mirror of
git://git.savannah.gnu.org/guix.git
synced 2023-12-14 03:33:07 +01:00
Merge branch 'wip-r'
This commit is contained in:
Ricardo Wurmus
commit
e640da33f3
8 changed files with 1596 additions and 1393 deletions
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@ -11094,6 +11094,15 @@ expression report comparing samples in an easily configurable manner.")
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(modify-phases %standard-phases
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||||
(add-before 'bootstrap 'autoreconf
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||||
(lambda _
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||||
;; This was fixed in commit
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||||
;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no
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||||
;; release with this fix.
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||||
(call-with-output-file "VERSION"
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||||
(lambda (port) (display ,version port)))
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||||
;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176
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(substitute* "m4/ax_r_package.m4"
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(("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
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"if(system.file(package=\"PKG\") == \"\")"))
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(invoke "autoreconf" "-vif")))
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||||
(add-before 'configure 'set-PYTHONPATH
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||||
(lambda _
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@ -11182,6 +11191,15 @@ in an easily configurable manner.")
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(modify-phases %standard-phases
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||||
(add-before 'bootstrap 'autoreconf
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(lambda _
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||||
;; This was fixed in commit
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;; d56ac732524da659afbbb0972f7a87fa178ae58e, but there is no
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;; release with this fix.
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(call-with-output-file "VERSION"
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(lambda (port) (display ,version port)))
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;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/181
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(substitute* "m4/ax_r_package.m4"
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(("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
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"if(system.file(package=\"PKG\") == \"\")"))
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(invoke "autoreconf" "-vif")))
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(add-before 'configure 'set-PYTHONPATH
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(lambda _
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||||
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@ -11249,8 +11267,20 @@ methylation and segmentation.")
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"1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885"))))
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(build-system gnu-build-system)
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||||
(arguments
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||||
'(#:phases
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||||
`(#:phases
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||||
(modify-phases %standard-phases
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||||
(add-before 'bootstrap 'autoreconf
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(lambda _
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||||
;; This was fixed in commit
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;; c4ac067438ae9312b5786a72e2bfb3d795e3ec8a, but there is no
|
||||
;; release with this fix.
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||||
(call-with-output-file "VERSION"
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||||
(lambda (port) (display ,version port)))
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||||
;; https://github.com/BIMSBbioinfo/pigx_scrnaseq/issues/59
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||||
(substitute* "m4/ax_r_package.m4"
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(("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
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"if(system.file(package=\"PKG\") == \"\")"))
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(invoke "autoreconf" "-vif")))
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||||
(add-before 'configure 'set-additional-environment-variables
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||||
(lambda _
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;; Needed because of loompy
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||||
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@ -11299,6 +11329,8 @@ methylation and segmentation.")
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r-singlecellexperiment
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r-stringr
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r-yaml))
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||||
(native-inputs
|
||||
(list autoconf automake))
|
||||
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
|
||||
(synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
|
||||
(description
|
||||
|
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@ -11327,6 +11359,13 @@ based methods.")
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`(#:tests? #f ;requires huge kraken database
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#:phases
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||||
(modify-phases %standard-phases
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||||
(add-before 'bootstrap 'autoreconf
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(lambda _
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;; https://github.com/BIMSBbioinfo/pigx_sars-cov-2/issues/123
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(substitute* "m4/ax_r_package.m4"
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(("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
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"if(system.file(package=\"PKG\") == \"\")"))
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(invoke "autoreconf" "-vif")))
|
||||
(add-before 'configure 'set-PYTHONPATH
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(lambda _
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(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
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||||
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@ -4207,7 +4207,7 @@ the SQL language using a syntax that reflects the resulting query.")
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|||
(define-public apache-arrow
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(package
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||||
(name "apache-arrow")
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(version "7.0.0")
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(version "8.0.0")
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(source
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(origin
|
||||
(method git-fetch)
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||||
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@ -4217,7 +4217,7 @@ the SQL language using a syntax that reflects the resulting query.")
|
|||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"19xx6mlddca79q6d3wga574m4y32ixmxx2rmk6j3f22i5c37mjzw"))))
|
||||
"1gwiflk72pq1krc0sjzabypmh7slfyf7ak71fiypy3xgzw8a777c"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f
|
||||
|
|
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|||
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@ -5,7 +5,7 @@
|
|||
;;; Copyright © 2014-2022 Eric Bavier <bavier@posteo.net>
|
||||
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
|
||||
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
|
||||
;;; Copyright © 2015–2021 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2015–2022 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
|
||||
;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
|
||||
|
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@ -152,6 +152,7 @@
|
|||
#:use-module (gnu packages serialization)
|
||||
#:use-module (gnu packages shells)
|
||||
#:use-module (gnu packages sphinx)
|
||||
#:use-module (gnu packages swig)
|
||||
#:use-module (gnu packages tcl)
|
||||
#:use-module (gnu packages texinfo)
|
||||
#:use-module (gnu packages tex)
|
||||
|
|
@ -1915,34 +1916,34 @@ with the provided training tools.")
