diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 295 |
1 files changed, 216 insertions, 79 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cc879be99c..04b49def54 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com> ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> @@ -9,6 +9,8 @@ ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017 Alex Kost <alezost@gmail.com> +;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,6 +47,8 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages curl) + #:use-module (gnu packages emacs) + #:use-module (gnu packages emacs-xyz) #:use-module (gnu packages gcc) #:use-module (gnu packages gtk) #:use-module (gnu packages gettext) @@ -60,6 +64,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) #:use-module (gnu packages ssh) #:use-module (gnu packages tcl) @@ -395,14 +400,14 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") (define-public r-class (package (name "r-class") - (version "7.3-14") + (version "7.3-15") (source (origin (method url-fetch) (uri (cran-uri "class" version)) (sha256 (base32 - "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q")))) + "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -439,14 +444,14 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (define-public r-codetools (package (name "r-codetools") - (version "0.2-15") + (version "0.2-16") (source (origin (method url-fetch) (uri (cran-uri "codetools" version)) (sha256 (base32 - "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) + "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/codetools") (synopsis "Code analysis tools for R") @@ -567,14 +572,14 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-25") + (version "1.8-26") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "1y2rq6v45pr2wcxihhgmingcdvcsilim2cvskrlb7k2n00qg6v2q")))) + "02bsz455fr5hyhpmgcrd266qafs2wbz3ygdipxg9gfazbdvq2v4q")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -649,14 +654,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "2.43-1") + (version "2.43-3") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "0220fjsq4ycx1n5zc5h39wdbj5j6xr8rzqbcixx2p25akzdn7kqk")))) + "0ldrjja1dj4n1ic0lbggm7jvk52sl5h85i8m23nrgndi60acsv4r")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -808,14 +813,14 @@ non-estimable cases correctly.") (define-public r-pheatmap (package (name "r-pheatmap") - (version "1.0.10") + (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "pheatmap" version)) (sha256 (base32 - "1jzxs5hwbz3r0z2pp09i7fd14sndxnrbm3zibaac3kny4nzydzf7")))) + "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) (build-system r-build-system) (propagated-inputs `(("r-gtable" ,r-gtable) @@ -1266,13 +1271,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.66.0-1") + (version "1.69.0-1") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "14kab6wp0c27d8x4jqyf065p4bj210s9b67c0bfsfjnp29aypn8p")))) + "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") @@ -1361,13 +1366,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "1vcgsh2m2f5kfgappgg71nbf04ff0j1sbk668krjs3r2n89dk3sk")))) + "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h")))) (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 @@ -1405,19 +1410,20 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.20") + (version "1.21") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1408dm25cxahk2clff8hlajaqdj5v1gs40nm3q6rf0ghd82hj93v")))) + "0xzymi4gkilqaa5b2ay9zk1advavzkwxf7mb064bqfb09y8rak0j")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) ("r-highr" ,r-highr) ("r-markdown" ,r-markdown) ("r-stringr" ,r-stringr) + ("r-xfun" ,r-xfun) ("r-yaml" ,r-yaml))) (home-page "http://yihui.name/knitr/") (synopsis "General-purpose package for dynamic report generation in R") @@ -1608,13 +1614,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.3.0.1") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "0j7kp6h25wbkvpzr7dpc0zgdpjiwsjjlgprj3mv7bgfalfq1si99")))) + "0lbi66bavca866k26dnpkxj3l106xr4a6khcsfn8i3i8w8mpnhih")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1626,20 +1632,22 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "1.4.2") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "05svbjkm1xqv56ybjgsqqg2pp8nn6hams1yxcr8aanbhzx9h6rqi")))) + "04rxf5x9awwa9c00v9p7d3a2lqnn7j2rjg4r219hmw7cbqlwrcks")))) (build-system