diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 163 |
1 files changed, 83 insertions, 80 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index eb5e5b4b76..cdd0caec4a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -75,6 +75,7 @@ #: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) @@ -180,7 +181,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "3.6.0") + (version "3.6.1") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -188,7 +189,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "02bmylmzrm9sdidirmwy233lghmd2346z725ca71ari68lzarz1n")))) + "128kifbq0w25y8aq77w289ddax5i5w2djcfsqgffrb3i7syrxajv")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -319,9 +320,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ("perl" ,perl) ("pkg-config" ,pkg-config) ("texinfo" ,texinfo) ; for building HTML manuals - ("texlive" ,(texlive-union (list texlive-fonts-amsfonts - texlive-fonts-ec - texlive-latex-amsfonts + ("texlive" ,(texlive-union (list texlive-fonts-ec + texlive-amsfonts texlive-latex-base texlive-latex-fancyvrb texlive-latex-graphics @@ -397,14 +397,14 @@ available, greatly increasing its breadth and scope.") (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") @@ -502,14 +502,14 @@ code for possible problems.") (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") @@ -588,14 +588,14 @@ and operations on them using LAPACK and SuiteSparse.") (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))) @@ -804,13 +804,13 @@ effects of different types of color-blindness.") (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. @@ -1138,13 +1138,13 @@ legends.") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.2.0") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "1cvk9pw59kxx19kamqwa15h26rbznp0vvqpn7y8kgjssnrzqkdii")))) + (base32 "0mjswqiqcwm0aqxll16bx2kwa6c9km3aql87bdj4347n1ali94g3")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -1404,13 +1404,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "19nrz0ba1yd5kicd65crkkz2r3kialm2hm6zdkp495l2s5r80b8p")))) + "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d")))) (build-system r-build-system) ;; Skip check phase because the tests require the r-knitr package to be ;; installed. This prevents installation failures. Knitr normally @@ -1418,7 +1418,8 @@ data derived from /etc/mime.types in UNIX-type systems.") ;; package. (arguments `(#:tests? #f)) (propagated-inputs - `(("r-mime" ,r-mime))) + `(("r-mime" ,r-mime) + ("r-xfun" ,r-xfun))) (home-page "https://github.com/rstudio/markdown") (synopsis "Markdown rendering for R") (description @@ -1448,13 +1449,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.23") + (version "1.24") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "16ba4258c915xydhniw4cw7fvv1vp4cnwd1w49ykx7zw00rznfq6")))) + "12bvs9fd61m7k7bq321qzrh2ccl9rq653s1anrvfb9s5ni1j0378")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) @@ -1603,18 +1604,19 @@ R packages that praise their users.") (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) @@ -1696,13 +1698,13 @@ and printing capabilities than traditional data frames.") (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) @@ -1979,13 +1981,13 @@ inference for statistical models.") (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))) @@ -2021,14 +2023,14 @@ and environmental data in the framework of Euclidean exploratory methods.") (define-public r-xml2 (package (name "r-xml2") - (version "1.2.0") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha")))) + "1x3q3a0xv8j0nx3hs4d3pfjm5g9nvaxmfrapba9f4nrkqi3z2l1h")))) (build-system r-build-system) (inputs `(("libxml2" ,libxml2) @@ -2136,14 +2138,14 @@ R version.") (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))) @@ -2333,14 +2335,14 @@ collation, and NAMESPACE files.") (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))) @@ -2366,13 +2368,13 @@ integers.") (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) @@ -2392,20 +2394,16 @@ functions make it easy to control additional request components.") (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))) @@ -2438,13 +2436,13 @@ informative error messages when it's not available.") (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) @@ -2457,9 +2455,11 @@ informative error messages when it's not available.") ("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") @@ -2490,18 +2490,19 @@ were originally a part of the r-devtools package.") (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 @@ -2597,13 +2598,13 @@ well as additional utilities such as panel and axis annotation functions.") (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 @@ -2695,14 +2696,14 @@ certain criterion, e.g., it contains a certain regular file.") (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 @@ -2788,17 +2789,18 @@ that package, other packages are unaffected.") (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 @@ -2810,13 +2812,13 @@ a column in data frame.") (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 @@ -3069,14 +3071,14 @@ standard R subsetting and Kronecker products.") (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") @@ -3089,14 +3091,14 @@ data.") (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) @@ -3117,14 +3119,14 @@ parallel.") (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 @@ -3140,14 +3142,14 @@ using the parallel package.") (define-public r-domc (package (name "r-domc") - (version "1.3.5") + (version "1.3.6") (source (origin (method url-fetch) (uri (cran-uri "doMC" version)) (sha256 (base32 - "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr")))) + "1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9")))) (properties `((upstream-name . "doMC"))) (build-system r-build-system) (propagated-inputs @@ -3163,13 +3165,13 @@ using the multicore functionality of the parallel package.") (define-public r-dt (package (name "r-dt") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx")))) + "08cfmv3d5awvd9h8648bvidcg2ak5pvl2p6vqwqwy1l82ia506ch")))) (properties `((upstream-name . "DT"))) (build-system r-build-system) @@ -3177,6 +3179,7 @@ using the multicore functionality of the parallel package.") `(("r-crosstalk" ,r-crosstalk) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) ("r-promises" ,r-promises))) (home-page "http://rstudio.github.io/DT") @@ -3315,14 +3318,14 @@ package registries.") (define-public r-rngtools (package (name "r-rngtools") - (version "1.3.1.1") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "rngtools" version)) (sha256 (base32 - "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr")))) + "1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -4566,19 +4569,19 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "0.9.4") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv")))) + "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) - ("r-plyr" ,r-plyr) + ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (home-page "https://github.com/wilkelab/cowplot") (synopsis "Streamlined plot theme and plot annotations for ggplot2") @@ -4640,14 +4643,14 @@ regression.") (define-public r-fastica (package (name "r-fastica") - (version "1.2-1") + (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 - "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg")))) + "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/fastICA") @@ -4749,14 +4752,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.4") + (version "5.4.5") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "039ymr57bq5327gypizw0v2qb81j6bkqhjdh8yj23qa5sh51phyc")))) + "0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4919,14 +4922,14 @@ generally.") (define-public r-robust (package (name "r-robust") - (version "0.4-18") + (version "0.4-18.1") (source (origin (method url-fetch) (uri (cran-uri "robust" version)) (sha256 (base32 - "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4")))) + "0xs098pfw5zdcdk3rsxkylfl6d2pyp566s5v92bzhgl7h8c90cfy")))) (build-system r-build-system) (propagated-inputs `(("r-fit-models" ,r-fit-models) @@ -5025,14 +5028,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (define-public r-pbapply (package (name "r-pbapply") - (version "1.4-0") + (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 - "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k")))) + "1bbws9n90cqnnp5k58hp852jwmm6513jnhn4vzhl9f8x314k6qxk")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") @@ -5138,14 +5141,14 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.41") + (version "5.51") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 (base32 - "110ax3ngn6i94h7iw7ha67kfsmj94hycp7lk62nmyvkp34vpfykh")))) + "1cdx51a9g6fjq2g9arr6wp6ghkyl2m6bs2dj4kcycvpn8p9304yz")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) |