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-rw-r--r--gnu/packages/statistics.scm295
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+)))
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-09 09:44:50 +0000