diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 971 |
1 files changed, 475 insertions, 496 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cf5ba0764b..3a66e611e4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -12,12 +12,13 @@ ;;; Copyright © 2017 Alex Kost <alezost@gmail.com> ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com> ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com> -;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2021, 2022, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com> ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net> ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com> ;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com> +;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -216,7 +217,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.3.1") + (version "4.3.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -224,7 +225,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "16dswjcymzr2mj1vjwqdyjaa9d4isa1p6c9viihnyg02y4jbzl4d")))) + "0aj51j34q2b28y28xvlf0dwdj8vpnhjwpvqf7xm05s7fq857dxdk")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -524,14 +525,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-60") + (version "7.3-60.0.1") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "1hphf8m1zny4582rvfnl262ydf3f2w0kayxj2b8n855hx87l20mq")))) + "1gdd2gyqngvgnm0bxc3a33nykrx2rbfmxj82i7bh7f1961cr7pvl")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "https://www.stats.ox.ac.uk/pub/MASS4/") @@ -567,14 +568,14 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") (define-public r-cluster (package (name "r-cluster") - (version "2.1.4") + (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "cluster" version)) (sha256 (base32 - "1dpmss4mdpw6la5kjf135h2jj5j5zmqvykpj6fl6n5wslbn0rwf6")))) + "0r1i243mjbsx00ccg3f46c5iwnfmjxmhhdjvrj3m799mzpx0xifi")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -608,14 +609,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-85") + (version "0.8-86") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "1azca97fhwb1pzgrjw2xscfh2k7bfryp6wjsdcx2y4h7305d4ych")))) + "1qf3x1vacc4sdcmw4mbh0251ii4xd8z1xmmd9isak75j100i4ad7")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -672,14 +673,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.6-1.1") + (version "1.6-5") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "1hlcxr38p4ybb67n25cc1ssh2q2r8cj0flc59lid8hclzvqv27ik")))) + "0zdrrss4q0g7jify9bp1vvzrdpy62fc6fx3awzbd2wvfc938sv3j")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -694,13 +695,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-163") + (version "3.1-164") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "12hj7icn0xgsm67awzf8x8afhckxmb98rci9c7gsizdp9x6gyikx")))) + (base32 "1s6lpp4hpjhyn7ygfngw2f60a40kbbikd0y2wqzbhdvhrqha19br")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -716,13 +717,13 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.9-0") + (version "1.9-1") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 - (base32 "0w1v0hdswb332xz3br1fcgacib7ddr4hb96cmlycxcpqq5w01cdj")))) + (base32 "0cnvbdda243as2bxfsgnnk7xjmp1msgr9i4vbd84jfnxpqvvq3vh")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-nlme)) @@ -757,14 +758,14 @@ single hidden layer, and for multinomial log-linear models.") (define-public r-rpart (package (name "r-rpart") - (version "4.1.21") + (version "4.1.23") (source (origin (method url-fetch) (uri (cran-uri "rpart" version)) (sha256 (base32 - "0av28n5as53qrxm41hcrwv59qdv7gfli668q32z0a5r1bdkiqz77")))) + "1bxbvbv3jwz1j6yhgswbr6qy574n9rbp3cnwl9badkm6dbnrmf7r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rpart") (synopsis "Recursive partitioning and regression trees") @@ -961,13 +962,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.33") + (version "0.6.34") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "06bq696wpmn8ivbrpxw0qlcf835kc515m8jfv9zbwf8ndf42qw5y")))) + (base32 "1na47pywh059g9ymf56z232h5yxbj0gn755cb10ms5igjd97awqb")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -1178,14 +1179,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.7.12") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "02g0464sbprrbjlacx727p9ad1s5nbxl2mnvfmm9h7q000lsrs7g")))) + "09a964g8q3iphq24ln9c9g5158ynr75pfh3ghddarn0xvn7bw0hn")))) (build-system r-build-system) (inputs (list icu4c)) (native-inputs (list pkg-config)) @@ -1204,13 +1205,13 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (define-public r-stringr (package (name "r-stringr") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "stringr" version)) (sha256 - (base32 "0fk34ql5ak57f06l10ai300kxay6r7kkkyfanh8r24qaf3bmkcaj")))) + (base32 "1pj5xwg8kq2jllmszgkw96qj37wlb0x0vx4f3m5j211zpd8yrbd4")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs)) @@ -1316,14 +1317,14 @@ agnes cluster diagrams.