r-build-system) (propagated-inputs - `(("r-rlang" ,r-rlang) - ("r-cli" ,r-cli) + `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) - ("r-pillar" ,r-pillar))) + ("r-fansi" ,r-fansi) + ("r-pkgconfig" ,r-pkgconfig) + ("r-pillar" ,r-pillar) + ("r-rlang" ,r-rlang))) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") (description @@ -1687,14 +1695,14 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "1.2.2") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "0j5w6a1qim972kv4vmvinp3j50yr4idmm9cd3w7y3zsz0nq0nhcx")))) + "07p23vyvi7s4abldhkyir05kcf7xnfc18igfryq12j67xd0jql0m")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -1800,13 +1808,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.11.8") + (version "1.12.0") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "1nb6wngrk1a30m984524gf26fa1nwgyf4y4an94dibcwb5jp8hnw")))) + "1xz388khklqqc39r1cmjvqm65azambgzqw0743aypm6v4chi26v1")))) (build-system r-build-system) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") @@ -2069,14 +2077,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8")))) + "1hac46xaawnqajlsfb5k7pfkc2ya9h76s5qv9ycj3jafh93d26z4")))) (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") @@ -2092,14 +2100,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "1.8.5") + (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1q6igk50lq4fp5d3imgcn1j063h3gsp214ra4nlf534hf4wjlkg9")))) + "1y4ylzn55kpyfpzcx9rxb9413d3ck6hair36ldl0ak61ia5kc75p")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) @@ -2234,14 +2242,14 @@ other packages.") (define-public r-commonmark (package (name "r-commonmark") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 - "1xymqncf8byqxzpx64zlp6vbx7gry572jkr2ax0zlavr8bli861x")))) + "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") @@ -2289,17 +2297,21 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "0ldxgcr33lawwr8wp14kdk2678gpkvqkzv6g333bhck1hn6qspzv")))) + "0ypa41qr58jgipzkqn3wjqdsjyi7qk57i46s5wy88xy3j8jl9jkv")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (propagated-inputs + `(("r-askpass" ,r-askpass))) (home-page "https://github.com/jeroenooms/openssl") (synopsis "Toolkit for encryption, signatures and certificates") (description @@ -2318,13 +2330,13 @@ integers.") (define-public r-httr (package (name "r-httr") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "httr" version)) (sha256 (base32 - "0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2")))) + "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -2344,19 +2356,19 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.23.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "01250jz255fnyy2ap90nskvzhd8nhlmbhwgpvb43mk1fax077lrz")))) + "0vfc25z4j53pc49cnp3zjwzjb72kvc0aq96wgyg10xpgvhl3z0gg")))) (build-system r-build-system) ;; This R package contains modified sources of libgit2. This modified ;; version of libgit2 is built as the package is built. Hence libgit2 is ;; not among the inputs of this package. (inputs - `(("libssh2" ,libssh2) + `(("libssh2" ,libssh2) ; for SSH transport ("openssl" ,openssl) ("zlib" ,zlib))) (native-inputs @@ -2372,13 +2384,13 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.8") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "0d6r0in13k0rcyr6asanwy0a9dv4lizq6l2w913rr222pq6vrrck")))) + "0gn1pvaxfh2gh2ikvxcr8f6k97ygcfr68iz6dhwlq4z71a1s4jai")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") @@ -2464,16 +2476,18 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.1.1") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s")))) + "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) + `(("r-clipr" ,r-clipr) + ("r-crayon" ,r-crayon) + ("r-rcpp" ,r-rcpp) ("r-hms" ,r-hms) ("r-tibble" ,r-tibble) ("r-r6" ,r-r6) @@ -2547,13 +2561,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.200.4.0") + (version "0.9.200.7.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1ayvpyi4hgaqrhx1kqi640iillc2byj4kam7vydlgqmdrzpgrfvz")))) + "11m04yvdh6086567dzzxchbf68fl5hxf2y32acf3f43bjqgwbv2p")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs @@ -2641,14 +2655,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.10") + (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "0mh2f3k98w7pgz0ri34149s4kx5y0kfm27nwq64k0qwxd16hwd9r")))) + "0yyjbh891mdqzpjkblz8510ng71i7mxmyiqr69x3rwlwk2vakk79")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2658,7 +2672,6 @@ certain criterion, e.g., it contains a certain regular file.") ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-mime" ,r-mime) - ("r-rprojroot" ,r-rprojroot) ("r-stringr" ,r-stringr) ("r-tinytex" ,r-tinytex) ("r-yaml" ,r-yaml) @@ -3311,14 +3324,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.7-0") + (version "1.7-0.1") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "0fk4pw67cw1663d0n9rf1qfdqzz8k5nqkjgp3hi5jr422qp9lsck")))) + "11fqm4shmksalkazcwvzfknp3amigw7fr8wdwanqa5v5kx7ihyq9")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class))) @@ -3746,18 +3759,17 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.2.5") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "0dc53zzan3km2l9lzxjixcv6yn7dhw2ppmz8qf2awhak7x2qm9m4")))) + "0mzbf9ca8qdrqkrh9x7yzqxiab9bk10ql46qr1wl2bgbflminzda")))) (build-system r-build-system) (propagated-inputs - `(("r-tibble" ,r-tibble) - ("r-magrittr" ,r-magrittr) + `(("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang))) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") @@ -3972,14 +3984,14 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.1-1") + (version "4.2-0") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 (base32 - "160l50ppjs69ipcaya1mlcz29zbn5rmqg91r09dvzzvkvwfb47cr")))) + "1n8i2jhc308hd6bvys9cd7nrz7pwjszs03r5bwlh1pc869ki95ly")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs @@ -4102,14 +4114,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-2") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0")))) + "1y25nnw09qfm66523w1z4q766lv15a6ykvsq30r154n7m7aggvsq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -4191,14 +4203,14 @@ including: (define-public r-gplots (package (name "r-gplots") - (version "3.0.1") + (version "3.0.1.1") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 - "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l")))) + "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx")))) (build-system r-build-system) (propagated-inputs `(("r-catools" ,r-catools) @@ -4443,13 +4455,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.6") + (version "2.6.1") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "1r6rivh9ba4gwnzryip0aiwsbm46zma7nvd9z5y456p2dgzp9lii")))) + "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) @@ -4512,14 +4524,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "1jrx1h0blkk577y4cvnjk7xccn7qmjiv2bnpgqlsjvjhsxglf41y")))) + "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -4718,14 +4730,14 @@ and resampling-based inference.") (define-public r-prabclus (package (name "r-prabclus") - (version "2.2-6") + (version "2.2-7") (source (origin (method url-fetch) (uri (cran-uri "prabclus" version)) (sha256 (base32 - "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1")))) + "0h2nml8ri27mhfs2p6ngb6kfd6lyq30sc6813yybpskkrb6gs1pb")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -4810,14 +4822,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.4-4") + (version "1.4-7") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "0wn5h8vi0zyk5ah898m37ysz4kiih6y792nb9zdvhvd8r07f0sc5")))) + "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -5016,14 +5028,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.3.4.0") + (version "0.3.3.5.0") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "1m6ssq6lvi36ggf26y4hhq996583pxxdb978jnn1x6r9gdb0q0hi")))) + "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs @@ -5086,14 +5098,14 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.36") + (version "5.38") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 (base32 - "023gdzahxp582rpabilpxbl3wyjrgjjnnrhcv9xhrqdfiq5l2yza")))) + "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5248,14 +5260,14 @@ to Applied regression, Second Edition, Sage, 2011.") (define-public r-caret (package (name "r-caret") - (version "6.0-80") + (version "6.0-81") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "0xhdhazzfh0hiqv2hgxglj9ffd2p4ls8acqn2sjn0ndx6158f187")))) + "1fibrskjzq2f06b8gbrfp3263svfc5s5apsjwaqdg9qzs7sy7fpc")))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) @@ -5395,14 +5407,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.10.1") + (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "12z67xkgdmr5cflpd6cln0mn5xxajanqbfwlckv6cfma0gvf2z1j")))) + "1yyg1nppq76jngzffd44brppqrlxqdhv92pyy0gn09rfc0ab37wr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -5711,6 +5723,64 @@ plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.") (license license:lgpl3+))) +(define-public python-rpy2 + (package + (name "python-rpy2") + (version "2.9.