|
|||
(define-public nlopt
|
||||
(package
|
||||
(name "nlopt")
|
||||
(version "2.4.2")
|
||||
(version "2.7.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
|
||||
version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/stevengj/nlopt/")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
|
||||
(build-system gnu-build-system)
|
||||
(base32 "1xpdza28i8w441fwv6a5f3qk4zi7ys6ws9fx6kr5ny27dfdz6rr1"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(;; Shared libraries are not built by default. They are required to
|
||||
;; build the Guile, Octave, and Python bindings.
|
||||
#:configure-flags '("--enable-shared")
|
||||
|
||||
#:phases
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'configure 'set-libnlopt-file-name
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
;; Make sure the Scheme module refers to the library by its
|
||||
;; absolute file name (we cannot do that from a snippet
|
||||
;; because the expansion of @libdir@ contains
|
||||
;; ${exec_prefix}.)
|
||||
;; absolute file name.
|
||||
(let ((out (assoc-ref outputs "out")))
|
||||
(substitute* "swig/nlopt.scm.in"
|
||||
(("libnlopt")
|
||||
(string-append out "/lib/libnlopt")))
|
||||
#t))))))
|
||||
(inputs (list guile-2.0))
|
||||
(native-inputs (list pkg-config))
|
||||
(substitute* "src/swig/nlopt-guile.i"
|
||||
(("\"nlopt_guile\"")
|
||||
(format #f "~s"
|
||||
`(format #f "~anlopt_guile"
|
||||
(if (getenv "NLOPT_UNINSTALLED")
|
||||
""
|
||||
,(format #f "~a/lib/guile/3.0/extensions/" out))))))
|
||||
(setenv "NLOPT_UNINSTALLED" "1")))))))
|
||||
(inputs (list guile-3.0 octave python))
|
||||
(native-inputs (list pkg-config swig))
|
||||
(home-page "http://ab-initio.mit.edu/wiki/")
|
||||
(synopsis "Library for nonlinear optimization")
|
||||
(description "NLopt is a library for nonlinear optimization, providing a
|
||||
|
|
|
|||
|
|
@ -68,6 +68,7 @@
|
|||
#:use-module (gnu packages java)
|
||||
#:use-module (gnu packages javascript)
|
||||
#:use-module (gnu packages libffi)
|
||||
#:use-module (gnu packages linux)
|
||||
#:use-module (gnu packages machine-learning)
|
||||
#:use-module (gnu packages maths)
|
||||
#:use-module (gnu packages multiprecision)
|
||||
|
|
@ -203,7 +204,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
|
|||
(define r-with-tests
|
||||
(package
|
||||
(name "r-with-tests")
|
||||
(version "4.1.3")
|
||||
(version "4.2.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://cran/src/base/R-"
|
||||
|
|
@ -211,7 +212,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1mpy4sar1amx5ai9rqr9s0nw8p65iqfrqbm5n9h402b17hrmpzqm"))))
|
||||
"123l17sv3smh5cz0vrjxjj8jf81bb860kah6iww9bl3skdqvgsiq"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:disallowed-references (,tzdata-for-tests)
|
||||
|
|
@ -237,6 +238,16 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
|
|||
(("uname") uname-bin))
|
||||
(substitute* "src/unix/sys-std.c"
|
||||
(("rm -Rf ") (string-append rm-bin " -Rf "))))))
|
||||
(add-after 'unpack 'patch-tests
|
||||
(lambda _
|
||||
;; This is needed because R is run during the check phase and
|
||||
;; /bin/sh doesn't exist in the build container.
|
||||
(substitute* "src/unix/sys-unix.c"
|
||||
(("\"/bin/sh\"")
|
||||
(string-append "\"" (which "sh") "\"")))
|
||||
;; This test fails because line numbers are off by two.
|
||||
(substitute* "tests/reg-packages.R"
|
||||
(("8 <= print" m) (string-append "## " m)))))
|
||||
(add-after 'unpack 'build-reproducibly
|
||||
(lambda _
|
||||
;; The documentation contains time stamps to demonstrate
|
||||
|
|
@ -315,6 +326,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
|
|||
(setenv "TZDIR"
|
||||
(search-input-directory inputs
|
||||
"share/zoneinfo"))))
|
||||
(add-before 'check 'set-home
|
||||
;; Some tests require that HOME be set.
