;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
+;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
;;;
;;; This file is part of GNU Guix.
;;;
("pango" ,pango)
("readline" ,readline)
("gtk" ,gtk+)
- ("gtksourceview" ,gtksourceview)
+ ("gtksourceview" ,gtksourceview-3)
("spread-sheet-widget" ,spread-sheet-widget)
("zlib" ,zlib)))
(native-inputs
(define-public libxls
(package
(name "libxls")
- (version "1.5.2")
+ (version "1.5.3")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/libxls/libxls/releases/download/"
"v" version "/libxls-" version ".tar.gz"))
(sha256
- (base32 "1akadsyl10rp101ccjmrxr7933c3v641k377bn74jv6cdkcm4zld"))))
+ (base32 "0rl513wpq5qh7wkmdk4g9c68rzffv3mcbz48p4xyg4969zrx8lnm"))))
(build-system gnu-build-system)
(home-page "https://github.com/libxls/libxls")
(synopsis "Read binary (.xls) Excel spreadsheet files")
(define r-with-tests
(package
(name "r-with-tests")
- (version "4.0.0")
+ (version "4.0.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
version ".tar.gz"))
(sha256
(base32
- "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"))))
+ "0xdy3dy2bzdiba8z94hjykyra8si8a5q15s0bri7c26scjrymg6k"))))
(build-system gnu-build-system)
(arguments
`(#:disallowed-references (,tzdata-for-tests)
("openblas" ,openblas)
("gfortran" ,gfortran)
("icu4c" ,icu4c)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libtiff" ,libtiff)
("libxt" ,libxt)
(define-public r-foreign
(package
(name "r-foreign")
- (version "0.8-78")
+ (version "0.8-80")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
- "01anirfbfa3ip5pyqv72cg4x7p0jsppmbvxrllw7bm28fl1hgiyq"))))
+ "0wjdi3qn9famsxmpdyyahidaid0yhxlpx4ad9k8vrxhxd6xspasp"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
(define-public r-kernsmooth
(package
(name "r-kernsmooth")
- (version "2.23-16")
+ (version "2.23-17")
(source
(origin
(method url-fetch)
(uri (cran-uri "KernSmooth" version))
(sha256
(base32
- "1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq"))))
+ "11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b"))))
(properties `((upstream-name . "KernSmooth")))
(build-system r-build-system)
(native-inputs
(define-public r-nlme
(package
(name "r-nlme")
- (version "3.1-147")
+ (version "3.1-148")
(source
(origin
(method url-fetch)
(uri (cran-uri "nlme" version))
(sha256
- (base32 "1rqc3wy3lmy0wczsvsn8yszzsxhppfwg4iznb1j6ki2qawpdij7g"))))
+ (base32 "1cmf43r82kar1hpj9dhqfi3rbjka0z5s6cbdy7fklwh99xj3phkp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(define-public r-nnet
(package
(name "r-nnet")
- (version "7.3-13")
+ (version "7.3-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "nnet" version))
(sha256
(base32
- "1z0rj5cm4ycw1y0gd5wwwg8c2298v90iybgqdqh17967jbi2125f"))))
+ "1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
(build-system r-build-system)
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "Feed-forward neural networks and multinomial log-linear models")
(define-public r-spatial
(package
(name "r-spatial")
- (version "7.3-11")
+ (version "7.3-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatial" version))
(sha256
(base32
- "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
+ "0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
(build-system r-build-system)
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "Functions for kriging and point pattern analysis")
(define-public r-survival
(package
(name "r-survival")
- (version "3.1-12")
+ (version "3.2-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "survival" version))
(sha256
(base32
- "07zj3gpwncw89hbiwjb6ih9axv5zwdqnbgz9yw9xzws6nrpdcbmn"))))
+ "07h76r2y23w889257krlijcw4n4d7ssx92x7i5qb1xyv5gyvl3rx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