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rpy2" version)) + (sha256 + (base32 + "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy")))) + (build-system python-build-system) + (arguments + '(#:modules ((ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26) + (guix build utils) + (guix build python-build-system)) + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key outputs inputs #:allow-other-keys) + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" + (getenv "PYTHONPATH")))) + (invoke "python" "-m" "rpy2.tests" "-v")))))) + (propagated-inputs + `(("python-six" ,python-six) + ("python-jinja2" ,python-jinja2) + ("python-pytz" ,python-pytz))) + (inputs + `(("readline" ,readline) + ("icu4c" ,icu4c) + ("pcre" ,pcre) + ("r-minimal" ,r-minimal) + ("r-survival" ,r-survival) + ("r-ggplot2" ,r-ggplot2) + ("r-rsqlite" ,r-rsqlite) + ("r-dplyr" ,r-dplyr) + ("r-dbplyr" ,r-dbplyr) + ("python-numpy" ,python-numpy))) + (native-inputs + `(("zlib" ,zlib))) + (home-page "https://rpy2.bitbucket.io/") + (synopsis "Python interface to the R language") + (description "rpy2 is a redesign and rewrite of rpy. It is providing a +low-level interface to R from Python, a proposed high-level interface, +including wrappers to graphical libraries, as well as R-like structures and +functions.") + ;; Any of these licenses can be picked for the R interface. The whole + ;; project is released under GPLv2+ according to the license declaration + ;; in "setup.py". + (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))) + (define-public java-jdistlib (package (name "java-jdistlib") @@ -5747,3 +5817,70 @@ Java package that provides routines for various statistical distributions.") ;; are under the GPLv3, which is a mistake. The author confirmed in an ;; email that this whole project should be under GPLv2+. (license license:gpl2+))) + +(define-public emacs-ess + (package + (name "emacs-ess") + (version "17.11") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/emacs-ess/ESS/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c")) + (file-name (string-append name "-" version ".tar.gz")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Stop ESS from trying to bundle an external julia-mode.el. + (substitute* "lisp/Makefile" + (("^\tjulia-mode.elc\\\\\n") "") + (("^dist: all julia-mode.el") + "dist: all")) + ;; No need to build docs in so many formats. Also, skipping + ;; pdf lets us not pull in texlive. + (substitute* "doc/Makefile" + (("all : info text html pdf") + "all : info") + (("install: install-info install-other-docs") + "install: install-info")) + ;; Test fails upstream + (substitute* "test/ess-r-tests.el" + (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()") + "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed")) + #t)))) + (build-system gnu-build-system) + (arguments + (let ((base-directory "/share/emacs/site-lisp/guix.d/ess")) + `(#:make-flags (list (string-append "PREFIX=" %output) + (string-append "ETCDIR=" %output "/" + ,base-directory "/etc") + (string-append "LISPDIR=" %output "/" + ,base-directory)) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'more-shebang-patching + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makeconf" + (("SHELL = /bin/sh") + (string-append "SHELL = " (which "sh")))) + #t)) + (replace 'check + (lambda _ + (invoke "make" "test"))))))) + (inputs + `(("emacs" ,emacs-minimal) + ("r-minimal" ,r-minimal))) + (native-inputs + `(("perl" ,perl) + ("texinfo" ,texinfo))) + (propagated-inputs + `(("emacs-julia-mode" ,emacs-julia-mode))) + (home-page "https://ess.r-project.org/") + (synopsis "Emacs mode for statistical analysis programs") + (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU +Emacs. It is designed to support editing of scripts and interaction with +various statistical analysis programs such as R, Julia, and JAGS.") + (license license:gpl2+))) |