|
||||
(lambda _ (setenv "HOME" "/tmp")))
|
||||
(add-after 'build 'make-info
|
||||
(lambda _ (invoke "make" "info")))
|
||||
(add-after 'build 'install-info
|
||||
|
|
@ -493,14 +507,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
|
|||
(define-public r-mass
|
||||
(package
|
||||
(name "r-mass")
|
||||
(version "7.3-56")
|
||||
(version "7.3-57")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "MASS" version))
|
||||
(sha256
|
||||
(base32
|
||||
"11gv5965ba6xr4qsp1945vd39rp0sggzpa103rwj1c5hw0abvnlv"))))
|
||||
"13asg609szqq8d1a4ybr508qcanr9gvqd439vfras6mw0l0qi2xx"))))
|
||||
(properties `((upstream-name . "MASS")))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
||||
|
|
@ -912,13 +926,13 @@ additions (tooltips, bipartite diagram type).")
|
|||
(define-public r-dichromat
|
||||
(package
|
||||
(name "r-dichromat")
|
||||
(version "2.0-0")
|
||||
(version "2.0-0.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "dichromat" version))
|
||||
(sha256
|
||||
(base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
|
||||
(base32 "10b0avdar3d1y8x2ya3x5kqxqg0z0mq872hdzvc1nn4amplph1d1"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "https://cran.r-project.org/web/packages/dichromat")
|
||||
(synopsis "Color schemes for dichromats")
|
||||
|
|
@ -1215,13 +1229,13 @@ using just two functions: melt and dcast (or acast).")
|
|||
(define-public r-ggplot2
|
||||
(package
|
||||
(name "r-ggplot2")
|
||||
(version "3.3.5")
|
||||
(version "3.3.6")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "ggplot2" version))
|
||||
(sha256
|
||||
(base32 "1si46bf9p09qzs208hqffwcb40305p361whmwhc1pwrsmx7jjxdh"))))
|
||||
(base32 "1aa377jdfajj8ld2fh159y8havlibsr4pjisf6mkzk8g5awlxjxz"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-digest
|
||||
|
|
@ -1537,13 +1551,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
|
|||
(define-public r-knitr
|
||||
(package
|
||||
(name "r-knitr")
|
||||
(version "1.38")
|
||||
(version "1.39")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "knitr" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1bg7nmd2bvfd2gscp4nly4a2c05bpgzq536bmmf93vaf860yhf6i"))))
|
||||
"0wmcj6xv0bcqzmp5vm8s574rfx366rkgm03lgyppk9ywxgnna6n9"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-evaluate r-highr r-stringr r-xfun r-yaml))
|
||||
|
|
@ -1680,13 +1694,13 @@ R packages that praise their users.")
|
|||
(define-public r-testthat
|
||||
(package
|
||||
(name "r-testthat")
|
||||
(version "3.1.3")
|
||||
(version "3.1.4")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "testthat" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0c7whxl6zwapqzdplwplvhs73w9blb419h2mdl21pwmqjhzjaq68"))))
|
||||
"02cwdix7v8zsvcmcl3h5hfi66w1ln9qi60risf5nl62f3c1yqzm4"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-brio
|
||||
|
|
@ -1760,14 +1774,14 @@ like tidy evaluation.")
|
|||
(define-public r-tibble
|
||||
(package
|
||||
(name "r-tibble")
|
||||
(version "3.1.6")
|
||||
(version "3.1.7")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "tibble" version))
|
||||
(sha256
|
||||
(base32
|
||||
"14l2i6ri3v5y0h8g0ahc4kz0pdqsp5yabxk2w8wavss6y44xjcsv"))))
|
||||
"0wn8j7slfqrdl126g536sg1xkrvjd9rlsk0bjqk3b03nyj8hi9g1"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-ellipsis
|
||||
|
|
@ -1790,13 +1804,13 @@ and printing capabilities than traditional data frames.")
|
|||
(define-public r-dplyr
|
||||
(package
|
||||
(name "r-dplyr")
|
||||
(version "1.0.8")
|
||||
(version "1.0.9")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "dplyr" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0xb04ckp29pva1h2rfahqhmk9gcwp2dbbx3av8ip40v7dnha6siv"))))
|
||||
"0sxl9yzccsdhlrrwj26lmh9frsijxyfaf7csv8mf7d0q4qqzgqg2"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-generics
|
||||
|
|
@ -2113,14 +2127,14 @@ chain.")
|
|||
(define-public r-ade4
|
||||
(package
|
||||
(name "r-ade4")
|
||||
(version "1.7-18")
|
||||
(version "1.7-19")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "ade4" version))
|
||||
(sha256
|
||||
(base32
|
||||
"09f5kh2mwygqpnvf53k0r54k0cvaafxm9x4nm819gwv05k2g9dpc"))))
|
||||
"1vv5y6badksnpjb3bcphhjdzzh6i2grmwnsalcf2cfpr3y412lf8"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-mass r-pixmap r-sp))
|
||||
|
|
@ -2245,17 +2259,19 @@ R version.")