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "00mak9js1s05j5bmkda24nl2z023jsyg8zc60nm4h2xs7w1l7mxa")))) + "155qa55wr9vf2j2j4qjqqlkdaqlvvlvsm2wmysnhli47bfh6vd4c")))) (build-system r-build-system) (native-inputs (list pkg-config)) @@ -1346,13 +1347,13 @@ and to generate base64 encoded string from raster matrix.") (define-public r-svglite (package (name "r-svglite") - (version "2.1.2") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "svglite" version)) (sha256 - (base32 "0c00djvlnf4qr30srh3xjnx1valqq8grm5ib0q4485z8gphn7hf2")))) + (base32 "0m0axxrkiih4wmrp9qh803p4l92fdgrsbxaww38z89widx75da7h")))) (properties `((upstream-name . "svglite"))) (build-system r-build-system) (inputs (list libpng zlib)) @@ -1408,13 +1409,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.1.3") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "13a2656w5j9shpcwa7gj2szy7nk9sajjhlisi5wdpgd57msk7frq")))) + "0w7dpp1zg8w0mback1mk0a0vp51hf4njmrxz1i3j1xq5b1jfyiz4")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1430,13 +1431,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.81.0-1") + (version "1.84.0-0") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "0r7zjxpbm2paliplprwf9769a57clqaiskiiadiy10gissnqn77m")))) + "1b7igvvy9f13l969a26j2bdzib2laq3m4w1x0xsxjb2pbxsn1dkg")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") @@ -1448,13 +1449,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.22") + (version "0.23") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "0sz4zimz4brbd9sawdazfgipkmfzzdmdq01b5m8pnrql5xrxhiwh")))) + "0p540jl6sixpgk08cp2h9470d28p7n66pfafiskvz3rba0vrrky9")))) (build-system r-build-system) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") @@ -1534,13 +1535,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "1.11") + (version "1.12") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "052zrb6bnr6k3p9pmm3vfh3g7z20g6pjvphjdiqyjb4mb9sn3z27")))) + "182b290dj0c6m4qf4azyih521ski0ssk1awzmbzfbqlcy3lf7p3x")))) (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 @@ -1560,13 +1561,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.3.7") + (version "2.3.8") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "1aw0cvaqw8a0d1r3cplj5kiabkcyz8fghcpi0ax8mi7rw0cv436j")))) + "1n1zlbnq3ldipnnm08whpvm8r21vxg4c9jzg7x7j3blw2pi7kl4y")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") @@ -1721,13 +1722,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.2.0") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "03k58p8kd7vddx7rlcyi28sy48bh3w4xy4c7wi190l7yjlrfa2sv")))) + "1ba80zk9jzs91xl82bykhrvvgamfvp1h189rfq099h813dhhx60x")))) (build-system r-build-system) (propagated-inputs (list r-brio @@ -1735,7 +1736,6 @@ R packages that praise their users.") r-cli r-desc r-digest - r-ellipsis r-evaluate r-jsonlite r-lifecycle @@ -1782,13 +1782,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "1.1.1") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "16fsibxbh4fy62x6fw358qbniw085qs1wjyr75n22xv9g6kwjpjy")))) + "02mz53g8lk26yi0js6qq57ijhl1mw7xm82vwbwzbvi62bm5l58r4")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1829,13 +1829,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0hhpzv66rqz7z8vdryzjdkp4flmjvzxrx1pwpxnbmjqgvd3s4hv8")))) + "1jsq8pj12bngy66xms486j8a65wxvyqs944q9rxkiaylsla08wyg")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -1991,13 +1991,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.14.8") + (version "1.14.10") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "1z9rf5anjvg3bmbbajb12nf65jsxdw35ad9piysrp76zcx9wxchl")))) + "0zk2g0lnjrw5wk6avwq07xw0cd7hpcpkmamf9d8avpd8f7ml2jq1")))) (properties `((upstream-name . "data.table"))) (build-system r-build-system) (inputs @@ -2182,7 +2182,7 @@ comparison and diagnostics.") (define-public python-pymc (package (name "python-pymc") - (version "5.7.2") + (version "5.10.0") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference @@ -2191,7 +2191,7 @@ comparison and diagnostics.") (file-name (git-file-name name version)) (sha256 (base32 - "1r3lxpfc782f0wphdqfgsskbz52i0gwgrmxb65307k6cqia69s3r")))) + "17gb7ny2isfgyps7qffdxq18a9p43qy1fhqhbh75cnqd5wv1yxzb")))) (build-system pyproject-build-system) (arguments (list #:tests? #f ; tests are too computationally intensive @@ -2296,13 +2296,13 @@ building design matrices.") (define-public python-mapie (package (name "python-mapie") - (version "0.7.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "MAPIE" version)) (sha256 (base32 - "1nvi547avvwrck1n7rf5jh7d0ml6jaqjs2p59iwcq2a5xjmdsmsc")))) + "185nnsl6ag2xzkfxpmc86d9dd8wf2v87b2psan10sma399fbqd0x")))) (build-system pyproject-build-system) (native-inputs (list python-pandas python-pytest)) (propagated-inputs (list python-numpy python-scikit-learn)) @@ -2317,6 +2317,29 @@ uncertainties and are backed by strong theoretical guarantees thanks to conformal prediction methods intervals.") (license license:bsd-3))) +(define-public python-emcee + (package + (name "python-emcee") + (version "3.1.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "emcee" version)) + (sha256 + (base32 "1vbz67cwzig28dlndkm6g246p1vcvj6yy2w65z8cdyffigf1j3lf")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy)) + (native-inputs (list python-coverage + python-pytest + python-pytest-cov + python-setuptools-scm)) + (home-page "https://emcee.readthedocs.io/en/stable/") + (synopsis "Ensemble sampling toolkit for MCMC") + (description + "@code{emcee} is a Python implementation of the affine-invariant ensemble +sampler for Markov chain Monte Carlo (MCMC).") + (license license:expat))) + (define-public python-statsmodels (package (name "python-statsmodels") @@ -2374,7 +2397,7 @@ inference for statistical models.") (define-public python-openturns (package (name "python-openturns") - (version "1.21") + (version "1.21.3") (source (origin (method git-fetch) @@ -2383,7 +2406,7 @@ inference for statistical models.