d2d0b7f8
gnu: patchutils: Update to 0.4.2.
* gnu/packages/patchutils.scm (patchutils): Update to 0.4.2.
[source]: Remove patch.
[inputs]: Add ‘python’.
[arguments]<#:phases>: Remove trailing #t.
* gnu/local.mk (dist_patch_DATA): Remove patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-09-21 15:15:52 +02:00
Andrew Tropin bac597cc96
home-services: Add Mcron.
* gnu/home-services/mcron.scm: New file.
* gnu/local.mk: Add this.
* doc/guix.texi: Add documentation about Mcron Home Service.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-13 22:41:25 +03:00
Philip McGrath fd22921490
gnu: racket: fix raco exe with non-minimal Racket
This commit backports an upstream repair for a bug exposed by Guix's
change in Racket 8.2 to make the `racket` package a layered/tethered
installation that chains to the `racket-minimal` package. When using a
layered/tethered installation, the `setup/variant` library would fail to
recognize the default Racet variant (CS, 3M, or CGC), leading to
confusing failures from `raco exe`, `create-embedding-executable`, and
other clients.

For further details, see <https://issues.guix.gnu.org/50118> and
<https://github.com/racket/racket/issues/3969>.

* gnu/packages/patches/racket-minimal-backport-1629887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/racket.scm (racket-minimal)[source]: Use it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-09-10 17:30:55 +02:00
Sarah Morgensen 63cc4dd579
gnu: go-github-com-urfave-cli-v2: Fix tests when building with Go 1.17.
* gnu/packages/patches/go-github-com-urfave-cli-v2-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/golang.scm (go-github-com-urfave-cli-v2)[origin]: Apply it.

Signed-off-by: Leo Famulari <leo@famulari.name>
2021-09-09 21:34:50 -04:00
Sarah Morgensen f161f111e0
gnu: go-github-com-urfave-cli: Fix tests when building with Go 1.17.
* gnu/packages/patches/go-github-com-urfave-cli-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/golang.scm (go-github-com-urfave-cli)[origin]: Apply it.

Signed-off-by: Leo Famulari <leo@famulari.name>
2021-09-09 21:34:50 -04:00
Maxim Cournoyer 173b6f6f15
gnu: mailutils: Update to 3.13.
* gnu/packages/patches/mailutils-fix-uninitialized-variable.patch: Remove
patch.
* gnu/local.mk (dist_patch_DATA): De-register it.
* gnu/packages/mail.scm (mailutils): Update to 3.13.  Remove the 2013
--with-sql option TODO comment; if someone needs that, they can send a patch.
[source]: Remove above patch.
[phases]{prepare-test-suite}: Also patch shell shebang in
'libmailutils/tests/lock.at' and 'imap4d/tests/testclient.c'.
[parallel-tests?]: Reinstate parallel tests.
[inputs]: Move m4 to...
[native-inputs]: ... here.  Add the autoconf, automake, gettext and libtool
quartet.
2021-09-09 20:48:31 -04:00
Andrew Tropin 6b5ff71b99
home-services: Add Shepherd.
* gnu/home-services/shepherd.scm: New file.
* gnu/local.mk: Add this.
* doc/guix.texi: Add documentation about Shepherd Home Service.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 20:28:03 +03:00
Oleg Pykhalov 3a10563d47
gnu: local.mk: Tabify.
* gnu/local.mk (GNU_SYSTEM_MODULES): Normalize to tabs.
2021-09-09 20:26:51 +03:00
Andrew Tropin 833a78b16c
home-services: Add utils module.
* gnu/home-services/utils.scm (maybe-object->string object->snake-case-string)
(object->snake-case-string): New variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/utils.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 20:26:50 +03:00
Andrew Tropin 7fcc64253c
home: Add home-environment.
* gnu/home.scm
(home-environment, home-environment?, this-home-environment)
(home-environment-derivation, home-environment-user-services)
(home-environment-essential-services, home-environment-services)
(home-environment-location, home-environment-with-provenance): New variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 20:26:50 +03:00
Andrew Tropin a9214267af
home-services: Add xdg.
* gnu/home-services/xdg.scm
(home-xdg-base-directories-service-type)
(home-xdg-base-directories-configuration)
(home-xdg-base-directories-configuration?)
(home-xdg-user-directories-service-type)
(home-xdg-user-directories-configuration)
(home-xdg-user-directories-configuration?)
(xdg-desktop-action, xdg-desktop-entry)
(home-xdg-mime-applications-service-type)
(home-xdg-mime-applications-configuration): New variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/xdg.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 20:26:43 +03:00
Andrew Tropin 9a2e9a6144
home-services: Add shells.
* gnu/home-services/shells.scm
(home-shell-profile-service-type, home-shell-profile-configuration)
(home-bash-service-type, home-bash-configuration, home-bash-extension)
(home-zsh-service-type, home-zsh-configuration, home-zsh-extension)
(home-fish-service-type, home-fish-configuration, home-fish-extension): New
variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/shells.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 19:54:54 +03:00
Andrew Tropin a0a914a9a4
home-services: Add helper functions for service configurations.
* gnu/home-services/configuration.scm (helper functions): New variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/configuration.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 19:54:54 +03:00
Andrew Tropin 6d2e3168ce
home-services: Add fontutils.
* gnu/home-services/fontutils.scm (home-fontconfig-service-type): New
variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/fontutils.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 19:54:54 +03:00
Andrew Tropin 1cc03081e8
home-services: Add symlink-manager.
* gnu/home-services/symlink-manager.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/symlink-manager.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 19:54:54 +03:00
Andrew Tropin 3588bb0f4a
home-services: Add most essential home services.
* gnu/home-services.scm (home-service-type, home-profile-service-type)
(home-environment-variables-service-type, home-files-service-type)
(home-run-on-first-login-service-type, home-activation-service-type): New
variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2021-09-09 19:54:53 +03:00
Xinglu Chen 550f4aa682
gnu: ocaml-ppx-variants-conv: Patch for building with ocaml-ppxlib.
The patch will make it build when building it with ocaml-ppxlib@0.23.0.