|
|||
(define-public r-checkmate
|
||||
(package
|
||||
(name "r-checkmate")
|
||||
(version "2.0.0")
|
||||
(version "2.1.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "checkmate" version))
|
||||
(sha256
|
||||
(base32
|
||||
"193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd"))))
|
||||
"1ii11lypfz8qwswaiagaxnfq6wqkg3cq4j7k9q40sdd0cd8xv15p"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-backports))
|
||||
(native-inputs
|
||||
(list r-knitr))
|
||||
(home-page "https://github.com/mllg/checkmate")
|
||||
(synopsis "Fast and versatile argument checks")
|
||||
(description
|
||||
|
|
@ -2406,16 +2422,17 @@ tables, autolinks and strikethrough text.")
|
|||
(define-public r-roxygen2
|
||||
(package
|
||||
(name "r-roxygen2")
|
||||
(version "7.1.2")
|
||||
(version "7.2.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "roxygen2" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1zf55wywlpy7mk7zfyi3s9fhhg1m9kvafzj46iqw5cbvnlg3ssdk"))))
|
||||
"12s436jn7aagjpc2lnlrhzwqgsdl8lbbwhkddih6rnxrczawzgrf"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-brew
|
||||
r-cli
|
||||
r-commonmark
|
||||
r-cpp11
|
||||
r-desc
|
||||
|
|
@ -2427,6 +2444,7 @@ tables, autolinks and strikethrough text.")
|
|||
r-rlang
|
||||
r-stringi
|
||||
r-stringr
|
||||
r-withr
|
||||
r-xml2))
|
||||
(native-inputs
|
||||
(list r-knitr))
|
||||
|
|
@ -2440,14 +2458,14 @@ collation, and NAMESPACE files.")
|
|||
(define-public r-openssl
|
||||
(package
|
||||
(name "r-openssl")
|
||||
(version "2.0.0")
|
||||
(version "2.0.2")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "openssl" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0jsnzxa72bfxsdai25xyklmmrraaf9yv2nmqmf0bgzrkbzkgsa7b"))))
|
||||
"1i7il5kkr1yp2xk8zw7max4llga4hfz0cx9sx0v2xnb9pg4ksbc6"))))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
(list
|
||||
|
|
@ -2482,13 +2500,13 @@ integers.")
|
|||
(define-public r-httr
|
||||
(package
|
||||
(name "r-httr")
|
||||
(version "1.4.2")
|
||||
(version "1.4.3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "httr" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6"))))
|
||||
"0skwi501rzndywn81704d68n1l6lrvqilf91q08cjfhpjvx171ls"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-curl r-jsonlite r-openssl r-mime r-r6))
|
||||
|
|
@ -2721,13 +2739,13 @@ well as additional utilities such as panel and axis annotation functions.")
|
|||
(define-public r-rcpparmadillo
|
||||
(package
|
||||
(name "r-rcpparmadillo")
|
||||
(version "0.11.0.0.0")
|
||||
(version "0.11.1.1.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "RcppArmadillo" version))
|
||||
(sha256
|
||||
(base32
|
||||
"13blvrlbw8194a96v38hnllnwvyhdw5x9m0dnkyw3xsi3jrhcxin"))))
|
||||
"15s8lx3s0g9npwmys509ahrqc786lg2cid21civ3wm219i4gq2zb"))))
|
||||
(properties `((upstream-name . "RcppArmadillo")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -2813,13 +2831,13 @@ certain criterion, e.g., it contains a certain regular file.")
|
|||
(define-public r-rmarkdown
|
||||
(package
|
||||
(name "r-rmarkdown")
|
||||
(version "2.13")
|
||||
(version "2.14")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "rmarkdown" version))
|
||||
(sha256
|
||||
(base32 "0i07p3dxxv2s2a4xmyhc3qxmwg86vakniq5jjjclmcq2sahvw5vj"))))
|
||||
(base32 "081j1hpxcwadn606ch5lq279s66c1b0f0mjvap7yimnrljpigv79"))))
|
||||
(properties `((upstream-name . "rmarkdown")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -2928,13 +2946,13 @@ a column in data frame.")
|
|||
(define-public r-rsqlite
|
||||
(package
|
||||
(name "r-rsqlite")
|
||||
(version "2.2.12")
|
||||
(version "2.2.14")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "RSQLite" version))
|
||||
(sha256
|
||||
(base32
|
||||
"12ka9cp591sc3hn5r6z4skbjzm3nfq338wlpjdmw6rz26mmr2c9s"))))
|
||||
"0z307d7rx7blh2apc9dbw9vgad2ldbf9vbdjhmwlj0mwbs3nmqra"))))
|
||||
(properties `((upstream-name . "RSQLite")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -2958,15 +2976,13 @@ engine (version 3.8.8.2) is included.")