(define-public r-ggplot2
(package
(name "r-ggplot2")
- (version "3.3.0")
+ (version "3.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggplot2" version))
(sha256
- (base32 "0j21am605kqqzlwhm45kaj0m2irnmy2vz0j7kzi9f0qdzrv3q3ij"))))
+ (base32 "0wsib5qpzn4d0w1ss3x158xmrawkms8vvsfvr3mh40pvd8g2ibad"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
("r-scales" ,r-scales)
("r-svglite" ,r-svglite) ; Needed for 'ggsave'
("r-withr" ,r-withr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://ggplot2.tidyverse.org")
(synopsis "An implementation of the grammar of graphics")
(description
(define-public r-svglite
(package
(name "r-svglite")
- (version "1.2.3")
+ (version "1.2.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "svglite" version))
(sha256
(base32
- "1zivykbi1pxdxhrkc1if1ihdn5p27j0nai2q0abca1dwry3wg2yl"))))
+ "00n8bg4iligl0h24v42cka417w26zmcxrr4r6k8wdal1riwhgmi5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
("r-gdtools" ,r-gdtools)
("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/hadley/svglite")
(synopsis "SVG graphics device")
(description
(define-public r-knitr
(package
(name "r-knitr")
- (version "1.28")
+ (version "1.29")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
- "0ai382fmpz25qrhdgchs3vph2cdvyd73xyryg4jby5fp67d03vh5"))))
+ "00rcwiq8znmk5h4qgrwd0639xyb38iwbjykqjk3disz3kvrcvbn1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-evaluate" ,r-evaluate)
(define-public r-rlang
(package
(name "r-rlang")
- (version "0.4.5")
+ (version "0.4.7")
(source (origin
(method url-fetch)
(uri (cran-uri "rlang" version))
(sha256
(base32
- "1a0h3dr519p3jj6aygbhwi9f2zwlan6d07f1gkh2db56y5vaq7yd"))))
+ "0f4rhnhyhgrv874l0yzm80ij6vcqdykfd7bzmnqs0wbgyhkxk8vq"))))
(build-system r-build-system)
(home-page "http://rlang.tidyverse.org")
(synopsis "Functions for base types, core R and Tidyverse features")
(define-public r-tibble
(package
(name "r-tibble")
- (version "3.0.1")
+ (version "3.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "tibble" version))
(sha256
(base32
- "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
+ "0f4yi87w6509lnaz1lhk9s8nm3bzx21ij3273s0zx7vpbp0qlxxz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
(define-public r-dplyr
(package
(name "r-dplyr")
- (version "0.8.5")
+ (version "1.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
- "0602b4a9nffxx67q57csqp87nkrv33nn9wlaw1458yys9fzx6l2p"))))
+ "1wxi7pzw1mqkgay2s9hwlkpkxfzydngf56wrf7k93n14rlqm3dmz"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-assertthat" ,r-assertthat)
- ("r-bh" ,r-bh)
- ("r-ellipsis" ,r-ellipsis)
+ `(("r-ellipsis" ,r-ellipsis)
+ ("r-generics" ,r-generics)
("r-glue" ,r-glue)
+ ("r-lifecycle" ,r-lifecycle)
("r-magrittr" ,r-magrittr)
- ("r-pkgconfig" ,r-pkgconfig)
- ("r-plogr" ,r-plogr)
("r-r6" ,r-r6)
- ("r-rcpp" ,r-rcpp)
("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)
- ("r-tidyselect" ,r-tidyselect)))
+ ("r-tidyselect" ,r-tidyselect)
+ ("r-vctrs" ,r-vctrs)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/hadley/dplyr")
(define-public r-dbplyr
(package
(name "r-dbplyr")
- (version "1.4.3")
+ (version "1.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "dbplyr" version))
(sha256
(base32
- "1si8sahr1kwq1xgjzi9klkahad07pyrsngy75y1f74f64907pb39"))))
+ "1v0p0557n6bz84nq9jc4182k00mdd1hvz7h4w3bbg81z0fmpj0d8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
+ ("r-blob" ,r-blob)
("r-dbi" ,r-dbi)
("r-dplyr" ,r-dplyr)
("r-glue" ,r-glue)
("r-lifecycle" ,r-lifecycle)
+ ("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
("r-r6" ,r-r6)
("r-rlang" ,r-rlang)
(define-public r-rversions
(package
(name "r-rversions")
- (version "2.0.1")
+ (version "2.0.2")
