diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 171 |
1 files changed, 97 insertions, 74 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index be7c42617b..6bf952734c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -183,7 +183,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "3.6.3") + (version "4.0.0") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -191,7 +191,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49")))) + "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -269,6 +269,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (("my \\$date = strftime \"%B %Y\", localtime" line) (string-append line " 1")))) #t)) + (add-before 'build 'set-locales + (lambda _ + (setlocale LC_ALL "C") + (setenv "LC_ALL" "C") + #t)) (add-before 'configure 'set-default-pager ;; Set default pager to "cat", because otherwise it is "false", ;; making "help()" print nothing at all. @@ -322,7 +327,9 @@ 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-ec + ("texlive" ,(texlive-union (list texlive-ae + texlive-inconsolata + texlive-fonts-ec texlive-amsfonts texlive-latex-base texlive-latex-fancyvrb @@ -331,7 +338,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ texlive-latex-oberdiek texlive-latex-tools texlive-latex-upquote - texlive-latex-url))) + texlive-latex-url + texlive-latex-xkeyval))) ("tzdata" ,tzdata-for-tests) ("xz" ,xz))) (inputs @@ -347,7 +355,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ("libpng" ,libpng) ("libtiff" ,libtiff) ("libxt" ,libxt) - ("pcre" ,pcre) + ("pcre2" ,pcre2) ("readline" ,readline) ;; This avoids a reference to the ungraftable static bash. R uses the ;; detected shell for the "system" procedure. @@ -504,14 +512,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-76") + (version "0.8-78") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "1z6x2x1z12wnv0z4p74d91r5wfaq30sdz4ynwx0lncz1q45mhbh5")))) + "01anirfbfa3ip5pyqv72cg4x7p0jsppmbvxrllw7bm28fl1hgiyq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -548,13 +556,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) (define-public r-lattice (package (name "r-lattice") - (version "0.20-40") + (version "0.20-41") (source (origin (method url-fetch) (uri (cran-uri "lattice" version)) (sha256 (base32 - "1w53sfzdy9zsifv44dqf9pl46fk14lnx3fha1k1p660h51lyv56m")))) + "1dapkmh4jlb9sxfrpvapvlfhczl4s8p3r20bn47gcgdk1izmbjjl")))) (build-system r-build-system) (home-page "http://lattice.r-forge.r-project.org/") (synopsis "High-level data visualization system") @@ -590,13 +598,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-145") + (version "3.1-147") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "1i9a3afdmn2ziks0imz0j09ay9n0zb9mhrymy9mg97vvlz5diwrh")))) + (base32 "1rqc3wy3lmy0wczsvsn8yszzsxhppfwg4iznb1j6ki2qawpdij7g")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -693,14 +701,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.1-11") + (version "3.1-12") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "1fbhbm3bnpg1nmj37h1d76x813ggvwk0cp51ixmmgb3pz47i5xj4")))) + "07zj3gpwncw89hbiwjb6ih9axv5zwdqnbgz9yw9xzws6nrpdcbmn")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -1066,13 +1074,13 @@ the input of another.") (define-public r-reshape2 (package (name "r-reshape2") - (version "1.4.3") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "reshape2" version)) (sha256 - (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa")))) + (base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) @@ -1148,14 +1156,14 @@ agnes cluster diagrams.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "1aax50wyrs4336zpf247l8wmp4spab2n70msziy1ip4gbjn26wa1")))) + "08njzin0c6biw62j5w30r9j85vr1m2cg4hmv5d76nym860yrlqjf")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -1505,7 +1513,7 @@ understand the language at a deeper level.") (home-page "https://github.com/hadley/memoise") (synopsis "Memoise functions for R") (description - "This R package allows to cache the results of a function so that when + "This R package caches the results of a function so that when you call it again with the same arguments it returns the pre-computed value.") (license license:expat))) @@ -1624,22 +1632,28 