|
|||
(define-public r-rcurl
|
||||
(package
|
||||
(name "r-rcurl")
|
||||
(version "1.95-0.1.2")
|
||||
(version "1.98-1.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||||
"release/extra/src/"
|
||||
"contrib/RCurl_" version ".tar.gz"))
|
||||
(uri (cran-uri "RCurl" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
|
||||
"18nif4phr5vfhri07mnchiym0qfm31ak9nxvb2v9ac84mij6idbc"))))
|
||||
(properties `((upstream-name . "RCurl")))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
|
|
@ -2979,10 +2995,11 @@ engine (version 3.8.8.2) is included.")
|
|||
(string-append "\
|
||||
certs = Sys.getenv(\"CURL_CA_BUNDLE\")
|
||||
if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
|
||||
" m)))
|
||||
#t)))))
|
||||
" m))))))))
|
||||
(native-inputs
|
||||
(list libxml2))
|
||||
(inputs
|
||||
`(("libcurl" ,curl)))
|
||||
(list curl))
|
||||
(propagated-inputs
|
||||
(list r-bitops))
|
||||
(home-page "http://www.omegahat.net/RCurl")
|
||||
|
|
@ -3122,14 +3139,14 @@ statements.")
|
|||
(define-public r-segmented
|
||||
(package
|
||||
(name "r-segmented")
|
||||
(version "1.4-1")
|
||||
(version "1.5-0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "segmented" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1aagn2v48ncwxx79h601nlalbgc40fc81nqaw6nbncqkqm0zaxi3"))))
|
||||
"1d8np6psnmqyq3bxxd17ivp6pq6p8rx5hal4bgz8ckc4d1i9lp6n"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs (list r-mass))
|
||||
(home-page "https://cran.r-project.org/web/packages/segmented")
|
||||
|
|
@ -3565,13 +3582,13 @@ using the multicore functionality of the parallel package.")
|
|||
"datatables-extensions/Select"))))
|
||||
(package
|
||||
(name "r-dt")
|
||||
(version "0.22")
|
||||
(version "0.23")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "DT" version))
|
||||
(sha256
|
||||
(base32
|
||||
"16ah0h60ygvj49cs6cxxhdxx68cs6v6m35w5r1j5h8nxz171q61z"))
|
||||
"0w6wgiwa3zgldp175a3q7zfw853xqc7mfj34n6hja48ln7yf42in"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(for-each delete-file
|
||||
|
|
@ -3716,13 +3733,13 @@ analysis of large sparse or dense matrices.")
|
|||
(define-public r-glmnet
|
||||
(package
|
||||
(name "r-glmnet")
|
||||
(version "4.1-3")
|
||||
(version "4.1-4")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "glmnet" version))
|
||||
(sha256
|
||||
(base32 "0nij8v44b5dvp1vc843sfkl9ds83n6g687m2p37q1rdn82m3bg34"))))
|
||||
(base32 "1y80a3b5s24ywhlil3r7b3a0vs9j59d7jkxrqa8zz09x1c5ggc7n"))))
|
||||
(build-system r-build-system)
|
||||
(native-inputs
|
||||
(list gfortran r-knitr))
|
||||
|
|
@ -3817,14 +3834,14 @@ the way current RNG settings can be changed.")
|
|||
(define-public r-rtsne
|
||||
(package
|
||||
(name "r-rtsne")
|
||||
(version "0.15")
|
||||
(version "0.16")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "Rtsne" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
|
||||
"1mgviwrqwapn8w7rq0sjxca5vi7ylgmm876ijwp22a3chbf5m82j"))))
|
||||
(properties `((upstream-name . "Rtsne")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -3905,17 +3922,19 @@ message passing.")
|
|||
(define-public r-bigmemory
|
||||
(package
|
||||
(name "r-bigmemory")
|
||||
(version "4.5.36")
|
||||
(version "4.6.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "bigmemory" version))
|
||||
(sha256
|
||||
(base32
|
||||
"03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
|
||||
"0hainqkm7cs8gjm42vkpdrr0284smsbwdfackp34yv7dhxy1avmm"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-bh r-rcpp r-bigmemory-sri))
|
||||
(list r-bh r-bigmemory-sri r-rcpp r-uuid))
|
||||
(inputs
|
||||
(list `(,util-linux "lib"))) ;for -luuid
|
||||
(home-page "http://www.bigmemory.org")
|
||||
(synopsis "Manage large matrices with shared memory or memory-mapped files")
|
||||
(description "This package provides methods to create, store, access, and
|
||||
|
|
@ -4075,13 +4094,13 @@ t-probabilities, quantiles, random deviates and densities.")