(source (origin
(method url-fetch)
(uri (cran-uri "rversions" version))
(sha256
(base32
- "1ic6sxnyya24d5xsxjg3fba73fhya9fhs0kaf66yha6nwxj1zv2i"))))
+ "0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
(define-public r-backports
(package
(name "r-backports")
- (version "1.1.6")
+ (version "1.1.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "backports" version))
(sha256
(base32
- "170rphqq28j0pcr28g6dxv3isp436ajhyzkpri31pn0lfm3szs6h"))))
+ "1irc9c23hwliwkky1b3hi0dkzwalhb7zgjj08562ff1k8dqv4qf6"))))
(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")
(define-public r-roxygen2
(package
(name "r-roxygen2")
- (version "7.1.0")
+ (version "7.1.1")
(source (origin
(method url-fetch)
(uri (cran-uri "roxygen2" version))
(sha256
(base32
- "00s1wzx5960k8pzgpz4kikjf4k061hyhnd278y65q6n0wzv3d6vy"))))
+ "0qc8akwfwmaqsjaza87f5fi0zk6sh3l6j3assbs6chvx0gnmvidx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-brew" ,r-brew)
("r-stringi" ,r-stringi)
("r-stringr" ,r-stringr)
("r-xml2" ,r-xml2)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/klutometis/roxygen")
(synopsis "In-source documentation system for R")
(description
(define-public r-openssl
(package
(name "r-openssl")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
- "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
+ "17fkc6pr8w5z3rpadg692a689p1v4j7xl5ak0y64is7c74cxgljx"))))
(build-system r-build-system)
(inputs
`(("libressl" ,libressl)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-askpass" ,r-askpass)))
(home-page "https://github.com/jeroenooms/openssl")
(define-public r-git2r
(package
(name "r-git2r")
- (version "0.26.1")
+ (version "0.27.1")
(source (origin
(method url-fetch)
(uri (cran-uri "git2r" version))
(sha256
(base32
- "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
+ "1h1vfzym6hi1fqs9p5z5v0f4xldggr425frw8k6dsidah3qhg4h9"))))
(build-system r-build-system)
(inputs
`(("libgit2" ,libgit2)
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.9.860.2.0")
+ (version "0.9.900.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "1rg9ak0zbv8d9cyj10jq52nrcbk1pvfz28kbkhpx79mpjhrl7pb5"))))
+ "1zisw2yrb9qmmrs7q8y83mrm7lh1c2786h70gs8jwc0si16x0lq5"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "2.1")
+ (version "2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
- (base32 "0pa5xs0vzwn9vsgysjqbks9v5lbqphxh5agciskllibc40hhwigg"))))
+ (base32 "0vdjq4kcyxkr2m27588kk6yi5g53symjshj4jz4n0j18wz53shji"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
("r-xfun" ,r-xfun)
("r-yaml" ,r-yaml)
("ghc-pandoc" ,ghc-pandoc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://rmarkdown.rstudio.com")
(synopsis "Convert R Markdown documents into a variety of formats")
(description
(define-public r-xml
(package
(name "r-xml")
- (version "3.99-0.3")
+ (version "3.99-0.4")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
- "0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1"))))
+ "1bw6wr17gp0vdnxc5hip47n15nhxwacin3a5992sc7yfb55kaxm5"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
(define-public r-segmented
(package
(name "r-segmented")
- (version "1.1-0")
+ (version "1.2-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "segmented" version))
(sha256
(base32
- "06cxdrqgnpk5fvbam5i7qa4n71wry0yvlj0jpwbxf267mvpx10fh"))))
+ "0r83p36l6m5sy4lxfjbfajn4gcqb0wv9zh7arny02s6c7fb4756y"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/segmented")
(synopsis "Regression models with breakpoints estimation")
(define-public r-dt
(package
(name "r-dt")
- (version "0.13")
+ (version "0.14")
(source (origin
(method url-fetch)
(uri (cran-uri "DT" version))
(sha256
(base32
- "1db35mi4m4q3kha4vhvh693bv04y7h9pdawhsx8f234qjvz7783r"))))