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "2.1.3") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "06jfayiip8j8ibdhw3fvxn4n8aqbqhwanrszpzlsf92xdfgfm34s")))) + "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) + ("r-ellipsis" ,r-ellipsis) ("r-fansi" ,r-fansi) + ("r-lifecycle" ,r-lifecycle) + ("r-magrittr" ,r-magrittr) ("r-pkgconfig" ,r-pkgconfig) ("r-pillar" ,r-pillar) - ("r-rlang" ,r-rlang))) + ("r-rlang" ,r-rlang) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") (description @@ -1688,25 +1702,28 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp")))) + "1si8sahr1kwq1xgjzi9klkahad07pyrsngy75y1f74f64907pb39")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-dbi" ,r-dbi) ("r-dplyr" ,r-dplyr) ("r-glue" ,r-glue) + ("r-lifecycle" ,r-lifecycle) ("r-purrr" ,r-purrr) ("r-r6" ,r-r6) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidyverse/dbplyr") (synopsis "Dplyr back end for databases") (description @@ -1983,14 +2000,14 @@ and environmental data in the framework of Euclidean exploratory methods.") (define-public r-xml2 (package (name "r-xml2") - (version "1.2.5") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "0mp61gg8s3zfq10g10vjk0mrcx6d5gm81n4ji8an2my11g61yq94")))) + "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz")))) (build-system r-build-system) (inputs `(("libxml2" ,libxml2) @@ -1998,8 +2015,6 @@ and environmental data in the framework of Euclidean exploratory methods.") (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/hadley/xml2") (synopsis "Parse XML with R") (description @@ -2076,14 +2091,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "0k19w68b2aihyj5mflw3732gkkzs78sssqdns960pdw3yfnkiv33")))) + "170rphqq28j0pcr28g6dxv3isp436ajhyzkpri31pn0lfm3szs6h")))) (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") @@ -2397,13 +2412,13 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "2.2.2") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "1bhb2j8ilpdzwd0c678mcgfpdw88vncsjma79afcikxmzcsz9279")))) + "1l6w765q180bg5mmdq5k2ymf6apz7ldhnknzf6ynfp1kf70pbhsg")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -2431,6 +2446,8 @@ informative error messages when it's not available.") ("r-testthat" ,r-testthat) ("r-usethis" ,r-usethis) ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/devtools") (synopsis "Tools to make developing R packages easier") (description "The devtools package is a collection of package development @@ -2440,14 +2457,16 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.1.2") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1")))) + "10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") (description @@ -2508,13 +2527,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.7-7") + (version "3.7-8") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54")))) + "104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2569,21 +2588,15 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.850.1.0") + (version "0.9.860.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0q9clhmbwwph47hrhx5827m7njrcl2klihyqbkf0ihwlbqrjijwz")))) + "1rg9ak0zbv8d9cyj10jq52nrcbk1pvfz28kbkhpx79mpjhrl7pb5")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) - ;; All needed for vignettes - (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/RcppCore/RcppArmadillo") @@ -3060,18 +3073,20 @@ data.") (define-public r-foreach (package (name "r-foreach") - (version "1.4.8") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "foreach" version)) (sha256 (base32 - "1xwf5l2fw62w80ji3dvgcc6m9m4s6zygkhi84ypb0gv0ppjffg5c")))) + "0584nv49x8d8m1cak5drb54sxs3y594gd521kjsdwk4c849sgy8s")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-iterators" ,r-iterators))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/foreach") (synopsis "Foreach looping construct for R") (description @@ -3741,18 +3756,20 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "17lyys7dxjrwsfkq7a7hw65iy3qn3pp1sn70srdy64jf8adahc8g")))) + "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") (description @@ -3763,13 +3780,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.9.2") + (version "4.9.2.1") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "19zw3qnhfgqdxlvma8xyikir46aiqhfcwxf072z9xgq0hknpblm5")))) + "1f0x83a2s7200iqi6gpngijks06fcvcbm6701d5r5rxpb8rawppl")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -4095,14 +4112,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-5") + (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "173qgm2bn84x544fc3x9gc2rv995sbsvji9lnn2drx8drvzyy8lf")))) + "04fvjdab6vyyghyqy0abxvfbyr1myz6yib7ibwiyjw9yf7fjrcjp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -4114,14 +4131,14 @@ Zurich, including many that are related to graphics.") (define-public r-gtools (package (name "r-gtools") - (version "3.8.1") + (version "3.8.2") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 - "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505")))) + "1pnwy412wvhhvnnx8qg6s9hrgcnsfhnfcpf2560ipipk845acfsh")))) (build-system r-build-system) (arguments `(#:phases @@ -4689,17 +4706,18 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.5") + (version "5.4.6") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm")))) + "1z46qask09x3xpv0wzvhn09218vwyrip4f5jrhnx96khpwvczzyl")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) (home-page "https://www.stat.washington.edu/mclust/") (synopsis "Gaussian mixture modelling for model-based clustering etc.") (description @@ -4775,7 +4793,7 @@ can be efficiently implemented directly in the R language.") (home-page "http://robustbase.r-forge.r-project.org/") (synopsis "Basic robust statistics") (description - "This package allows to analyze data with robust methods such as + "This package analyzes data with robust methods such as regression methodology including model selections and multivariate statistics.") (license license:gpl2+))) @@ -5076,13 +5094,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.54") + (version "5.55") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "19nh79qrkb75q348nk148l8wqjwnq5jgq29wpzqym5cfv1kjqfvh")))) + (base32 "1zjc8p95kb0ypxa6nxp0lkdq8armkjmmhf8484m25n5f14a59qfb")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5131,14 +5149,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-21") + (version "1.1-23") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "035j2hqkwv939xl07pm2vykvf3wlx8qj317846n9pkpqkyv58mbz")))) + "0qh29kqli0l3naylgb6jha6jllx4nwryr3hv9yk37blgyyql5mcr")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -5149,7 +5167,10 @@ algorithms.") ("r-nloptr" ,r-nloptr) ("r-nlme" ,r-nlme) ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + ("r-rcppeigen" ,r-rcppeigen) + ("r-statmod" ,r-statmod))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/lme4") (synopsis "Linear mixed-effects models using eigen and S4") (description @@ -5251,7 +5272,7 @@ to Applied regression, Second Edition, Sage, 2011.") (home-page "https://github.com/kforner/rcpp_progress") (synopsis "Interruptible progress bar for C++ in R packages") (description - "This package allows to display a progress bar in the R console for long running + "This package displays a progress bar in the R console for long running computations taking place in C++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.") (license license:gpl3+))) @@ -5302,18 +5323,19 @@ first and second order derivatives.") (define-public r-sn (package (name "r-sn") - (version "1.5-5") + (version "1.6-1") (source (origin (method url-fetch) (uri (cran-uri "sn" version)) (sha256 (base32 - "0ymyyc0di1g2b11wzljiih05z3rxck48wn74bygg3fiby973z49f")))) + "0snri2k8qslb7478c5jz4a5xxmmb1ipmp8x1jizi8mhj2cjic1w0")))) (build-system r-build-system) (propagated-inputs `(("r-mnormt" ,r-mnormt) - ("r-numderiv" ,r-numderiv))) + ("r-numderiv" ,r-numderiv) + ("r-quantreg" ,r-quantreg))) (home-page "http://azzalini.stat.unipd.it/SN") (synopsis "The skew-normal and skew-t distributions") (description @@ -5396,14 +5418,14 @@ genome-wide association studies can be analyzed efficiently.") (define-public r-cairo (package (name "r-cairo") - (version "1.5-11") + (version "1.5-12") (source (origin (method url-fetch) (uri (cran-uri "Cairo" version)) (sha256 (base32 - "1k9kpxcg5n4g6x2gydv344f4w0snqbhww14fnbbj1bny0mmv28xg")))) + "02v29am4fac3fyq6y1w6r89zwbqqkxjsxrafcwb5s124ikxyl22f")))) (properties `((upstream-name . "Cairo"))) (build-system r-build-system) (inputs @@ -5432,20 +5454,21 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.4") + (version "1.7.8") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i")))) + "0g2m9dyhgds4shdrk76w7rqdl9msam4rii2qrhz12gipzhi9k89x")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr))) - (home-page - "https://cran.r-project.org/web/packages/lubridate") + `(("r-generics" ,r-generics) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/lubridate/") (synopsis "Make dealing with dates a little easier") (description "This package provides functions to work with date-times and time-spans: |