#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages java)
+ #:use-module (gnu packages libffi)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages base)
+ #:use-module (gnu packages version-control)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
(define-public r-boot
(package
(name "r-boot")
- (version "1.3-22")
+ (version "1.3-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "boot" version))
(sha256
(base32
- "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
+ "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/boot")
(synopsis "Bootstrap functions for R")
(define-public r-foreign
(package
(name "r-foreign")
- (version "0.8-71")
+ (version "0.8-72")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
- "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
+ "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
(define-public r-nlme
(package
(name "r-nlme")
- (version "3.1-140")
+ (version "3.1-141")
(source
(origin
(method url-fetch)
(uri (cran-uri "nlme" version))
(sha256
(base32
- "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
+ "0ml00g79bimjcl0sgn6h55l5b4gfmnsnc1vvmivggn0318k4c04i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(define-public r-digest
(package
(name "r-digest")
- (version "0.6.19")
+ (version "0.6.20")
(source
(origin
(method url-fetch)
(uri (cran-uri "digest" version))
(sha256
- (base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
+ (base32 "1irhk2jaj9cg57cxprgyn1if06x121xwcxh1fzzn3148bl5lnrq5"))))
(build-system r-build-system)
;; Vignettes require r-knitr, which requires r-digest, so we have to
;; disable them and the tests.
(define-public r-testthat
(package
(name "r-testthat")
- (version "2.1.1")
+ (version "2.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "testthat" version))
(sha256
(base32
- "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
+ "0y0bvggm4pzkzp6xn7b8cf3ybqp9ijxkhhyp3z49a9iipc90bvk7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
("r-crayon" ,r-crayon)
("r-digest" ,r-digest)
+ ("r-evaluate" ,r-evaluate)
("r-magrittr" ,r-magrittr)
("r-praise" ,r-praise)
("r-r6" ,r-r6)
(define-public r-dplyr
(package
(name "r-dplyr")
- (version "0.8.1")
+ (version "0.8.3")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
- "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
+ "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
(define-public r-coda
(package
(name "r-coda")
- (version "0.19-2")
+ (version "0.19-3")
(source (origin
(method url-fetch)
(uri (cran-uri "coda" version))
(sha256
(base32
- "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
+ "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(define-public r-xml2
(package
(name "r-xml2")
- (version "1.2.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "xml2" version))
(sha256
(base32
- "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
+ "0186d7r36xw1z9f8ajz35a0dz4ch6hmrjl9536yc7vq78v4vn5an"))))
(build-system r-build-system)
(inputs
`(("libxml2" ,libxml2)
(define-public r-checkmate
(package
(name "r-checkmate")
- (version "1.9.3")
+ (version "1.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "checkmate" version))
(sha256
(base32
- "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
+ "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)))
(define-public r-openssl
(package
(name "r-openssl")
- (version "1.4")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
- "0mh4xwb9wnn5j2n1zzmjldqjqv2nn4wdidiixxciaqrqsi0l9834"))))
+ "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
(build-system r-build-system)
(inputs
`(("libressl" ,libressl)))
(define-public r-httr
(package
(name "r-httr")
- (version "1.4.0")
+ (version "1.4.1")
(source (origin
(method url-fetch)
(uri (cran-uri "httr" version))
(sha256
(base32
- "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
+ "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
(define-public r-git2r
(package
(name "r-git2r")
- (version "0.25.2")
+ (version "0.26.1")
(source (origin
(method url-fetch)
(uri (cran-uri "git2r" version))
(sha256
(base32
- "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
+ "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
(build-system r-build-system)
- ;; This R package contains modified sources of libgit2. This modified
- ;; version of libgit2 is built as the package is built. Hence libgit2 is
- ;; not among the inputs of this package.
(inputs
- `(("libssh2" ,libssh2) ; for SSH transport
- ("openssl" ,openssl)
+ `(("libgit2" ,libgit2)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(define-public r-devtools
(package
(name "r-devtools")
- (version "2.0.2")
+ (version "2.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "devtools" version))
(sha256
(base32
- "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
+ "0393v7nr22gr5g9afgrhq4ab3lwbqy6fd3shnmlhdpqam5357xy1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
("r-pkgbuild" ,r-pkgbuild)
("r-pkgload" ,r-pkgload)
("r-rcmdcheck" ,r-rcmdcheck)
+ ("r-roxygen2" ,r-roxygen2)
("r-remotes" ,r-remotes)
("r-rstudioapi" ,r-rstudioapi)
("r-sessioninfo" ,r-sessioninfo)
+ ("r-testthat" ,r-testthat)
("r-usethis" ,r-usethis)
("r-withr" ,r-withr)))
(home-page "https://github.com/hadley/devtools")
(define-public r-hms
(package
(name "r-hms")
- (version "0.4.2")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "hms" version))
(sha256
(base32
- "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
+ "06snfqdczr0x0nbp7qnvwhlp2pw0wx9c2y3xb4gr1wrvbik74y58"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)
- ("r-pkgconfig" ,r-pkgconfig)))
+ ("r-pkgconfig" ,r-pkgconfig)
+ ("r-vctrs" ,r-vctrs)))
(home-page "https://github.com/rstats-db/hms")
(synopsis "Pretty time of day")
(description
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.9.500.2.0")
+ (version "0.9.600.4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv"))))
+ "07jg2667xyhmp1fbcdi5nnhmkk81da76s9rlswfq4k2sjsmbfmr0"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