|
|||
(define-public r-matrixstats
|
||||
(package
|
||||
(name "r-matrixstats")
|
||||
(version "0.61.0")
|
||||
(version "0.62.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "matrixStats" version))
|
||||
(sha256
|
||||
(base32
|
||||
"16pxsba5i51ifbbgvxln2w6nigbwd3290b2ckgzn5bmib7nc1lyv"))))
|
||||
"1jjfsi5vzx6js7phlnd3v64fd05fg0jyz8iq5pivy36jdmmh3ql5"))))
|
||||
(properties `((upstream-name . "matrixStats")))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
|
|
@ -4466,13 +4485,13 @@ package instead.")
|
|||
(define-public r-hmisc
|
||||
(package
|
||||
(name "r-hmisc")
|
||||
(version "4.6-0")
|
||||
(version "4.7-0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "Hmisc" version))
|
||||
(sha256
|
||||
(base32 "1bd1c8sichyijprfpnqj5g72nmgs9jvi0zyw8v4nsg1kn83fj71c"))))
|
||||
(base32 "1gc71wg6f17x6nriphs1kk39ix7lpqk32clk1qshqy8wl6f2vv19"))))
|
||||
(properties `((upstream-name . "Hmisc")))
|
||||
(build-system r-build-system)
|
||||
(native-inputs
|
||||
|
|
@ -4592,14 +4611,14 @@ Zurich, including many that are related to graphics.")
|
|||
(define-public r-gtools
|
||||
(package
|
||||
(name "r-gtools")
|
||||
(version "3.9.2")
|
||||
(version "3.9.2.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "gtools" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0lx97yafrms2mjym8rhcq5586z7s1iqgy8qfm4px3xl1yn5qkc83"))))
|
||||
"0pxg0ang9q26hlwgf53pp1hq6rlarq5rnrrr9dl14f5kgfnynpzc"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "https://cran.r-project.org/web/packages/gtools")
|
||||
(synopsis "Various R programming tools")
|
||||
|
|
@ -4614,14 +4633,14 @@ tests for whether a value is missing, empty or contains only @code{NA} and
|
|||
(define-public r-gdata
|
||||
(package
|
||||
(name "r-gdata")
|
||||
(version "2.18.0")
|
||||
(version "2.18.0.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "gdata" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
|
||||
"1n9jw136kk5ld27qvny7cx2s8l34jdgmzlx40x62mmcqjddksbsy"))))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
(list perl))
|
||||
|
|
@ -4654,14 +4673,14 @@ including:
|
|||
(define-public r-gplots
|
||||
(package
|
||||
(name "r-gplots")
|
||||
(version "3.1.1")
|
||||
(version "3.1.3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "gplots" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr"))))
|
||||
"05k7a8x62qs5g6mps62vb3mwjdnfjzvjb20yws3x0r2j42g3p1cz"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-catools r-gtools r-kernsmooth))
|
||||
|
|
@ -4997,14 +5016,14 @@ mixture models.")
|
|||
(define-public r-lars
|
||||
(package
|
||||
(name "r-lars")
|
||||
(version "1.2")
|
||||
(version "1.3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "lars" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
|
||||
"17al1g0pvfz9frs2kxicqr8dyp7ciz3x87yx2l4lqd53ls6nm7n6"))))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
(list gfortran))
|
||||
|
|
@ -5044,14 +5063,14 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.")
|
|||
(define-public r-randomforest
|
||||
(package
|
||||
(name "r-randomforest")
|
||||
(version "4.7-1")
|
||||
(version "4.7-1.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "randomForest" version))
|
||||
(sha256
|
||||
(base32
|
||||
"04q6gb917md4yw837cf9vlx1q8ljl06jw7yhykzb6nl47w55jnkq"))))
|
||||
"1micz9794j7xmj755ln2692rzip8azndflxgdg6xn3j86issi7pm"))))
|
||||
(properties `((upstream-name . "randomForest")))
|
||||
(build-system r-build-system)
|
||||
(home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
|
||||
|
|
@ -5130,14 +5149,14 @@ models, generalized linear models and model-based clustering.")
|
|||
(define-public r-mclust
|
||||
(package
|
||||
(name "r-mclust")
|
||||
(version "5.4.9")
|
||||
(version "5.4.10")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "mclust" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0s4mva0n04f3pl41msmzhlh7pnk0zbmf06n826smxkw6mz327wb5"))))
|
||||
"0wh6nsbma4b0wsmqm2ynbznl2wlwdly4vg583f6z0zd1qkrvn6ra"))))
|
||||
(build-system r-build-system)
|
||||
(native-inputs
|
||||
(list gfortran r-knitr))
|
||||
|
|
@ -5222,14 +5241,14 @@ regression methodology including model selections and multivariate statistics.")