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "05lbx8npvvk7jyakvfpgi9ggdp6cnzwv2hjmjrkji2s42axv0q6d")))) + (base32 "0nf77p6zv2br23n3c0yidnclb0234ni07y67h1h1f2bng4kdn8jp")))) (build-system cmake-build-system) (arguments (list @@ -2504,17 +2527,19 @@ and environmental data in the framework of Euclidean exploratory methods.") (define-public r-xml2 (package (name "r-xml2") - (version "1.3.5") + (version "1.3.6") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "10p214gzzcy2zzcq2xkh1vz2wrjsys5gplvk9c1crq3nmfki0six")))) + "13rhvmrjdqwc5psn501vz9jfmqwlf4rc30w6vrnn3wxzk7zr26g8")))) (build-system r-build-system) (inputs (list libxml2 zlib)) + (propagated-inputs + (list r-cli r-rlang)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/hadley/xml2") @@ -2615,14 +2640,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1m41idv7iwq6mby8dyvsbljj5jkyhj65k7caz2na17a83s2inwl8")))) + "1xl4313kav3fy32ff9mdlm03za1mrwlym6d5abrkf0a0r86bmrp7")))) (build-system r-build-system) (propagated-inputs (list r-backports)) @@ -2714,13 +2739,13 @@ SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") (define-public r-brew (package (name "r-brew") - (version "1.0-8") + (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "brew" version)) (sha256 (base32 - "09kq14nbaw0mmpb2vbfklz786q6lyizzkyg5bg64bmj2f1d2sr8i")))) + "13x3vnrhfcvr479r4dya61a5vcky2gb4kv2xbivy0ah39qrzg0a1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/brew") (synopsis "Templating framework for report generation") @@ -2733,17 +2758,17 @@ module, Java Server Pages, and Python's psp module.") (define-public r-desc (package (name "r-desc") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 - "0z1259ghccmrjylydra4bpryqasirsky7bc4gsx0k327pqacz2km")))) + "09ig14bm68cps6d1mrmj6hhjr01i6gz1ri35qpkwk3yp7nkqsijl")))) (build-system r-build-system) (propagated-inputs - (list r-cli r-r6 r-rprojroot)) + (list r-cli r-r6)) (home-page "https://github.com/r-pkgs/desc") (synopsis "Manipulate DESCRIPTION Files") (description @@ -2778,13 +2803,13 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.2.3") + (version "7.3.0") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "1nhn0jhnxzlyqx0qnpd7k7q3azzngyn0j4zs8awmlmyjfywzli6q")))) + "05vzmln9cwcns1pcs568ivxpvf823xcw671d3wi77c3ixzmj3p7q")))) (build-system r-build-system) (propagated-inputs (list r-brew @@ -2882,13 +2907,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.32.0") + (version "0.33.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "0wa6k1g7y0sx6s7map7mn579c1h07n185m163msmcjk81i62ap8v")))) + "158q1rzh9j0xb6l09j6banzvx8l26bhvip2z4lf6ymi21s6vcm8q")))) (build-system r-build-system) (inputs (list libgit2 zlib)) @@ -2966,13 +2991,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.5.2") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "01a27nqlrrf1pws57hi9631f3aj33a9dashd640m5nlgf9nzmdnm")))) + "1rz0pgm1bg3cnc09s8q8yyg83lmf8bv9arlasciqqr0fdpgfwy4c")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3008,13 +3033,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "2.1.4") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "03gbzf29kdvf4rdqgdq2jm7c9ifjla3qzpiyqzw1x9jgijj4y54q")))) + "02p1jjal73j39r49ba4jlvbx8bdqmm96nsdp47igyv54w1gmm9hg")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -3023,9 +3048,9 @@ time-of-day values, based on the @code{difftime} class.") r-crayon r-hms r-lifecycle - r-tibble r-r6 r-rlang + r-tibble r-tzdb r-vroom)) (native-inputs @@ -3040,13 +3065,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.8-2") + (version "3.8-4") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "07xwq3505qb2yak7pfda22yqwifj6m78f8b5rm0ym74808qrawmv")))) + "1mp8mb79prgf5fzlaix4fvslr4q67hrzxqdv3kr7mik1mf9jv8p6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -3103,13 +3128,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.12.6.4.0") + (version "0.12.6.6.1") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1k7xq2yl4pkc7krz1bcdnx5kfj6n4zjmnm40nly2da2ji87agv49")))) + "1h7z1l2zf4qv8azi9c4wj0klshhcqihpabvjhln7ra61i8lvssls")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -3172,14 +3197,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (define-public r-rprojroot (package (name "r-rprojroot") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "rprojroot" version)) (sha256 (base32 - "15zq606s544wmbvk5dw13xq0sspr9dsxyxlvzvn0r48f8x3l4q2h")))) + "16bf6ga5fgm83j3m67plw5i54az2vdbvw5m99ixaqkd24pxn7x5m")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3317,13 +3342,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.3.2") + (version "2.3.4") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "09vbx3akqws8a07ai6qbp3jn1w05qsmazl79wl2dyvvjpzs8b62x")))) + "1sy4zgacr7f7svv0a1vd7s40llk7g2989qwf19l6zkngncdwikbk")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -3333,7 +3358,8 @@ a column in data frame.") r-dbi r-memoise r-pkgconfig - r-plogr)) + r-plogr + r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/rstats-db/RSQLite") @@ -3347,13 +3373,13 @@ engine (version 3.8.8.2) is included.") (define-public r-rcurl (package (name "r-rcurl") - (version "1.98-1.12") + (version "1.98-1.14") (source (origin (method url-fetch) (uri (cran-uri "RCurl" version)) (sha256 (base32 - "1ci6lsxm0f13yzw712gcbq23syl54x5llvhs2w1b8wwm9vqgx0qs")))) + "1kq3ydvm7hvy8pxk9iy13pkq5mxyxqlx4mpjsadzl7a7jj32gbgf")))) (properties `((upstream-name . "RCurl"))) (build-system r-build-system) (arguments @@ -3367,10 +3393,8 @@ engine (version 3.8.8.2) is included.") certs = Sys.getenv(\"CURL_CA_BUNDLE\") if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) } " m)))))))) - (native-inputs - (list libxml2)) (inputs - (list curl)) + (list curl libxml2)) (propagated-inputs (list r-bitops)) (home-page "https://www.omegahat.net/RCurl") @@ -3389,13 +3413,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.14") + (version "3.99-0.16") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "1ygi65ddgbsamxw2rm0p2clfak1xj44xyisgk48y72cd9ldaddic")))) + "0ny93jlx0fpv0hs9qjm9cbcv4fh5rh0kkyhk6g0dm8wvp6x3f39m")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -3510,14 +3534,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.6-4") + (version "2.0-1") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "14ci6hd5xlrz22gvnvy2fzpnp50fbds3wpx4mf2fgi5i7sp0hb27")))) + "0r3l39sihncrmhs6y3nydr6izp5ss86rfwjyhwf2x0clvqq2gkz9")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") @@ -3666,324 +3690,102 @@ using the multicore functionality of the parallel package.") 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(let ((file (string-append dir "/js/" (basename url ".js") ".min.js"))) (delete-file file)))) ',javascript-sources) + ;; Preserve pdfmake.js and vfs_fonts.js + (copy-file "datatables-extensions/Buttons/js/pdfmake.js" + "/tmp/pdfmake.js") + (copy-file "datatables-extensions/Buttons/js/vfs_fonts.js" + "/tmp/vfs_fonts.js") + (for-each (lambda (extension) + (let ((name (assoc-ref extension 'name))) + (delete-file-recursively + (string-append "datatables-extensions/" name "/js")))) + (append ',extensions ',ts-extensions)) + (mkdir-p "datatables-extensions/Buttons/js/") + (copy-file "/tmp/pdfmake.js" + "datatables-extensions/Buttons/js/pdfmake.js") + (copy-file "/tmp/vfs_fonts.js" + "datatables-extensions/Buttons/js/vfs_fonts.js") (delete-file "nouislider/jquery.nouislider.min.js") (delete-file "selectize/selectize.min.js") (with-directory-excursion "datatables-plugins/features/" @@ -4026,6 +3843,56 @@ using the multicore functionality of the parallel package.") (mkdir-p dir) (minify source #:target target)))) ',javascript-sources) + + ;; Minify JS for each extension + (for-each (lambda (extension) + (let* ((name (assoc-ref extension 'name)) + (version (assoc-ref extension 'version)) + (hash (assoc-ref extension 'hash)) + (label (string-append "js:" name)) + (dir (string-append "datatables-extensions/" + name "/js"))) + (mkdir-p dir) + (with-directory-excursion dir + (for-each + (lambda (file) + (minify file + #:target + (string-append (basename file ".js") ".min.js"))) + (find-files (string-append (assoc-ref inputs label) "/js") + "\\.js$"))))) + ',extensions) + ;; Process typescript extensions + (for-each (lambda (extension) + (let* ((name (assoc-ref extension 'name)) + (version (assoc-ref extension 'version)) + (hash (assoc-ref extension 'hash)) + (label (string-append "ts:" name)) + (dir (string-append "datatables-extensions/" + name "/js"))) + (mkdir-p dir) + (with-directory-excursion dir + (apply invoke "esbuild" + "--bundle" + (string-append + "--tsconfig=" + (string-append (assoc-ref inputs label) + "/tsconfig.json")) + (string-append "--outdir=" (getcwd)) + (find-files + (string-append (assoc-ref inputs label) "/src/") + "\\.ts$")) + (rename-file "index.js" (string-append "dataTables." + (string-downcase name 0 1) + ".js")) + (for-each + (lambda (file) + (minify file + #:target + (string-append (basename file ".js") ".min.js")) + (delete-file file)) + (find-files "." "\\.js$"))))) + ',ts-extensions) (minify (string-append (assoc-ref inputs "datatables-plugins") "/dataRender/ellipsis.js") #:target "datatables-plugins/dataRender/ellipsis/source.min.js") @@ -4068,7 +3935,7 @@ using the multicore functionality of the parallel package.") `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) ("datatables-plugins" - ,(let ((version "1.13.4")) + ,(let ((version "1.13.6")) (origin (method git-fetch) (uri (git-reference @@ -4077,7 +3944,7 @@ using the multicore functionality of the parallel package.") (file-name (git-file-name "datatables-plugins" version)) (sha256 (base32 - "0igrd7pghvk2w8mpad4mnw8ldflw47wma4qpp7ymkzvxy2100k49"))))) + "02ijp9671al2fpb5sahy1z4nx1q75jp8p0i77vv87r8lqmsvsjis"))))) ("js-nouislider" ,(let ((version "7.0.10")) (origin @@ -4093,7 +3960,21 @@ using the multicore functionality of the parallel package.") ,(origin (method url-fetch) (uri url) (sha256 (base32 hash)))))) - javascript-sources))) + javascript-sources) + ,@(map (lambda (extension) + (let ((name (assoc-ref extension 'name)) + (version (assoc-ref extension 'version)) + (hash (assoc-ref extension 'hash))) + `(,(string-append "js:" name) + ,(extension-origin name version hash)))) + extensions) + ,@(map (lambda (extension) + (let ((name (assoc-ref extension 'name)) + (version (assoc-ref extension 