diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 405 |
1 files changed, 227 insertions, 178 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 89bed30916..af64cbd99d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com> ;;; Copyright © 2023 Felix Gruber <felgru@posteo.net> ;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com> +;;; Copyright © 2024 Vinicius Monego <monego@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -227,7 +228,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.3.3") + (version "4.4.1") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -235,7 +236,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0c03abq3kqg6d2yhrijy9j3fsl77har3k7pffwwbz19v74qi51c0")))) + "0kfrn8v8l555n5xrpf753jar5wa3vs622p967ffjkdxfx9fngjxl")))) (build-system gnu-build-system) (arguments (list @@ -410,7 +411,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ pkg-config texinfo ; for building HTML manuals (texlive-updmap.cfg - (list texlive-fancyvrb + (list texlive-etoolbox + texlive-fancyvrb texlive-inconsolata texlive-upquote texlive-xkeyval)) @@ -539,14 +541,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-60.0.1") + (version "7.3-61") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "1gdd2gyqngvgnm0bxc3a33nykrx2rbfmxj82i7bh7f1961cr7pvl")))) + "140ah1719zad8gd0glvy9qlkxxakgz12i5r5gk2bgmwxayzwhi1i")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "https://www.stats.ox.ac.uk/pub/MASS4/") @@ -623,14 +625,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-86") + (version "0.8-87") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "1qf3x1vacc4sdcmw4mbh0251ii4xd8z1xmmd9isak75j100i4ad7")))) + "0mi8vf3bsvrn2nh9kxjlgsmvxrc8icw51scr0mscqyp8r3saq90s")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -643,14 +645,14 @@ for reading and writing some dBase files.") (define-public r-kernsmooth (package (name "r-kernsmooth") - (version "2.23-22") + (version "2.23-24") (source (origin (method url-fetch) (uri (cran-uri "KernSmooth" version)) (sha256 (base32 - "1sblhl7b9d3m6034xd3254ddkj9ssqxawknzksfbgjh68s849q3n")))) + "0pxc53sw9f4hhxnl3zkalkkk0fvzcfxw7c4ibrb95zbzahwyrcyh")))) (properties `((upstream-name . "KernSmooth"))) (build-system r-build-system) (native-inputs @@ -687,14 +689,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.6-5") + (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "0zdrrss4q0g7jify9bp1vvzrdpy62fc6fx3awzbd2wvfc938sv3j")))) + "0dxd13y6x6pz54ccbcalw2sm646h9pls4bby9zmj40ipvyhbp5zv")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -709,13 +711,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-164") + (version "3.1-166") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "1s6lpp4hpjhyn7ygfngw2f60a40kbbikd0y2wqzbhdvhrqha19br")))) + (base32 "0qlpj3hjnlvd7x3ayjhvvpxlc2z4bfwk9qpglw8mnxbqipp18yi3")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -811,14 +813,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.5-8") + (version "3.7-0") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "1d0qvw4200mjldna9n0acis0fk8xj28wwzqb8c3d4537l92zivbi")))) + "1vzy8kg159yqnvg733air11la2qrirwcqhn9d67h5c18r67b15nd")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) @@ -976,13 +978,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.35") + (version "0.6.37") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "07vqv2mnf8ppan2a3gydh4yr84n8489hypfas1rlk7050nxkycyc")))) + (base32 "0883iyjbd50f0gwz6hgdmcsrk0i0fkjaix9hz6d4m2jbk54x3i42")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -1007,13 +1009,13 @@ OpenSSL should be used.") (define-public r-estimability (package (name "r-estimability") - (version "1.5") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "estimability" version)) (sha256 (base32 - "0s6w8vnq0jc136d2mpf6pgg45rbxccrlsgdy89pgksnbaxhmyb5k")))) + "1sa42rczhzfj0dkn8v1pq6b752rh6h7x553gcgl7g27x75mbk9iw")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/estimability") @@ -1194,14 +1196,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.8.