+ "0xhinw7wasrai5wfswp3r48qfv7ppdfd9jc7py2rp63dn0bnvbab"))))
(properties
`((upstream-name . "DT")))
(build-system r-build-system)
(define-public r-glmnet
(package
(name "r-glmnet")
- (version "3.0-2")
+ (version "4.0-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "glmnet" version))
(sha256
- (base32 "0b3nnfzp8dxcdkvxr0yvy6d58yk3xg4kz1wqa42bxqppbakmd2gl"))))
+ (base32 "0qdswxvdwjcnw0by15p9yfzw8laq4f2j0ivpma6q8c5zywldpxxc"))))
(build-system r-build-system)
(native-inputs
- `(("gfortran" ,gfortran)))
+ `(("gfortran" ,gfortran)
+ ("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-foreach" ,r-foreach)
("r-matrix" ,r-matrix)
- ("r-shape" ,r-shape)))
+ ("r-shape" ,r-shape)
+ ("r-survival" ,r-survival)))
(home-page "https://www.jstatsoft.org/article/view/v033i01")
(synopsis "Lasso and elastic-net regularized generalized linear models")
(description
(define-public r-r-rsp
(package
(name "r-r-rsp")
- (version "0.43.2")
+ (version "0.44.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.rsp" version))
(sha256
(base32
- "128zqyvbq9hm9gy86jzhj609lkfw57vr24mdxgh46ncmx66ag4gj"))))
+ "0n9sxrffahgxcc8h9vgxg5i446g14cibixpf82nkpm5bvidhfsc9"))))
(properties `((upstream-name . "R.rsp")))
(build-system r-build-system)
(propagated-inputs
(define-public r-mvtnorm
(package
(name "r-mvtnorm")
- (version "1.1-0")
+ (version "1.1-1")
(source (origin
(method url-fetch)
(uri (cran-uri "mvtnorm" version))
(sha256
(base32
- "0pfb6qk4yb6xaya8i1wvx6dnc3jj4s2g94sq2kzv4p8zn4pf24l1"))))
+ "1pj51mi0g6ip7a2nhzc93yv9289kaayvspjvsbgbgarvx7axlrg9"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(define-public r-tidyselect
(package
(name "r-tidyselect")
- (version "1.0.0")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyselect" version))
(sha256
(base32
- "1bwwsljkg1bxh7xnqxv7n0n1s9y8x407i6lsv826vy1ss1k1fxpy"))))
+ "14rqx4dq574hilmdwrr34wyjg8rlw4rvndpsqd9plgxm3wwfsdg6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ellipsis" ,r-ellipsis)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/tidyselect")
(synopsis "Select from a set of strings")
(description
(define-public r-tidyr
(package
(name "r-tidyr")
- (version "1.0.2")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
(base32
- "0safj8bcf8libwr0jx4059bmarngvhfddrcv8k5iw39m9lpxs0r4"))))
+ "0vqj5dakb35axv4l0yrihpa16vnz2b5bhaaqg7l0gsqbb04qcb00"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-stringi" ,r-stringi)
("r-tibble" ,r-tibble)
("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/hadley/tidyr")
(synopsis "Tidy data with `spread()` and `gather()` functions")
(description
(define-public r-preprocesscore
(package
(name "r-preprocesscore")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "preprocessCore" version))
(sha256
(base32
- "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm"))))
+ "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
(properties
`((upstream-name . "preprocessCore")))
(build-system r-build-system)
(define-public r-sfsmisc
(package
(name "r-sfsmisc")
- (version "1.1-6")
+ (version "1.1-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "sfsmisc" version))
(sha256
(base32
- "04fvjdab6vyyghyqy0abxvfbyr1myz6yib7ibwiyjw9yf7fjrcjp"))))
+ "12g6m8sf17q3qmm133nm4fa296w5n5d9ly3fvb2nvc0w4llkif3l"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/sfsmisc")
(synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
(define-public r-gplots
(package
(name "r-gplots")
- (version "3.0.3")
+ (version "3.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "gplots" version))
(sha256
(base32
- "0hs6mk48i9yd43rg9wfjc2nxsjjwrnpifxqvxkv8ah18kvpd6xnp"))))
+ "15ip3v4xiqzbanf8bc5fj90cbwdgixr72aj5jrp34jfdzdx0gxwg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-catools" ,r-catools)