'version)) + (hash (assoc-ref extension 'hash))) + `(,(string-append "ts:" name) + ,(extension-origin name version hash)))) + ts-extensions))) (home-page "https://rstudio.github.io/DT") (synopsis "R wrapper of the DataTables JavaScript library") (description @@ -4253,14 +4134,14 @@ the way current RNG settings can be changed.") (define-public r-rtsne (package (name "r-rtsne") - (version "0.16") + (version "0.17") (source (origin (method url-fetch) (uri (cran-uri "Rtsne" version)) (sha256 (base32 - "1mgviwrqwapn8w7rq0sjxca5vi7ylgmm876ijwp22a3chbf5m82j")))) + "02srqmfkdj7v9gyhssaqdarg4ljn2ds77w25a5w0dm66sqa6ibis")))) (properties `((upstream-name . "Rtsne"))) (build-system r-build-system) (propagated-inputs @@ -4277,14 +4158,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.7-13") + (version "1.7-14") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "0bvbgcbj8a5z3rv4z4cx6dlwhk374fwd8l1jkq7slsbfmy8y356s")))) + "15aiwr1jhv3a2r9jqqy8d5rf0c8y09zzi45116whgk1s0ymrfkbm")))) (build-system r-build-system) (propagated-inputs (list r-class r-proxy)) @@ -4299,13 +4180,13 @@ computation, bagged clustering, naive Bayes classifier, and more.") (define-public r-bigmemory-sri (package (name "r-bigmemory-sri") - (version "0.1.6") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "bigmemory.sri" version)) (sha256 - (base32 "03468ak0lgd9m0f7synxms2zzr8f7n2nm1gmhcraj3nfcv4nmyiv")))) + (base32 "0wbpk3naipl0ab3wnixnp2n874kazrapv1c31fi3cxm19b94x6h2")))) (properties `((upstream-name . "bigmemory.sri"))) (build-system r-build-system) @@ -4319,14 +4200,14 @@ bigmemory and synchronicity packages.") (define-public r-synchronicity (package (name "r-synchronicity") - (version "1.3.5") + (version "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "synchronicity" version)) (sha256 (base32 - "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx")))) + "12svf4xzb9s3m1h2ddqgl6q2v57ifsj2p80j8cg2k0543a43pww2")))) (build-system r-build-system) (propagated-inputs (list r-bh r-bigmemory-sri r-rcpp r-uuid)) @@ -4341,14 +4222,14 @@ message passing.") (define-public r-bigmemory (package (name "r-bigmemory") - (version "4.6.1") + (version "4.6.4") (source (origin (method url-fetch) (uri (cran-uri "bigmemory" version)) (sha256 (base32 - "0hainqkm7cs8gjm42vkpdrr0284smsbwdfackp34yv7dhxy1avmm")))) + "0b80c2nsgphgr3cnvf75a0z3bzqx4q1a4dplq0h2izc71mn5fgzy")))) (build-system r-build-system) (propagated-inputs (list r-bh r-bigmemory-sri r-rcpp r-uuid)) @@ -4419,13 +4300,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.12.2") + (version "2.12.3") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "0dl8rc7s7vg4g2pkmrwwqx7dkm02096jk439x4s0cm21hsmg2g7y")))) + "03640a1v8jk9k9s5xirdia9lngb53gh4p9gyj2j82cx2jmxfgmkl")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs @@ -4501,13 +4382,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.2-3") + (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "1iy65fc2y0af6ma9f6lvzd5zh7zm60cqihdhr58ksc75ymfxrnia")))) + "1zws7myh61622v46gir6bs0dpyp6siz0hx7lrsvymshn02xqg0l4")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -4520,13 +4401,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0vxd7g1fm4x0f72bs1xfik1d4yklvpjdyg1hpx86pl8fwr86i1wl")))) + "0ws5lmzqm42vrn5791l21zr05l78x0xi6b89jw0gi0vjb4pc20z4")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments @@ -4964,7 +4845,12 @@ from within R.") (add-after 'mkdist 'no-mtune (lambda _ (substitute* "src/Makevars" - (("-mtune=native") ""))))))) + (("-mtune=native") "")))) + (add-after 'no-mtune 'use-c++11 + (lambda _ + (substitute* "src/Makevars" + (("-DUSE_BLAS_LIB" m) + (string-append m " -std=c++11")))))))) (native-inputs (list hevea perl @@ -5098,14 +4984,14 @@ hierarchical clustering dendrograms.") (define-public r-fastcluster (package (name "r-fastcluster") - (version "1.2.3") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "fastcluster" version)) (sha256 (base32 - "009amz7i5yndqw2008fgd3p11n4fsb291k2ypg3pip6dw4lr28hz")))) + "06cd3w62ijf0yx2yq0xgx6qw5lcrnn1033ygx6bl9dmhix2haal5")))) (build-system r-build-system) (home-page "http://danifold.net/fastcluster.html") (synopsis "Fast hierarchical clustering routines") @@ -5142,14 +5028,14 @@ Zurich, including many that are related to graphics.") (define-public r-gtools (package (name "r-gtools") - (version "3.9.4") + (version "3.9.5") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 - "04gihp78x2caahqvf0mlv1cqy1m121l6hkdvbp01r2z99wcqpksr")))) + "0jqpvygxgr4m1rgaj5rzd048fwxvpcr4n1vx8bfabc9d2p0vdsfy")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gtools") (synopsis "Various R programming tools") @@ -5187,7 +5073,6 @@ including: @item character vector operations @item factor manipulation @item obtaining information about R objects -@item manipulating MS-Excel formatted files @item generating fixed-width format files @item extricating components of date and time objects @item operations on columns of data frames @@ -5304,13 +5189,13 @@ with alternating row colors) in LaTeX and HTML formats easily from (define-public r-vipor (package (name "r-vipor") - (version "0.4.5") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "vipor" version)) (sha256 (base32 - "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx")))) + "17hb6y1i9bva0fr4k9m6wncmnzdjad1b7fhsvfhva4xavpll3bds")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/vipor") (synopsis "Plot categorical data using noise and density estimates") @@ -5383,16 +5268,21 @@ data at that region, and avoids over-plotting.") (define-public r-ggthemes (package (name "r-ggthemes") - (version "4.2.4") + (version "5.