;; All needed for vignettes
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "1.13")
+ (version "1.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32
- "1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
+ "0qfw5rkvwqpgix32g6qy9xrr50awmm146aqbm836xravih2b2dpn"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
(define-public r-blob
(package
(name "r-blob")
- (version "1.1.1")
+ (version "1.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "blob" version))
(sha256
(base32
- "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
+ "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-prettyunits" ,r-prettyunits)
- ("r-tibble" ,r-tibble)))
+ ("r-rlang" ,r-rlang)
+ ("r-vctrs" ,r-vctrs)))
(home-page "https://github.com/hadley/blob")
(synopsis "Simple S3 Class for representing vectors of binary data")
(description "Raw vectors in R are useful for storing a single binary
(define-public r-rsqlite
(package
(name "r-rsqlite")
- (version "2.1.1")
+ (version "2.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
- "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
+ "1inrhap5cs0wry2jbw42fx9wwxb3qdzlpy0ba4f6a29bs8jx9nk6"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
(define-public r-iterators
(package
(name "r-iterators")
- (version "1.0.10")
+ (version "1.0.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "iterators" version))
(sha256
(base32
- "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
+ "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/iterators")
(synopsis "Iterator construct for R")
(define-public r-foreach
(package
(name "r-foreach")
- (version "1.4.4")
+ (version "1.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreach" version))
(sha256
(base32
- "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
+ "0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
(define-public r-doparallel
(package
(name "r-doparallel")
- (version "1.0.14")
+ (version "1.0.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "doParallel" version))
(sha256
(base32
- "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
+ "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
(properties `((upstream-name . "doParallel")))
(build-system r-build-system)
(propagated-inputs
(license license:lgpl3+)))
(define-public python-rpy2
- (package
- (name "python-rpy2")
- (version "2.9.4")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "rpy2" version))
- (sha256
- (base32
- "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy"))))
- (build-system python-build-system)
- (arguments
- '(#:modules ((ice-9 ftw)
- (srfi srfi-1)
- (srfi srfi-26)
- (guix build utils)
- (guix build python-build-system))
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key outputs inputs #:allow-other-keys)
- (let ((cwd (getcwd)))
- (setenv "PYTHONPATH"
- (string-append cwd "/build/"
- (find (cut string-prefix? "lib" <>)
- (scandir (string-append cwd "/build")))
- ":"
- (getenv "PYTHONPATH"))))
- (invoke "python" "-m" "rpy2.tests" "-v"))))))
- (propagated-inputs
- `(("python-six" ,python-six)
- ("python-jinja2" ,python-jinja2)
- ("python-pytz" ,python-pytz)))
- (inputs
- `(("readline" ,readline)
- ("icu4c" ,icu4c)
- ("pcre" ,pcre)
- ("r-minimal" ,r-minimal)
- ("r-survival" ,r-survival)
- ("r-ggplot2" ,r-ggplot2)
- ("r-rsqlite" ,r-rsqlite)
- ("r-dplyr" ,r-dplyr)
- ("r-dbplyr" ,r-dbplyr)
- ("python-numpy" ,python-numpy)))
- (native-inputs
- `(("zlib" ,zlib)))
- (home-page "https://rpy2.bitbucket.io/")
- (synopsis "Python interface to the R language")
- (description "rpy2 is a redesign and rewrite of rpy. It is providing a
+ ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because
+ ;; it fixes a regression when using ggplot 3.2.0.
+ (let ((changeset "19868a8")
+ (revision "1"))
+ (package
+ (name "python-rpy2")
+ (version (git-version "3.0.4" revision changeset))
+ (source
+ (origin
+ (method hg-fetch)
+ (uri (hg-reference
+ (url "https://bitbucket.org/rpy2/rpy2")
+ (changeset changeset)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:modules ((ice-9 ftw)
+ (srfi srfi-1)
+ (srfi srfi-26)
+ (guix build utils)
+ (guix build python-build-system))
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let ((cwd (getcwd)))
+ (setenv "TZ" "UTC")
+ (setenv "PYTHONPATH"
+ (string-append cwd "/build/"
+ (find (cut string-prefix? "lib" <>)
+ (scandir (string-append cwd "/build")))
+ ":"
+ (getenv "PYTHONPATH"))))
+ (invoke "pytest" "-v" "rpy/tests/"))))))
+ (propagated-inputs
+ `(("python-cffi" ,python-cffi)
+ ("python-six" ,python-six)
+ ("python-jinja2" ,python-jinja2)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-pytz" ,python-pytz)
+ ("python-ipython" ,python-ipython)
+ ("python-tzlocal" ,python-tzlocal)))
+ (inputs
+ `(("readline" ,readline)
+ ("icu4c" ,icu4c)
+ ("pcre" ,pcre)
+ ("r-minimal" ,r-minimal)
+ ("r-survival" ,r-survival)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dbplyr" ,r-dbplyr)
+ ("python-numpy" ,python-numpy)))
+ (native-inputs
+ `(("zlib" ,zlib)
+ ("python-pytest" ,python-pytest)))
+ (home-page "https://rpy2.bitbucket.io/")
+ (synopsis "Python interface to the R language")
+ (description "rpy2 is a redesign and rewrite of rpy. It is providing a
low-level interface to R from Python, a proposed high-level interface,
including wrappers to graphical libraries, as well as R-like structures and
functions.")
- ;; Any of these licenses can be picked for the R interface. The whole
- ;; project is released under GPLv2+ according to the license declaration
- ;; in "setup.py".
- (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
+ ;; Any of these licenses can be picked for the R interface. The whole
+ ;; project is released under GPLv2+ according to the license declaration
+ ;; in "setup.py".
+ (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))))
(define-public java-jdistlib
(package
HCoop / jackhill / guix / guix.git / blobdiff