("r-gdata" ,r-gdata)
("r-gtools" ,r-gtools)
("r-kernsmooth" ,r-kernsmooth)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/gplots")
(synopsis "Various R programming tools for plotting data")
(description
(define-public r-rocr
(package
(name "r-rocr")
- (version "1.0-7")
+ (version "1.0-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "ROCR" version))
(sha256
(base32
- "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
+ "0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p"))))
(properties `((upstream-name . "ROCR")))
(build-system r-build-system)
(propagated-inputs
`(("r-gplots" ,r-gplots)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://rocr.bioinf.mpi-sb.mpg.de/")
(synopsis "Visualizing the performance of scoring classifiers")
(description
mechanism.")
(license license:gpl2+)))
-(define-public r-zoo
- (package
- (name "r-zoo")
- (version "1.8-7")
- (source (origin
- (method url-fetch)
- (uri (cran-uri "zoo" version))
- (sha256
- (base32
- "1w4542zs53bm261g95086a60576v334g1jrhnbgdqni4izf2s1wy"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-lattice" ,r-lattice)))
- (home-page "http://zoo.R-Forge.R-project.org/")
- (synopsis "S3 infrastructure for regular and irregular time series")
- (description "This package contains an S3 class with methods for totally
-ordered indexed observations. It is particularly aimed at irregular time
-series of numeric vectors/matrices and factors.")
- (license license:gpl2+)))
-
(define-public r-ztable
(package
(name "r-ztable")
(define-public r-fit-models
(package
(name "r-fit-models")
- (version "0.5-14")
+ (version "0.63")
(source
(origin
(method url-fetch)
(uri (cran-uri "fit.models" version))
(sha256
(base32
- "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
+ "0wrrfsgngsfrqnm247f0h6g01807i7lbf5chpyx7hkfdfmm4xbxn"))))
(properties `((upstream-name . "fit.models")))
(build-system r-build-system)
(propagated-inputs
(define-public r-fpc
(package
(name "r-fpc")
- (version "2.2-5")
+ (version "2.2-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "fpc" version))
(sha256
(base32
- "10504hzivbn89ip0cd5bcxd36ivbgin1lw1xhyh3xfckcm25v1a5"))))
+ "1xnp3j36hggfg675v39mnr6rgvp7i11pfng7nmyy3k2ldgklz0j9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)
(define-public r-vgam
(package
(name "r-vgam")
- (version "1.1-2")
+ (version "1.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "VGAM" version))
(sha256
- (base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq"))))
+ (base32 "1hwlrdx3nhdp83pvy1h23i16vbbhi4kizdhr58c8nvg7kqdzb7qc"))))
(properties `((upstream-name . "VGAM")))
(build-system r-build-system)
- (inputs
+ (native-inputs
`(("gfortran" ,gfortran)))
(home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
(synopsis "Vector generalized linear and additive models")
(define-public r-quantreg
(package
(name "r-quantreg")
- (version "5.55")
+ (version "5.61")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantreg" version))
(sha256
- (base32 "1zjc8p95kb0ypxa6nxp0lkdq8armkjmmhf8484m25n5f14a59qfb"))))
+ (base32 "0kby1crnzkdg5sczwqapfpkr58apyzrrx85khigcqggmhhwl44wk"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(propagated-inputs
- `(("r-matrix" ,r-matrix)
+ `(("r-conquer" ,r-conquer)
+ ("r-matrix" ,r-matrix)
("r-matrixmodels" ,r-matrixmodels)
("r-sparsem" ,r-sparsem)))
(home-page "https://www.r-project.org")
(define-public r-nloptr
(package
(name "r-nloptr")
- (version "1.2.2.1")
+ (version "1.2.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "nloptr" version))
(sha256
(base32
- "1bhh2v14phzndjhiq7yw9vych6vzn5yy3vk9q35zcp3jhjjbwdyh"))))