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggthemes" version)) (sha256 (base32 - "0rw5f6axyz1pqn6qx9jwm38hjzn8bqs1nfjkvm96z3xnyn61cdbv")))) + "1iddxlcxbj5pq0llbhjh5gvxq8j4kzby0cahy0sgzzca074i7aan")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 r-purrr r-scales r-stringr r-tibble)) + (list r-ggplot2 + r-lifecycle + r-purrr + r-scales + r-stringr + r-tibble)) (home-page "https://cran.rstudio.com/web/packages/ggthemes") (synopsis "Extra themes, scales and geoms for @code{ggplot2}") (description "This package provides extra themes and scales for @@ -5500,14 +5390,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "0j7d5vhzdxn1blrsfafx5z8lhq122rp8230hp9czrpsnnhjydp67")))) + "1ppsg3rbqz9a16zq87izdj5w8ylb6jb6v13xb01k7m3n2h4mv4f6")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gtable r-rlang r-scales)) @@ -5571,14 +5461,14 @@ regression.") (define-public r-fastica (package (name "r-fastica") - (version "1.2-3") + (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 - "0l49cmxm1n4dzrv8q3q3mq4drcjgby4f1dmpwfdb8jxn9ij85vz9")))) + "0bszvwsfal83phwsk81vwcbs8q56qp5fs9a99yzpa6hd87m8hsgd")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/fastICA") @@ -5614,14 +5504,14 @@ forest of trees using random inputs, for classification and regression.") (define-public r-diptest (package (name "r-diptest") - (version "0.76-0") + (version "0.77-0") (source (origin (method url-fetch) (uri (cran-uri "diptest" version)) (sha256 (base32 - "10629vwn6r2949jjrmj5slbb5v0vnm3w0v8mrl7ws68m2sxmx2jh")))) + "0cnaz1akl86vg5p0g4yl4r66407dxssfki130rrwxpbbbqakbj63")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/diptest") (synopsis "Hartigan's dip test statistic for unimodality") @@ -5678,14 +5568,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "6.0.0") + (version "6.0.1") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0ahj5161lmid0gxyw6vidd4ig50l1374iisn9970zvx1rdp30z6y")))) + "0zsk89r2l73zi1dy0195k84n4dqdp97yisll5kg16amxs5pxx4hf")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5747,14 +5637,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.99-0") + (version "0.99-1") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "0xshwfv6vq47857xfhwnlxcl1511ghn6pyjylrg39i19xhp44za3")))) + "0n3qxw633hk391mr07pd7c9572v3zgdffvmaq4q2w5q4x3n1n6mf")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -5770,14 +5660,14 @@ regression methodology including model selections and multivariate statistics.") (define-public r-pcapp (package (name "r-pcapp") - (version "2.0-3") + (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "pcaPP" version)) (sha256 (base32 - "00ynanxpngzsvq5fsyalyzqz6axqcryy94300afvylwp0d7mbb0s")))) + "0cw18pcbpsr5rc8fxbwnzfag5g76j4hscij7j08zlbyr2436gifn")))) (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) (propagated-inputs @@ -5843,14 +5733,14 @@ generally.") (define-public r-robust (package (name "r-robust") - (version "0.7-2") + (version "0.7-3") (source (origin (method url-fetch) (uri (cran-uri "robust" version)) (sha256 (base32 - "1kryflq2p0c78pggnj5yghjivy4npxfkzcqhxh9jvrngkpxhsrb6")))) + "0pj7qinp11rjsibixl7axvxp9alaqr4pjr1l52vq8cl8h6j159w9")))) (build-system r-build-system) (propagated-inputs (list r-fit-models r-lattice r-mass r-robustbase r-rrcov)) @@ -5888,14 +5778,14 @@ of the points.") (define-public r-fpc (package (name "r-fpc") - (version "2.2-10") + (version "2.2-11") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 - "1lj7j74yx747iic1hcngzbym0sqxppja8bxw64m0j6na5s7m9d4r")))) + "06j1dzlf96qcaiqg8m5iah9rmwdppky04xjhs8k4rh0k12wr0mc2")))) (build-system r-build-system) (propagated-inputs (list r-class @@ -5987,18 +5877,18 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.3.9.3") + (version "0.3.3.9.4") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "0xhwgn77166ir7qnzl25mj0byskkqr0b36hihrpr2zaqsrzs8wsq")))) + "1faz1phvg7g14bchi88vizn5mfhgiwmsjg7jzkyf1yjg0f6vpsj1")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs - (list r-rcpp r-matrix)) + (list r-rcpp)) (home-page "http://eigen.tuxfamily.org") (synopsis "Rcpp integration for the Eigen templated linear algebra library") (description @@ -6033,14 +5923,14 @@ metrics for evaluating models.") (define-public r-matrixmodels (package (name "r-matrixmodels") - (version "0.5-2") + (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "MatrixModels" version)) (sha256 (base32 - "0ap3mfzb2psjwlksfjzs2ycl5598bllwzx5hfmf9db4yjsydn1hw")))) + "03zjfxjk4l2dl1117slz163w0ky675d23sjfni4d7fdhqq359ny2")))) (properties `((upstream-name . "MatrixModels"))) (build-system r-build-system) (propagated-inputs @@ -6115,14 +6005,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-34") + (version "1.1-35.1") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "1bbaxkrd5m3d40y6jdyrdr4vsjyzkfixbqjwj6c8inmks98f2wp8")))) + "0nzv1a22pfsf2ryw91h16ic4cb8y8g6wh0gx3msr7gv8dwwi3974")))) (build-system r-build-system) (propagated-inputs (list r-boot @@ -6345,14 +6235,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.5-4") + (version "1.5-5") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "1a3i6kvfzc2d6rdf75w03n5172jihhqa8mvzcb4m8l0w6mgdlm9b")))) + "15jl1srsn0m0r5qafbkqsvnh44j30nh3yhipw030mdfa4qkbz3gw")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs @@ -6368,14 +6258,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "0bibv9xf6w8k8nsc13f2yd4kx99aq0i758h3wfh089szgkpdjrad")))) + "12c52gqqwaaid5b062gad18ir1vala1z3a0z5j4af1xqzlxgk583")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-matrix r-rcppeigen)) @@ -6409,14 +6299,14 @@ genome-wide association studies can be analyzed efficiently.") (define-public r-cairo (package (name "r-cairo") - (version "1.6-1") + (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "Cairo" version)) (sha256 (base32 - "051pqbhfsr3dki2wiycbwvka850y4h4gyhvnjjf907q8sz2cykg6")))) + "0qjdsj6mpbwvnp8cimc4yrqfq3z68pfcd78ahsai52hpjdplqvvb")))) (properties `((upstream-name . "Cairo"))) (build-system r-build-system) (inputs @@ -6557,7 +6447,7 @@ can load multiple parameters to the current environment.") (license license:gpl3+)))) (define-public r-tgutil - (let ((commit "0e4a2e84e5cf1f74bc66df0a3d8eac89633fd7b1") + (let ((commit "db4ff8b98082f8e4dbdeacb452641d215fd3c7ff") (revision "1")) (package (name "r-tgutil") @@ -6570,7 +6460,7 @@ can load multiple parameters to the current environment.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0pmacpzhrigprlpl8b5j4xz7l110ifw98017xwk569dghbf8zrq1")))) + (base32 "00rsqs7f896piywh84jr8fkphbbx4jb7radf6znhhj6fip63yn91")))) (properties `((upstream-name . "tgutil"))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -6590,7 +6480,9 @@ can load multiple parameters to the current environment.") r-tidyr)) (home-page "https://github.com/tanaylab/tgutil") (synopsis "Simple utility functions for Tanay lab code") - (description "Shared utility functions for multiple Tanay lab packages.") + (description + "This package provides simple utility functions that are shared +across several packages maintained by the Tanay lab.") (license license:gpl3)))) (define-public r-catterplots @@ -6864,11 +6756,9 @@ Java package that provides routines for various statistical distributions.") (license license:gpl2+))) (define-public emacs-ess - ;; Latest release is old. This is not the latest commit either due to bug - ;; reported here: <https://github.com/emacs-ess/ESS/issues/987>. - (let ((commit "24da603184ce39246611dd5b8602e769d7ebd5bf") + (let ((commit "3691ecc642eab5d016887e42699648e0eeeef566") (version "18.10.2") - (revision "0")) + (revision "1")) (package (name "emacs-ess") (version (git-version version revision commit)) @@ -6879,62 +6769,107 @@ Java package that provides routines for various statistical distributions.") (url "https://github.com/emacs-ess/ESS") (commit commit))) (sha256 - (base32 "0j98lv07nzwzd54d4dgcfz01wy5gj48m0mnirxzh5r45ik2myh1r")) + (base32 "19p8djsbgvahpsx1w8i6h3qvpbdr4isjwm3wi82yk2648ri0qsq1")) (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet - '(begin - ;; Stop ESS from trying to bundle an external julia-mode.el. - (substitute* "lisp/Makefile" - ((" \\$\\(JULIAS)") "") - (("\ttest.*julia-mode.*\\.el") "")) - ;; Only build docs in info format. - (substitute* "doc/Makefile" - (("all : info text") - "all : info") - (("install: install-info install-other-docs") - "install: install-info")) - ;; Stop install-info from trying to update the info directory. - (substitute* "doc/Makefile" - ((".*/dir.*") "")) - ;; Fix r-help-mode test. - (substitute* "test/ess-test-r.el" - (("\\(equal ess-help-object \"plot.default\")") "t")) - ;; Avoid generating ess-autoloads.el twice. - (substitute* "Makefile" - (("all: lisp doc etc autoloads") - "all: lisp doc etc")) - ;; Install to correct directories. - (substitute* "Makefile" - (("mkdir -p \\$\\(ESSDESTDIR)") - "$(MAKE) -C lisp install; $(MAKE) -C doc install") - (("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/") - "$(MAKE) -C etc install")) - #t)) - (patches - (search-patches "emacs-ess-fix-obsolete-function-alias.patch")))) + #~(begin + ;; Stop ESS from trying to bundle an external julia-mode.el. + (substitute* "lisp/Makefile" + ((" \\$\\(JULIAS)") "") + (("\ttest.*julia-mode.*\\.el") "")) + ;; Only build docs in info format. + (substitute* "doc/Makefile" + (("all : info text") + "all : info") + (("install: install-info install-other-docs") + "install: install-info")) + ;; Stop install-info from trying to update the info directory. + (substitute* "doc/Makefile" + ((".*/dir.