|
|||
(define-public r-pcapp
|
||||
(package
|
||||
(name "r-pcapp")
|
||||
(version "1.9-74")
|
||||
(version "2.0-1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "pcaPP" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1dlrz5plb8b89vr3j6sn9jwryyhcwflqkiilxkybbr379m1pp0sh"))))
|
||||
"06hjhr0dzdp5yhd421q9scbv6w6bchicbn2bl7am490ncgrf544n"))))
|
||||
(properties `((upstream-name . "pcaPP")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -5244,14 +5263,14 @@ analysis} (PCA) by projection pursuit.")
|
|||
(define-public r-rrcov
|
||||
(package
|
||||
(name "r-rrcov")
|
||||
(version "1.6-2")
|
||||
(version "1.7-0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "rrcov" version))
|
||||
(sha256
|
||||
(base32
|
||||
"18x8y2b9n2plpn4086nkjk9c27p7gb78kbrv5pj9r8fb0idl5rn5"))))
|
||||
"1z98j9973hl19b70dcwfcf55ifxr2a9v53daaq2sagynh95aik6b"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-lattice r-mvtnorm r-pcapp r-robustbase))
|
||||
|
|
@ -5507,18 +5526,24 @@ using modular prediction and response module classes.")
|
|||
(define-public r-quantreg
|
||||
(package
|
||||
(name "r-quantreg")
|
||||
(version "5.88")
|
||||
(version "5.93")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "quantreg" version))
|
||||
(sha256
|
||||
(base32 "0grsha18zkiil0qnxc1d7kc3w26i6aaa4av9n9ahdm8yf59yah0r"))))
|
||||
(base32 "0fg5x6sa8mz2hh9nak0wajh4l6h03x216462vs94rgq0ln24kafl"))))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'set-HOME
|
||||
(lambda _ (setenv "HOME" "/tmp"))))))
|
||||
(native-inputs
|
||||
(list gfortran))
|
||||
(list gfortran
|
||||
r-r-rsp)) ;for vignettes
|
||||
(propagated-inputs
|
||||
(list r-matrix r-matrixmodels r-sparsem))
|
||||
(list r-mass r-matrix r-matrixmodels r-sparsem r-survival))
|
||||
(home-page "https://www.r-project.org")
|
||||
(synopsis "Quantile regression")
|
||||
(description
|
||||
|
|
@ -5532,14 +5557,14 @@ expected shortfall risk are also included.")
|
|||
(define-public r-nloptr
|
||||
(package
|
||||
(name "r-nloptr")
|
||||
(version "2.0.0")
|
||||
(version "2.0.3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "nloptr" version))
|
||||
(sha256
|
||||
(base32
|
||||
"16k124ll14p3ygny6i1zd7yza83bv2sk87x922n1bfn9rx4k3jk5"))))
|
||||
"1mqnjswm0dl6vqc8b2s5k3n1mhanaha3l33vh68dh6zx8q9aq9kv"))))
|
||||
(build-system r-build-system)
|
||||
(native-inputs
|
||||
(list r-knitr ; for building vignettes
|
||||
|
|
@ -5642,13 +5667,13 @@ Companion to Applied Regression, Third Edition, Sage.")
|
|||
(define-public r-car
|
||||
(package
|
||||
(name "r-car")
|
||||
(version "3.0-12")
|
||||
(version "3.0-13")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "car" version))
|
||||
(sha256
|
||||
(base32 "00kk8l71508f73kyn21is1mx6kjbrzdq3ls94c5ajhiqmvpsd6dq"))))
|
||||
(base32 "1ss7kvi5hf9s4b6i7y06zl4iip1w1h8ff4zzf529wk18h3dfhnnk"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
(list r-abind
|
||||
|
|
@ -5792,14 +5817,14 @@ multivariate case.")
|
|||
(define-public r-tclust
|
||||
(package
|
||||
(name "r-tclust")
|
||||
(version "1.4-2")
|
||||
(version "1.5-1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "tclust" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1nb5iky4kc832627jf28lzj19wrvgwg5da6fyl3kyf0npmyx1p4m"))))
|
||||
"09zk38gih67a8lk72k46mfgv21jpnxh2nzrxc5ypdc2bfwq8nckk"))))
|
||||
(build-system r-build-system)
|
||||
;; These are all suggested packages, not build dependencies.
|
||||
(propagated-inputs
|
||||
|
|
@ -6454,14 +6479,14 @@ mediation and estimating power.")
|
|||
(define-public r-clubsandwich
|
||||
(package
|
||||
(name "r-clubsandwich")
|
||||
(version "0.5.5")
|
||||
(version "0.5.6")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "clubSandwich" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1ifnc2rg5agf7lpilmm27iq0af7ghfhkvwykajhvykgf6h4clvhf"))))
|
||||
"0mll8q61vnb980dck8ihxcy89z8m7f8i16mqdvr4l2ljywkhpzvd"))))
|
||||
(properties `((upstream-name . "clubSandwich")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -6603,14 +6628,14 @@ or eta squared effect size.")