+ "0whkilb85k4wixvr3k7rygfw1rcs1fs9h8c18kz4p3y1k9hsj3p8"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr) ; for building vignettes
(define-public r-cardata
(package
(name "r-cardata")
- (version "3.0-3")
+ (version "3.0-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "carData" version))
(sha256
- (base32 "0cg2yxzn0pdjqykr60my1fzpfkqac21fll5hv3m9w5c9sayq8swq"))))
+ (base32 "09270j39n4jpswxqps20b12zaj8dz4rrqpk2l2j5bnf1xzizb9nd"))))
(properties `((upstream-name . "carData")))
(build-system r-build-system)
(home-page "https://r-forge.r-project.org/projects/car/")
(define-public r-car
(package
(name "r-car")
- (version "3.0-7")
+ (version "3.0-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "car" version))
(sha256
- (base32 "11sfk1l41j27mrfy16g7b02c570n3gy9icvpcrfjh1biykqa565d"))))
+ (base32 "0ig1691kxbzkrsq8xi5a6fq2f0vq22j1dn54jxdkldqr5vri1m57"))))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
even in multithreaded code, typically using OpenMP.")
(license license:gpl3+)))
+(define-public r-tmvnsim
+ (package
+ (name "r-tmvnsim")
+ (version "1.0-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tmvnsim" version))
+ (sha256
+ (base32
+ "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp"))))
+ (properties `((upstream-name . "tmvnsim")))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://www.r-project.org")
+ (synopsis "Truncated multivariate normal simulation")
+ (description
+ "This package implements importance sampling from the truncated
+multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK)
+simulator. Unlike Gibbs sampling which can get stuck in one truncation
+sub-region depending on initial values, this package allows truncation based
+on disjoint regions that are created by truncation of absolute values. The
+GHK algorithm uses simple Cholesky transformation followed by recursive
+simulation of univariate truncated normals hence there are also no convergence
+issues. Importance sample is returned along with sampling weights, based on
+which, one can calculate integrals over truncated regions for multivariate
+normals.")
+ (license license:gpl2)))
+
(define-public r-mnormt
(package
(name "r-mnormt")
- (version "1.5-6")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "mnormt" version))
(sha256
(base32
- "0k8y08gj6z525yvc7y3dl2kzgnafbj3i7lvpamypsmqxf74zql99"))))
+ "00nn0b6nksn2jbpg0np5wphryp4f9v95vqxf5v628yysnawgkcwq"))))
(build-system r-build-system)
+ (propagated-inputs
+ `(("r-tmvnsim" ,r-tmvnsim)))
(native-inputs
`(("gfortran" ,gfortran)))
(home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
(define-public r-sn
(package
(name "r-sn")
- (version "1.6-1")
+ (version "1.6-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sn" version))
(sha256
(base32
- "0snri2k8qslb7478c5jz4a5xxmmb1ipmp8x1jizi8mhj2cjic1w0"))))
+ "179xb7yb8br99aa5awm2yxsy0v5w1kdhv6a7ifaliz2y64677m1g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mnormt" ,r-mnormt)
(define-public r-cairo
(package
(name "r-cairo")
- (version "1.5-12")
+ (version "1.5-12.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "Cairo" version))
(sha256
(base32
- "02v29am4fac3fyq6y1w6r89zwbqqkxjsxrafcwb5s124ikxyl22f"))))
+ "14hgz5wmnhlbqkd1g662n1agmjnlj3pq69gfng1vb0ivr02l2lnx"))))
(properties `((upstream-name . "Cairo")))
(build-system r-build-system)
(inputs
(define-public r-lubridate
(package
(name "r-lubridate")
- (version "1.7.8")
+ (version "1.7.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "lubridate" version))
(sha256
(base32
- "0g2m9dyhgds4shdrk76w7rqdl9msam4rii2qrhz12gipzhi9k89x"))))
+ "0wnjzvfkrgp2hkr8g5r5vcgcxmsq8bhdmkzkk0m93wr3fgh5xyfb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-generics" ,r-generics)
parameters.")