* gnu/packages/patches/ocaml-ppx-variants-ppxlib-api-change.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/ocaml.scm (ocaml-ppx-variants-conv): Apply the patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-09-06 23:27:40 +02:00
Danny Milosavljevic dd7df191b6
gnu: u-boot-nintendo-nes-classic-edition: Make it actually boot again.
* gnu/packages/patches/u-boot-nintendo-nes-serial.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add u-boot-nintendo-nes-serial.patch.
* gnu/packages/bootloaders.scm (u-boot-nintendo-nes-classic-edition): Downgrade to 2018.11.
[source]: Add patch.
[description]: Modify.
[native-inputs]: Add python-2.
2021-09-05 23:45:29 +02:00
Lars-Dominik Braun 46ba1bb068
gnu: beets: Update to 1.5.0.
* gnu/packages/music.scm (beets) [version]: Update to 1.5.0.
[#:phases]: Keep testcase, switch to pytest and respect tests?.
[native-inputs]: Move plugin dependencies…
[inputs]: …here.
* gnu/packages/music.scm (beets-next): Mark as deprecated.
* gnu/packages/patches/beets-werkzeug-compat.patch: Delete patch.
* gnu/local.mk: Deregister it.
2021-09-04 14:53:35 +02:00
Simon Streit ab12354c0a
gnu: python-mediafile: Update to 0.7.0.
Remove patch. It is now included in upstream release.

* gnu/packages/music.scm (python-mediafile): Update to 0.7.0.
* gnu/packages/patches/python-mediafile-wavpack.patch: Delete patch.
* gnu/local.mk: Deregister it.
2021-09-04 14:53:34 +02:00
Ludovic Courtès a5fb1f4eeb
gnu: mailutils: Look up Scheme variables in the right module.
Fixes <https://issues.guix.gnu.org/49295>.
Reported by Maxime Devos <maximedevos@telenet.be>.

* gnu/packages/patches/mailutils-variable-lookup.patch: New file.
* gnu/packages/mail.scm (mailutils)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
2021-09-01 23:41:41 +02:00
Ludovic Courtès b4452ffe9b
build: Build (gnu packages rocm).
This is a followup to df90cb1d5c.

* gnu/local.mk (GNU_SYSTEM_MODULES): Add %D%/packages/rocm.scm.
2021-08-30 14:27:30 +02:00
Ludovic Courtès 8e8d85f722
build: Build (gnu system setuid).
This is a followup to 45235e67e4.

* gnu/local.mk (GNU_SYSTEM_MODULES): Add %D%/system/setuid.scm.
2021-08-30 12:26:03 +02:00
Maxim Cournoyer b1ef8b410c
gnu: python-pytest-asyncio: Enable tests and patch for Python 3.8.
* gnu/packages/patches/python-pytest-asyncio-python-3.8.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/check.scm (python-pytest-asyncio)
[source]: Fetch from git and apply above patch.
[phases]: Override the check phase, enabling tests.
2021-08-29 01:05:28 -04:00
Maxim Cournoyer 1d94000d87
gnu: python-execnet: Update to 1.9.0 and enable tests.
* gnu/packages/patches/python-execnet-read-only-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/python-xyz.scm (python-execnet): Update to 1.9.0.
[source]: Fix indentation.
[arguments]: Enable tests, replacing the default check phase.
2021-08-29 01:05:27 -04:00