|
|||
(define-public r-logspline
|
||||
(package
|
||||
(name "r-logspline")
|
||||
(version "2.1.16")
|
||||
(version "2.1.17")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "logspline" version))
|
||||
(sha256
|
||||
(base32
|
||||
"12hkdi77vkic05p2vhap025xdcg1n53ywm239v18713pihdlj63l"))))
|
||||
"05c8l22zcvb086909h9vw7icphww703vkcxp2h881y4n1232pdq3"))))
|
||||
(properties `((upstream-name . "logspline")))
|
||||
(build-system r-build-system)
|
||||
(native-inputs (list gfortran))
|
||||
|
|
@ -6778,14 +6803,14 @@ Michael Lim & Trevor Hastie (2015)")
|
|||
(define-public r-datasaurus
|
||||
(package
|
||||
(name "r-datasaurus")
|
||||
(version "0.1.4")
|
||||
(version "0.1.6")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "datasauRus" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1w1yhwwrmh95bklacz44wjwynxd8cj3z8b9zvsnzmk18m5a4k0fl"))))
|
||||
"0vgylf3bab0xcfg08xwvfq9yhxy6w0fxi7wp4kkxfyjb0pw15qxk"))))
|
||||
(properties `((upstream-name . "datasauRus")))
|
||||
(build-system r-build-system)
|
||||
(native-inputs (list r-knitr))
|
||||
|
|
@ -6894,13 +6919,13 @@ Calculates confidence intervals for the difference in proportion.")
|
|||
(define-public r-desctools
|
||||
(package
|
||||
(name "r-desctools")
|
||||
(version "0.99.44")
|
||||
(version "0.99.45")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "DescTools" version))
|
||||
(sha256
|
||||
(base32 "04wp3sp6sahgq167465y38y13h1ia5a4zqazysacpjxd1if0578j"))))
|
||||
(base32 "01gbmikpzjmymvb7p76k7wqvfvwznl6v0qa78jy7bi6fzmbp1zld"))))
|
||||
(properties `((upstream-name . "DescTools")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -6910,9 +6935,11 @@ Calculates confidence intervals for the difference in proportion.")
|
|||
r-exact
|
||||
r-expm
|
||||
r-gld
|
||||
r-httr
|
||||
r-mass
|
||||
r-mvtnorm
|
||||
r-rcpp
|
||||
r-readxl
|
||||
r-rstudioapi))
|
||||
(native-inputs (list gfortran))
|
||||
(home-page "https://andrisignorell.github.io/DescTools/")
|
||||
|
|
@ -7016,13 +7043,13 @@ the presence of variance components/nonparametric terms for models fit with
|
|||
(define-public r-binom
|
||||
(package
|
||||
(name "r-binom")
|
||||
(version "1.1-1")
|
||||
(version "1.1-1.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "binom" version))
|
||||
(sha256
|
||||
(base32 "0mjj92dqf5q69jxzqya4izb1mly3mkydbnmlm4wb3zqqg82a324c"))))
|
||||
(base32 "1yxyhsd0savwirlmgnq6973slfakqyfvjm0zz60cmc9v490my8gf"))))
|
||||
(properties `((upstream-name . "binom")))
|
||||
(build-system r-build-system)
|
||||
(home-page "https://cran.r-project.org/package=binom")
|
||||
|
|
|
|||
|
|
@ -61,7 +61,7 @@ release corresponding to NAME and VERSION."
|
|||
"/src/contrib/"
|
||||
name "_" version ".tar.gz")
|
||||
;; TODO: use %bioconductor-version from (guix import cran)
|
||||
(string-append "https://bioconductor.org/packages/3.14"
|
||||
(string-append "https://bioconductor.org/packages/3.15"
|
||||
type-url-part
|
||||
"/src/contrib/"
|
||||
name "_" version ".tar.gz"))))
|
||||
|
|
|
|||
|
|
@ -156,9 +156,9 @@ package definition."
|
|||
(define %cran-canonical-url "https://cran.r-project.org/package=")
|
||||
(define %bioconductor-url "https://bioconductor.org/packages/")
|
||||
|
||||
;; The latest Bioconductor release is 3.14. Bioconductor packages should be
|
||||
;; The latest Bioconductor release is 3.15. Bioconductor packages should be
|
||||
;; updated together.
|
||||
(define %bioconductor-version "3.14")
|
||||
(define %bioconductor-version "3.15")
|
||||
|
||||
(define* (bioconductor-packages-list-url #:optional type)
|
||||
(string-append "https://bioconductor.org/packages/"
|
||||
|
|
|
|||
Loading…
Reference in a new issue