(license license:gpl3))))
-(define-public r-directlabels
- (package
- (name "r-directlabels")
- (version "2020.1.31")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "directlabels" version))
- (sha256
- (base32
- "08s1gnwp4bn8xahwjaq0f1qzhwh2dvybzhq3z7xyzn8cnyzmis6c"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-quadprog" ,r-quadprog)))
- (home-page "http://directlabels.r-forge.r-project.org/")
- (synopsis "Direct labels for multicolor plots")
- (description
- "This package provides an extensible framework for automatically placing
-direct labels onto multicolor plots. Label positions are described using
-positioning methods that can be re-used across several different plots. There
-are heuristics for examining @code{trellis} and @code{ggplot} objects and
-inferring an appropriate positioning method.")
- (license license:gpl3)))
-
(define-public r-catterplots
(let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
(revision "3"))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Gibbsdavidl/CatterPlots.git")
+ (url "https://github.com/Gibbsdavidl/CatterPlots")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jalvesaq/colorout.git")
+ (url "https://github.com/jalvesaq/colorout")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(define-public emacs-ess
(package
(name "emacs-ess")
- (version "17.11")
+ (version "18.10.2")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
- version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/emacs-ess/ESS")
+ (commit (string-append "v" version))))
(sha256
(base32
- "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
- (file-name (string-append name "-" version ".tar.gz"))
+ "1yq41l2bicwjrc0b731iic20cpcnz6ppigri1jn621qv2qv22vy3"))
+ (file-name (git-file-name name version))
(modules '((guix build utils)))
(snippet
'(begin
;; Stop ESS from trying to bundle an external julia-mode.el.
(substitute* "lisp/Makefile"
- (("^\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.
+ (("^ess-julia.elc: julia-mode.elc") "")
+ (("^all: julia-mode.el")
+ "all:"))
+ ;; Include *.el files in install target.
+ (substitute* "lisp/Makefile"
+ (("\t\\$\\(INSTALL) \\$\\(ELC\\) \\$\\(LISPDIR\\)" elc)
+ (string-append "\t$(INSTALL) $(ELS) ess-autoloads.el "
+ "$(LISPDIR)\n" elc)))
+ ;; Only build docs in info format.
(substitute* "doc/Makefile"
- (("all : info text html pdf")
+ (("all : info text")
"all : info")
(("install: install-info install-other-docs")
"install: install-info"))
- ;; Test fails upstream
+ ;; Stop install-info from trying to update the info directory.
+ (substitute* "doc/Makefile"
+ ((".*\\$\\(INFODIR\\)/dir.*") ""))
+ ;; Fix roxygen preview test.
(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"))
+ (("Add together two numbers.\n")
+ "Add together two numbers. ")
+ (("##' add\\(10, 1\\)") "add(10, 1)"))
#t))))
(build-system gnu-build-system)
(arguments
(let ((base-directory "/share/emacs/site-lisp"))
`(#:make-flags (list (string-append "PREFIX=" %output)
- (string-append "ETCDIR=" %output "/"
+ (string-append "ETCDIR=" %output
,base-directory "/etc")
- (string-append "LISPDIR=" %output "/"
+ (string-append "LISPDIR=" %output
,base-directory))
#:phases
(modify-phases %standard-phases
("r-minimal" ,r-minimal)))
(native-inputs
`(("perl" ,perl)
+ ("r-roxygen2" ,r-roxygen2)
("texinfo" ,texinfo)))
(propagated-inputs
`(("emacs-julia-mode" ,emacs-julia-mode)))
HCoop / jackhill / guix / guix.git / blobdiff