*") "")) + ;; Fix r-help-mode test. + (substitute* "test/ess-test-r.el" + (("\\(equal ess-help-object \"plot.default\")") "t")) + ;; Avoid generating ess-autoloads.el twice. + (substitute* "Makefile" + (("all: lisp doc etc autoloads") + "all: lisp doc etc")) + ;; Install to correct directories. + (substitute* "Makefile" + (("mkdir -p \\$\\(ESSDESTDIR)") + "$(MAKE) -C lisp install; $(MAKE) -C doc install") + (("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/") + "$(MAKE) -C etc install")))))) (build-system gnu-build-system) (arguments (let ((base-directory "/share/emacs/site-lisp")) - `(#:make-flags (list (string-append "PREFIX=" %output) - (string-append "ETCDIR=" %output - ,base-directory "/etc") - (string-append "LISPDIR=" %output - ,base-directory) - (string-append "INFODIR=" %output - "/share/info")) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (replace 'check - (lambda _ (invoke "make" "test"))))))) - (native-inputs - (list perl r-roxygen2 texinfo)) - (inputs - `(("emacs" ,emacs-minimal) - ("r-minimal" ,r-minimal))) - (propagated-inputs - (list emacs-julia-mode)) + (list + #:modules '((guix build gnu-build-system) + (guix build utils) + (guix build emacs-utils)) + #:imported-modules `(,@%gnu-build-system-modules + (guix build emacs-build-system) + (guix build emacs-utils)) + #:make-flags + #~(list (string-append "PREFIX=" #$output) + (string-append "ETCDIR=" #$output #$base-directory "/etc") + (string-append "LISPDIR=" #$output #$base-directory) + (string-append "INFODIR=" #$output "/share/info")) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-before 'check 'skip-failing-tests + ;; The command-without-trailing-newline-test and other + ;; tests fail for unknown reasons (see: + ;; https://github.com/emacs-ess/ESS/issues/1272). + (lambda _ + (let-syntax + ((disable-tests + (syntax-rules () + ((_ file ()) + (syntax-error "test names list must not be empty")) + ((_ file (test-name ...)) + (substitute* file + (((string-append "^\\(ert-deftest " test-name ".*") + all) + (string-append all "(skip-unless nil)\n")) + ...)))) + (disable-etests ;different test syntax + (syntax-rules () + ((_ file ()) + (syntax-error "test names list must not be empty")) + ((_ file (test-name ...)) + (emacs-batch-edit-file file + '(progn + (mapc (lambda (test) + (goto-char (point-min)) + (search-forward + (format "etest-deftest %s " test)) + (beginning-of-line) + (kill-sexp)) + (list test-name ...)) + (basic-save-buffer))))))) + (disable-tests (list "test/ess-test-inf.el" + "test/ess-test-r.el") + ("ess--derive-connection-path" + "ess-eval-line-test" + "ess-eval-region-test" + "ess-mock-remote-process" + "ess-r-load-ESSR-github-fetch-no" + "ess-r-load-ESSR-github-fetch-yes" + "ess-set-working-directory-test" + "ess-test-r-startup-directory")) + (disable-etests "test/ess-test-r-eval.el" + ("ess-r-eval-ns-env-roxy-tracebug-test" + "ess-r-eval-sink-freeze-test")) + (disable-etests + "test/ess-test-inf.el" + ("command-without-trailing-newline-test"))))) + (replace 'check + (lambda _ (invoke "make" "test"))))))) + (native-inputs (list perl r-roxygen2 texinfo)) + (inputs (list emacs-minimal r-minimal)) + (propagated-inputs (list emacs-julia-mode)) (home-page "https://ess.r-project.org/") (synopsis "Emacs mode for statistical analysis programs") (description @@ -6992,6 +6927,50 @@ files, including Rmarkdown files.") popular stats packages like SAS, Stata and SPSS.") (license license:expat))) +(define-public python-pyreadstat + (package + (name "python-pyreadstat") + (version "1.2.4") + ;; No tests in the PyPI tarball. + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Roche/pyreadstat") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zysrzixvqw2lwwykxqg5yj8a0zyv5s2bmk22x30f4rj2hgvq1pv")) + (patches (search-patches "python-pyreadstat-link-libiconv.patch")))) + (arguments + '(#:phases (modify-phases %standard-phases + (add-before 'check 'change-home-dir + (lambda _ + ;; test_sav_expand and test_sav_write_basic_expanduser need a + ;; home directory with write permissions. + (setenv "HOME" "/tmp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; The source also contains tests/test_version.py + ;; which checks the version in __init__.py against the + ;; one in setup.py. Since this requires texlive + ;; dependencies to run and is also not mentioned in + ;; how_to_test.md, this test is skipped. + (invoke "python" "tests/test_basic.py"))))))) + (build-system python-build-system) + (propagated-inputs (list python-pandas)) + (inputs (list libiconv zlib)) + (native-inputs (list python-cython-3)) + (home-page "https://github.com/Roche/pyreadstat") + (synopsis + "Read and write SAS, SPSS and Stata files into/from Pandas DataFrames") + (description + "This Python package can be used to read and write SAS, SPSS and Stata +files into/from Pandas DataFrames. It is a wrapper around the C library +@code{readstat}.") + (license license:asl2.0))) + (define-public r-quantpsyc (package (name "r-quantpsyc") @@ -7227,14 +7206,14 @@ various statistical models with linear predictors.") (define-public r-bayesfactor (package (name "r-bayesfactor") - (version "0.9.12-4.5") + (version "0.9.12-4.6") (source (origin (method url-fetch) (uri (cran-uri "BayesFactor" version)) (sha256 (base32 - "10bclqzczawpssjwa3b177xpab4mdhczfj1qj23xn2yvrrw1z9mh")))) + "1nvm26m5m8xi8iw1fj8ca79z3aqln4l3c0hvh38yvm9p584nwpzx")))) (properties `((upstream-name . "BayesFactor"))) (build-system r-build-system) (propagated-inputs @@ -7461,18 +7440,18 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.50") + (version "0.99.52") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "1awfhbv7klvkwxki4lvxj086yiwqyys95jnss8q5qqn7wyfz170v")))) + (base32 "147p9brnzyhibffq15wcn0dza3cx14w57b2zc9na8wmmc3wpv6cl")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (propagated-inputs - (list r-bh - r-boot + (list r-boot + r-cli r-data-table r-exact r-expm |