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "09a964g8q3iphq24ln9c9g5158ynr75pfh3ghddarn0xvn7bw0hn")))) + "1wv9qqxl84l44kpvkx0lmyciinrh9pa5512jm56gsaqs9pvgh6f2")))) (build-system r-build-system) (inputs (list icu4c)) (native-inputs (list pkg-config)) @@ -1268,13 +1270,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.5.0") + (version "3.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "1qlh231dwsa7j0pzlw6xdm68d7r0v64916p66bg9lh1dw3a1ryh7")))) + (base32 "08a72kizg42mdm35170fnpn8l6r4n3j1yvbgiq1k8dlvz4jb8n3w")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -1424,13 +1426,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "10d7sl9nk1gkkbinmvplyp2hg9zgxgs03llamrvbf4a5cnrs0mcd")))) + "1gid1mfzq1j3n5fsnpzdb50p2m73z92s6njp0sgr503aaskhhryg")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1464,13 +1466,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.23") + (version "0.24.0") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "0p540jl6sixpgk08cp2h9470d28p7n66pfafiskvz3rba0vrrky9")))) + "1mkzb2f8rv0qd33h3gqq7idkpxnnx7zcr93xsmbm4lp7b157cgg2")))) (build-system r-build-system) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") @@ -1506,13 +1508,13 @@ There is also a Shiny app as a user interface in this package.") (define-public r-highr (package (name "r-highr") - (version "0.10") + (version "0.11") (source (origin (method url-fetch) (uri (cran-uri "highr" version)) (sha256 (base32 - "0yrlpjs8qzq1d7iy4gypnf4x1gvxq6vaghkdh1kfv433yqgvqmgc")))) + "19z0gwdy46z6gb46b3fs2ljxa2cn0bpvx7aam0jk75h180l183g9")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -1580,13 +1582,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "1.12") + (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "182b290dj0c6m4qf4azyih521ski0ssk1awzmbzfbqlcy3lf7p3x")))) + "1nfgngskgb4r34r3cnkm0gn7p1axpcb7rpyi0jxg4nygfk322m1q")))) (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 @@ -1606,13 +1608,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.3.8") + (version "2.3.10") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "1n1zlbnq3ldipnnm08whpvm8r21vxg4c9jzg7x7j3blw2pi7kl4y")))) + "0v9al1fh82vpjhml91j73sim7gfyc0154kxaam41sdkf6qnx8dp2")))) (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") @@ -1624,13 +1626,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.46") + (version "1.48") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "0ng8kw79csvcg46lsm3yf147jh6rf91jbj8qlryaihd8jcyc6lcg")))) + "15zipywk2ayrmy0p7q4d18512c2cgr9kk1lmc7gyi8bxv8k5j6sh")))) (build-system r-build-system) (propagated-inputs (list r-evaluate r-highr r-xfun r-yaml)) @@ -1728,13 +1730,13 @@ you call it again with the same arguments it returns the pre-computed value.") (define-public r-crayon (package (name "r-crayon") - (version "1.5.2") + (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "crayon" version)) (sha256 (base32 - "0yjsnhifr3nipaid0q11jjglvqmp51g9d2xdh9kfxh5knl2sbabh")))) + "0sfsx4k77fsx1dx9c186dg273psrr3awz4ivfvmbbvs1amla0x1y")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/crayon") (synopsis "Colored terminal output for R") @@ -1828,13 +1830,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "02mz53g8lk26yi0js6qq57ijhl1mw7xm82vwbwzbvi62bm5l58r4")))) + "1qd6chyciwhj6f6w56d3pcy4q8qdvqkyn2s709qjiwwba0klbmzj")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1998,14 +2000,14 @@ side.") (define-public r-locfit (package (name "r-locfit") - (version "1.5-9.9") + (version "1.5-9.10") (source (origin (method url-fetch) (uri (cran-uri "locfit" version)) (sha256 (base32 - "1m7ji1ykvffqvs9ly1pzadiwhwxcyv4xivziikmahp0w0sv45lck")))) + "01mcfsqqqwdf9iggabyckid7rf5c9f0v0hjz8g58fflr2hc6c82c")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -2037,13 +2039,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.15.4") + (version "1.16.0") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "0lyb82kl2bn70l9ag5xdr8q7rh4majbimygaynmfqnbdjkznb05b")))) + "1kgrdv2iijn7qd39prwvcrglcp992xf2jl5a9zc81plr032sxy2q")))) (properties `((upstream-name . "data.table"))) (build-system r-build-system) (inputs @@ -2180,7 +2182,7 @@ machine learning, computer vision, and high-dimensional statistics.") (define-public python-arviz (package (name "python-arviz") - (version "0.17.1") + (version "0.19.0") (source (origin (method git-fetch) ; PyPI misses some test files (uri (git-reference @@ -2189,7 +2191,7 @@ machine learning, computer vision, and high-dimensional statistics.") (file-name (git-file-name name version)) (sha256 (base32 - "1rpm2a9swzhnqn84dfsbc8kvz6qnn8w2icr3p08gwax9h9pg4ksp")))) + "0wj1yxr6as368vkr4mk9fz4584nyy12gq2v20l7542lnaabw403z")))) (build-system pyproject-build-system) (arguments ;; FIXME: matplotlib tests fail because of the "--save" test flag. @@ -2208,7 +2210,8 @@ machine learning, computer vision, and high-dimensional statistics.") ;; 3 tests require write permission. (setenv "HOME" "/tmp")))))) (native-inputs (list python-cloudpickle python-pytest)) - (propagated-inputs (list python-h5netcdf + (propagated-inputs (list python-dm-tree + python-h5netcdf python-matplotlib python-numpy python-packaging @@ -2348,17 +2351,58 @@ building design matrices.") ;; and is covered by the PSFL. (license (list license:bsd-2 license:psfl)))) +(define-public python-lifelines + (package + (name "python-lifelines") + (version "0.28.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "lifelines" version)) + (sha256 + (base32 "0pmjb3z1rw1ia64gw87r6y9x1g4kwpw239gqzsa9qh7xadj75kzf")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; This accuracy test fails because 0.012 is not < 0.01. + '(list "-k" "not test_weibull_with_delayed_entries"))) + (propagated-inputs (list python-autograd + python-autograd-gamma + python-formulaic + python-matplotlib + python-numpy + python-pandas + python-scipy)) + (native-inputs (list python-dill + python-flaky + python-joblib + python-pytest)) + (home-page "https://github.com/CamDavidsonPilon/lifelines") + (synopsis + "Survival analysis including Kaplan Meier, Nelson Aalen and regression") + (description + "This package enables survival analysis in Python, including Kaplan +Meier, Nelson Aalen and regression.") + (license license:expat))) + (define-public python-mapie (package (name "python-mapie") - (version "0.8.3") + (version "0.8.6") (source (origin (method url-fetch) (uri (pypi-uri "MAPIE" version)) (sha256 (base32 - "13kgyqk1hp603n9zym835kp1pqs83k0j7ymayw4fk0zx4z1nmvdx")))) + "013ljcjjl3k9yb3166fnvr6nsb9ph4rhidpdjjks78qw0w1j7faa")))) (build-system pyproject-build-system) + ;; See https://github.com/scikit-learn-contrib/MAPIE/issues/432 + (arguments + (list + #:test-flags + '(list "-k" (string-append "not test_correct_results" + " and not test_correct_results_binary")))) (native-inputs (list python-pandas python-pytest)) (propagated-inputs (list python-numpy python-scikit-learn)) (home-page "https://github.com/scikit-learn-contrib/MAPIE") @@ -2375,13 +2419,13 @@ conformal prediction methods intervals.") (define-public python-emcee (package (name "python-emcee") - (version "3.1.4") + (version "3.1.6") (source (origin (method url-fetch) (uri (pypi-uri "emcee" version)) (sha256 - (base32 "1vbz67cwzig28dlndkm6g246p1vcvj6yy2w65z8cdyffigf1j3lf")))) + (base32 "0zb3ihja3hyj6zjbhkpxhyyppnv58q2jjg0yd1lwmydqdaplvbqi")))) (build-system pyproject-build-system) (propagated-inputs (list python-numpy)) (native-inputs (list python-coverage @@ -2673,14 +2717,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.4.1") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "0x144hij0rzhrxdq3k5ph8fk7pdgl1avjca25j4mlpmhzdckqp44")))) + "18kwi50bvha6p5jfl833grmhqzi55adnd3glcy4yh18mizdxjghd")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") @@ -2696,14 +2740,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "2.3.1") + (version "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1xl4313kav3fy32ff9mdlm03za1mrwlym6d5abrkf0a0r86bmrp7")))) + "1qw81bs3lhwr1m6wlbs0l0j669051n60x4ca2821599ddhnp6mbj")))) (build-system r-build-system) (propagated-inputs (list r-backports)) @@ -2859,13 +2903,13 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.3.1") + (version "7.3.2") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "1j72arkadw93f4wrzxhryn3666jwnablr1bhk0zv6g77q2lrypi1")))) + "0701v8dglv0mdsjs1mijpylpciiijb2schplavkf5drjj6gqg25p")))) (build-system r-build-system) (propagated-inputs (list r-brew @@ -2894,14 +2938,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "2.1.2") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "0mm0rlf3m6wkvz5p8prxwjr37rn30lmhddsdi4ffnsmrysfl3rbp")))) + "13gp6q8s0pdjvnd7mnmdqhmmsb0mf4m3snq99j6js8c4sll27895")))) (properties `((upstream-name . "openssl") (updater-extra-inputs . ("openssl")))) @@ -3047,13 +3091,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "3.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "1rz0pgm1bg3cnc09s8q8yyg83lmf8bv9arlasciqqr0fdpgfwy4c")))) + "0h9qbaa4i63awk176i3pm7bia7wgssav9zk9jvc7sg3k5yng2wym")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3184,13 +3228,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.12.8.2.1") + (version "14.0.0-1") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "11w92xjjwfhb3sv3g0m6hdhm27nnx73ahb404zm79a29ihwrj55w")))) + "145sci5fkwzrngqx2ykpxvvy3wn5wjfjfl7wmw92gn9yvkxd9i40")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -3212,13 +3256,13 @@ the header files from the templated Armadillo library.") (define-public r-bitops (package (name "r-bitops") - (version "1.0-7") + (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "bitops" version)) (sha256 (base32 - "1i0phmq5yynla5x0frqll1gbf5ww59p3sgz1s06a354zqf9grdg9")))) + "0f1744pi3qb1av41man6xp2xalwcjslz3qbk35gccpb4d6glp8bq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bitops") (synopsis "Bitwise operations") @@ -3276,13 +3320,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.26") + (version "2.28") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "1q6z2j1y6pjdz4nzw44srv9j62irnxqhkvrsi46ma7xrzq6ig34g")))) + (base32 "11d0fpzcwgi84dfbvjpg33gn155g3m2pa1jsih1h6hidm41sa0m1")))) (properties `((upstream-name . "rmarkdown") (updater-extra-propagated-inputs . ("pandoc")))) @@ -3311,13 +3355,13 @@ variety of formats.") (define-public r-gtable (package (name "r-gtable") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "gtable" version)) (sha256 (base32 - "0xvrkhcv1896mf3n43mva2mrmk0d8np7sjrykpg1pv54f69h6ckh")))) + "0wpavsypw2yp0pklmqw0qcwsh8smx5gr2kkxmgdmm52r0fiw37xi")))) (properties `((upstream-name . "gtable"))) (build-system r-build-system) (propagated-inputs @@ -3397,13 +3441,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.3.6") + (version "2.3.7") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "1wpqr71wckxrh8ih5f01wkqqqnq5s3zaj0m8b40g76pliyjvgcgv")))) + "1kllna6hfnyy3rizr8wkpfn7p5sxv3sra12x9vz68hp6i4jmgq15")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -3428,13 +3472,13 @@ engine (version 3.8.8.2) is included.") (define-public r-rcurl (package (name "r-rcurl") - (version "1.98-1.14") + (version "1.98-1.16") (source (origin (method url-fetch) (uri (cran-uri "RCurl" version)) (sha256 (base32 - "1kq3ydvm7hvy8pxk9iy13pkq5mxyxqlx4mpjsadzl7a7jj32gbgf")))) + "19qddkyasfwa61mj0r0m4wk2xhpsqxf2dikih0s1fdjr207c938s")))) (properties `((upstream-name . "RCurl"))) (build-system r-build-system) (arguments @@ -3468,13 +3512,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.16.1") + (version "3.99-0.17") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "1i7fs9i2f6bdkxb45w2bck7sshlwxy2s32hi9fwa4nfmw2iy62m3")))) + "1n52k06jrgyjmz96mv4sv6kczqkhmz2spr3gymcjzzv9zxjk48vf")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -3589,14 +3633,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "2.0-4") + (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "0a7qfs83kgn7g98kiwlk8zm2q9pzgkvmms9l15sgc5y952yig926")))) + "1p83g6qj8y4xblggm12bhr9zpsqbrrc7lbbigxcafhhi9c8v08v7")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") @@ -3631,17 +3675,17 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.81") + (version "1.84-2") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "0csbqd9wm6r4162mday1iaigzf9wv2rp1zq8hnihys6f38w8z0xx")))) + "0rc6x466jhalb6baxxhffmmcpi03nndvvighp696rrvrhsxzv015")))) (properties `((upstream-name . "SparseM"))) (native-inputs - (list gfortran)) + (list gfortran r-knitr)) (build-system r-build-system) (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") (synopsis "Sparse linear algebra") @@ -4437,13 +4481,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.2-4") + (version "1.2-6") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "1zws7myh61622v46gir6bs0dpyp6siz0hx7lrsvymshn02xqg0l4")))) + "0cfdd8l58yn48vc4zf4n5vfs3g02wdnvmkdf5zyybn3f54ydrpn4")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -4770,14 +4814,14 @@ data behind them) can be viewed and modified in a web browser.") (define-public r-biased-urn (package (name "r-biased-urn") - (version "2.0.11") + (version "2.0.12") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "0dvmkrdmhfh4swilyxf10y856kx0zf9sj1gc0g62bm6r5jhz35b2")))) + "14jpijms81pgl4zyqrhwwdfj0jmlmml21blspvin8lqw8fbbbcr9")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://www.agner.org/random/") @@ -4957,13 +5001,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "5.1-2") + (version "5.1-3") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "088gniwbymzhqg3vp0kpkbazryjzy9iq6wdvf9hg9qf0sjbibpg7")))) + (base32 "1sq5qvlr9swhdvf3l420y9fxq5s1qw8aiyl9a62sb357ywppfq9w")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs @@ -5064,14 +5108,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-17") + (version "1.1-19") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "06ih8zljs57scy7jfnv32yxijgv1i60vggmlyyblwnff6mr2fm60")))) + "0fzjbicaa3x16skxgil84b4h6ylbcfi6vf30z7r8rqfj6pfk36c6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -5376,13 +5420,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj")))) + "0wlpkf6vilw871ac2bxy5nr790cfs6sax5k8m0fhasxbansxbxvf")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) @@ -5516,14 +5560,14 @@ regression.") (define-public r-fastica (package (name "r-fastica") - (version "1.2-4") + (version "1.2-5.1") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 - "0bszvwsfal83phwsk81vwcbs8q56qp5fs9a99yzpa6hd87m8hsgd")))) + "11frycqqv4hsky2yaf2rb850wwqizgjnvna31kasb625lklnx4b5")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/fastICA") @@ -5623,14 +5667,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "6.1") + (version "6.1.1") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0mchdxkc3y0v6dw8fzjnlqd6f3zrafm3xf1c53s6ps529b66kx2x")))) + "0xb726ssy224mzfg37nq5hffkdwi2hwjp1y9gwngk9vfbs703myx")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5692,14 +5736,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.99-2") + (version "0.99-4") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "0i6dzri3bfkpmp7h0h5nyzigs9rjzdd3c4ilapmvadmfywl9d9mn")))) + "1g0cykxx5glq0sljjwl6f3cs872apfd5xw59px77mvjbrm7x0y59")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -5715,14 +5759,14 @@ regression methodology including model selections and multivariate statistics.") (define-public r-pcapp (package (name "r-pcapp") - (version "2.0-4") + (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "pcaPP" version)) (sha256 (base32 - "0cw18pcbpsr5rc8fxbwnzfag5g76j4hscij7j08zlbyr2436gifn")))) + "043w3g3f57j2d0irnrxm58mzzisg7xmnsl17v7wijsh1czcswkv7")))) (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) (propagated-inputs @@ -5737,14 +5781,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.7-5") + (version "1.7-6") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "0cxhs0plbd8b01hmnpaphshhk34rw1bwg56rackb2pmngw3rbifz")))) + "1pj8w4w4yd730qy7bl8h3z7d5xj05avnq0fbj2gnxrz489yc18mq")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mvtnorm r-pcapp r-robustbase)) @@ -5788,14 +5832,14 @@ generally.") (define-public r-robust (package (name "r-robust") - (version "0.7-4") + (version "0.7-5") (source (origin (method url-fetch) (uri (cran-uri "robust" version)) (sha256 (base32 - "0qh816ha18v0n021cccjan1kplmyj0xyb7jmkmrnb6gxf8kma3b3")))) + "1k0s5i9r0lyz3qsw76dd514qclggqj9k2axmgj86df81j6f2mh53")))) (build-system r-build-system) (propagated-inputs (list r-fit-models r-lattice r-mass r-robustbase r-rrcov)) @@ -5833,14 +5877,14 @@ of the points.") (define-public r-fpc (package (name "r-fpc") - (version "2.2-11") + (version "2.2-12") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 - "06j1dzlf96qcaiqg8m5iah9rmwdppky04xjhs8k4rh0k12wr0mc2")))) + "11s7211mnb9c72061mrcdfdwfph6nmbwcnpjgl32i2p7qys9cnam")))) (build-system r-build-system) (propagated-inputs (list r-class @@ -5865,13 +5909,13 @@ groupings.") (define-public r-vgam (package (name "r-vgam") - (version "1.1-10") + (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 - (base32 "04yy5rxid3fwn42sak9rjbxd1h4d7iigiznpbrvwxl06b1xficyb")))) + (base32 "199kicvlxciff9x243h357n4bjl00yg9k5jgs9awzz5wsadr17fy")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (native-inputs @@ -5909,14 +5953,14 @@ showing the progress is useful e.g. bootstrap.") (define-public r-minqa (package (name "r-minqa") - (version "1.2.6") + (version "1.2.8") (source (origin (method url-fetch) (uri (cran-uri "minqa" version)) (sha256 (base32 - "0421b4ysslaqmdgwlz080abis8m4xkcvjq7lx1wywbsz1s2vi9si")))) + "0rslvg4imaijzb5z6vzsx4zqhrna1jk6qkp2kxnzqy0rn2wy8har")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -5932,14 +5976,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.4.0.0") + (version "0.3.4.0.2") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "0djiyimgka7g3kfakb6mfaq7cxna9kn6kgib59x9p7qj24ha1m18")))) + "1fs2wmsq2s6nzhkrx59li4x1zvcjhk9mhmc2pdz8pm4z2ai7pbgc")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs @@ -6000,13 +6044,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.97") + (version "5.98") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "18bdcxm2f8gc2bxdxrk80dcafl8d5snckp0913pkdsfyfrbxxrw7")))) + (base32 "0qbad2wzw7qvsrm821k2vr0dsx75jj3qbs2sl9k3ymngv1cv5359")))) (build-system r-build-system) (arguments (list @@ -6032,21 +6076,18 @@ expected shortfall risk are also included.") (define-public r-nloptr (package (name "r-nloptr") - (version "2.0.3") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 - "1mqnjswm0dl6vqc8b2s5k3n1mhanaha3l33vh68dh6zx8q9aq9kv")))) + "1snqvav2pxjhssn1nld49mjj89cn2zv7gjn2y8ch22gbzmfzbnjc")))) (build-system r-build-system) (native-inputs - (list r-knitr ; for building vignettes - pkg-config gfortran)) - (inputs - (list nlopt)) - (propagated-inputs (list r-testthat)) + (list gfortran pkg-config r-knitr)) + (inputs (list nlopt)) (home-page "https://cran.r-project.org/web/packages/nloptr") (synopsis "R interface to NLopt") (description @@ -6060,14 +6101,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-35.3") + (version "1.1-35.5") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "0ij37wly0d28x143xdkjry5jsj4chlbli2fl9zbp8fkcgh95r1xl")))) + "0w2i2d3q19kbx3scd7p7dyfpfpcqb3d5h47y5rb2jr59gvdn8rkx")))) (build-system r-build-system) (propagated-inputs (list r-boot @@ -6093,17 +6134,18 @@ C++ library for numerical linear algebra and RcppEigen glue.") (define-public r-pbkrtest (package (name "r-pbkrtest") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "pbkrtest" version)) (sha256 (base32 - "1qxnd4pfpsq762x81s3vkw09wdwpfj25bba5474g7z506pqasycf")))) + "0qxswrk54r40qmi9ky7jzv53mrlr2w2mrlf1czma597nzrb52gmh")))) (build-system r-build-system) (propagated-inputs (list r-broom + r-doby r-dplyr r-lme4 r-mass @@ -6290,14 +6332,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "2.0-3") + (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "0l0m77a4r7izzw8akx7cz1qcxpvbjgg364yjapazji290741rfs6")))) + "0y05aqpmal7ky33hs8n1phai94d7f48ich43jvy4m5wbfxkp2rm6")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs @@ -6415,14 +6457,14 @@ easy and fun.") (define-public r-fdrtool (package (name "r-fdrtool") - (version "1.2.17") + (version "1.2.18") (source (origin (method url-fetch) (uri (cran-uri "fdrtool" version)) (sha256 (base32 - "1pf554vb902vavgqc4c0kgghywbgcvr3lkkr414bxngavcd60lil")))) + "1vxswr56c63vvl2q6m0j0a5psdw724vspf6zxlr1k9zsdfcnd6b4")))) (build-system r-build-system) (home-page "https://strimmerlab.org/software/fdrtool/") (synopsis "Estimation of false discovery rates and higher criticism") @@ -6865,7 +6907,7 @@ Java package that provides routines for various statistical distributions.") #:modules '((guix build gnu-build-system) (guix build utils) (guix build emacs-utils)) - #:imported-modules `(,@%gnu-build-system-modules + #:imported-modules `(,@%default-gnu-imported-modules (guix build emacs-build-system) (guix build emacs-utils)) #:make-flags @@ -6881,32 +6923,33 @@ Java package that provides routines for various statistical distributions.") (let-syntax ((disable-tests (syntax-rules () - ((_ file ()) + ((_ ()) (syntax-error "test names list must not be empty")) - ((_ file (test-name ...)) - (substitute* file + ((_ (test-name ...)) + (substitute* (find-files "test" "\\.el$") (((string-append "^\\(ert-deftest " test-name ".*") all) (string-append all "(skip-unless nil)\n")) ...)))) (disable-etests ;different test syntax (syntax-rules () - ((_ file ()) + ((_ ()) (syntax-error "test names list must not be empty")) - ((_ file (test-name ...)) - (emacs-batch-edit-file file - '(progn - (mapc (lambda (test) - (goto-char (point-min)) - (search-forward - (format "etest-deftest %s " test)) - (beginning-of-line) - (kill-sexp)) - (list test-name ...)) - (basic-save-buffer))))))) - (disable-tests (list "test/ess-test-inf.el" - "test/ess-test-r.el") - ("ess--derive-connection-path" + ((_ (test-name ...)) + (for-each + (lambda (file) + (emacs-batch-edit-file file + '(progn + (dolist (test (list test-name ...)) + (goto-char (point-min)) + (let ((s (format "etest-deftest %s " + test))) + (when (search-forward s nil t) + (beginning-of-line) + (kill-sexp)))) + (basic-save-buffer)))) + (find-files "test" "\\.el$")))))) + (disable-tests ("ess--derive-connection-path" "ess-eval-line-test" "ess-eval-region-test" "ess-mock-remote-process" @@ -6914,9 +6957,10 @@ Java package that provides routines for various statistical distributions.") "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 ("ess-r-eval-ns-env-roxy-tracebug-test" + "ess-r-eval-sink-freeze-test" + ;; Looks like an off-by-one error. + "ess--command-browser-unscoped-essr"))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "make" "test")))))))) @@ -7052,18 +7096,18 @@ mediation and estimating power.") (define-public r-clubsandwich (package (name "r-clubsandwich") - (version "0.5.10") + (version "0.5.11") (source (origin (method url-fetch) (uri (cran-uri "clubSandwich" version)) (sha256 (base32 - "0qx4qq0k01q06hrs348n417pf338dyfbcy2vsi0y3ap6y1rb7w6s")))) + "1y9iy86w2440y22279is7vgi9m9v876p5954nhq5lg9ghpzbwzdq")))) (properties `((upstream-name . "clubSandwich"))) (build-system r-build-system) (propagated-inputs - (list r-sandwich)) + (list r-lifecycle r-sandwich)) (native-inputs (list r-knitr)) (home-page "https://github.com/jepusto/clubSandwich") (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample @@ -7201,14 +7245,14 @@ or eta squared effect size.") (define-public r-logspline (package (name "r-logspline") - (version "2.1.21") + (version "2.1.22") (source (origin (method url-fetch) (uri (cran-uri "logspline" version)) (sha256 (base32 - "0xqbk3h28gkx3haj7hdg314616x673cmg9ia148g0q9j3zqkqflf")))) + "00pdcfj1hmafxzs7gqw3n072p6pxp9hvsdm062n0xkiby6igffkp")))) (properties `((upstream-name . "logspline"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -7465,13 +7509,13 @@ L-Moments and Distributional Least Absolutes.") (define-public r-exact (package (name "r-exact") - (version "3.2") + (version "3.3") (source (origin (method url-fetch) (uri (cran-uri "Exact" version)) (sha256 - (base32 "0a33gbhzd580i31xxsjxigg0nl8ag1x4xz3jqmq5jqappc6f5d2k")))) + (base32 "0hikz8f19blywxs66xj6zf4krwyivsy3w165qvrnb0m2l6dx1l7v")))) (properties `((upstream-name . "Exact"))) (build-system r-build-system) (propagated-inputs (list r-rootsolve)) @@ -7494,29 +7538,35 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.54") + (version "0.99.56") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "16qbm1l1281yj1cg6fp8xgd8xdshpz9a09f0b9cyimsjbm01c2j7")))) + (base32 "1lvh19q3f4yidcxilba6bw2l2lllm6zc0aiqjgh8bvz01rq19f09")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - (list r-boot - r-cli - r-data-table - r-exact - r-expm - r-gld - r-httr - r-mass - r-mvtnorm - r-rcpp - r-readxl - r-rstudioapi - r-withr)) + (list r-boot + r-cli + r-data-table + r-exact + r-expm + r-gld + r-httr + r-mass + r-mvtnorm + r-rcpp + r-readxl + r-rstudioapi + r-withr)) (native-inputs (list gfortran r-r-rsp)) (home-page "https://andrisignorell.github.io/DescTools/") (synopsis "Tools for Descriptive Statistics") @@ -7695,12 +7745,11 @@ models, using simulation. It was designed to work with models fit using the (synopsis "Pilotdata based simulations for estimating power in linear mixed models") (description - "Implementation of a simulation based aproach to power analysis. -Mixedpower uses lotdata and a linear mixed model fitted with lme4 to -simulate new data sets. wer is computed separate for every effect in the -model output as the relation significant simulations to all simulations. -More conservative simulations as protection against a bias in the -pilotdata are available aswell as methods for otting the results.") + "Mixedpower uses pilotdata and a linear mixed model fitted with lme4 to +simulate new data sets. Power is computed seperate for every effect in the +model output as the relation of significant simulations to all simulations. +More conservative simulations as a protection against a bias in the pilotdata +are available as well as methods for plotting the results.") (license license:gpl3)))) (define-public r-colorway @@ -7753,13 +7802,13 @@ Neyman, 1936; cf. Spiller et al., 2012), etc.") (define-public r-mumin (package (name "r-mumin") - (version "1.47.5") + (version "1.48.4") (source (origin (method url-fetch) (uri (cran-uri "MuMIn" version)) (sha256 (base32 - "0xqasb79lmdhff25zalzrpjwv6qs9qnxr54ypnqjjgshi96mbwvg")))) + "04zn63snv218c44nllfh8bqh5xg0gamd9fcpwxisvi9gwb3f20i0")))) (properties `((upstream-name . "MuMIn"))) (build-system r-build-system) (propagated-inputs (list r-insight r-matrix r-nlme)) |