;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 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>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix hg-download)
+ #:use-module (guix git-download)
#:use-module (guix utils)
+ #:use-module (guix build-system ant)
#:use-module (guix build-system gnu)
#:use-module (guix build-system r)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages bash)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
(define-public r-minimal
(package
(name "r-minimal")
- (version "3.4.3")
+ (version "3.4.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
version ".tar.gz"))
(sha256
(base32
- "09pl0w01fr09bsrwd7nz2r5psysj0z93w4chz3hm2havvqqvhg3s"))))
+ "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"))))
(build-system gnu-build-system)
(arguments
- `(#:disallowed-references (,tzdata-2017a)
+ `(#:disallowed-references (,tzdata-for-tests)
#:make-flags
(list (string-append "LDFLAGS=-Wl,-rpath="
(assoc-ref %outputs "out")
;; queries the mtime of a given file and records it in an object.
;; This is acceptable at runtime to detect stale source files,
;; but it destroys reproducibility at build time.
- ;;
- ;; Instead of disabling this feature, which may have unexpected
- ;; consequences, we reset the mtime of generated files before
- ;; passing them to the "srcfile" procedure.
- (substitute* "src/library/Makefile.in"
- (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
- (string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
- (("@\\$\\(MAKE\\) Rdobjects" line)
- (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n "
- line)))
- (substitute* "src/library/tools/Makefile.in"
- (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
- (string-append
- line
- "\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n")))
+
+ ;; Similarly, the "srcfilecopy" procedure records the current
+ ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
+ (substitute* "src/library/base/R/srcfile.R"
+ (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
+ (string-append "timestamp <- \
+as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
+ as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
+} else { " time "}, origin=\"1970-01-01\")\n")))
;; This library is installed using "install_package_description",
;; so we need to pass the "builtStamp" argument.
("perl" ,perl)
("pkg-config" ,pkg-config)
("texinfo" ,texinfo) ; for building HTML manuals
- ("tzdata" ,tzdata-2017a)
+ ("tzdata" ,tzdata-for-tests)
("xz" ,xz)))
(inputs
`(;; We need not only cairo here, but pango to ensure that tests for the
("libxt" ,libxt)
("pcre" ,pcre)
("readline" ,readline)
+ ;; This avoids a reference to the ungraftable static bash. R uses the
+ ;; detected shell for the "system" procedure.
+ ("bash" ,bash-minimal)
("which" ,which)
("zlib" ,zlib)))
(native-search-paths
(list (search-path-specification
(variable "R_LIBS_SITE")
(files (list "site-library/")))))
- (home-page "http://www.r-project.org/")
+ (home-page "https://www.r-project.org/")
(synopsis "Environment for statistical computing and graphics")
(description
"R is a language and environment for statistical computing and graphics.
(define-public r-mass
(package
(name "r-mass")
- (version "7.3-47")
+ (version "7.3-49")
(source
(origin
(method url-fetch)
(uri (cran-uri "MASS" version))
(sha256
(base32
- "1gy6z7ly9wn86rfn9xrmqiqq1ijw3pkasrr2299kbzsgx2mwsi7d"))))
+ "1yjbnj1p4z0vw84wga8q5fyqiw4n6r7pc6rdwam7vsbiamyzfcqs"))))
(properties `((upstream-name . "MASS")))
(build-system r-build-system)
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
(define-public r-nlme
(package
(name "r-nlme")
- (version "3.1-131")
+ (version "3.1-131.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "nlme" version))
(sha256
(base32
- "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
+ "1xafi670a9jzb52kqxkacxfmy0viac3aql5byfq86kgkgla2sg0y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(define-public r-mgcv
(package
(name "r-mgcv")
- (version "1.8-22")
+ (version "1.8-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "mgcv" version))
(sha256
(base32
- "1546p6aflg3z6xl2mns1n2c3j8q2spr9cjggj9rn33vrrhsv4fss"))))
+ "1lsrhf1yzn25pfn3f5x8yxjqnfryim4jx3iqd7ah8aalh5asqwbp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)
(define-public r-rpart
(package
(name "r-rpart")
- (version "4.1-11")
+ (version "4.1-13")
(source
(origin
(method url-fetch)
(uri (cran-uri "rpart" version))
(sha256
(base32
- "165djqj7lk81jr7z5fwccq3h7ayys26hx1kj9hndvg2rkyaq1arq"))))
+ "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/rpart")
(synopsis "Recursive partitioning and regression trees")
(define-public r-digest
(package
(name "r-digest")
- (version "0.6.13")
+ (version "0.6.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "digest" version))
(sha256
- (base32 "1bsgl07bvf4nk6bn7n3l2ilvk4qvn3nk7yxp22miil7x405xdks6"))))
+ (base32 "1ia4ak956gnn0f5aqhwgam6g9z6f1y57zz8jv45jc8h79yxp8bl8"))))
(build-system r-build-system)
;; Vignettes require r-knitr, which requires r-digest, so we have to
;; disable them and the tests.
(define-public r-estimability
(package
(name "r-estimability")
- (version "1.2")
+ (version "1.3")
(source (origin
(method url-fetch)
(uri (cran-uri "estimability" version))
(sha256
(base32
- "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
+ "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/estimability")
(synopsis "Tools for assessing estimability of linear predictions")
(define-public r-stringi
(package
(name "r-stringi")
- (version "1.1.6")
+ (version "1.1.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
- "122im5m8x9bqpahc0hbxmvdq6hnsmgnxwwyjpvbihyv2jq5kd44m"))))
+ "0nck1s2iglmkrn15ay2chrrwsy5lngcylz2sc87fxy5skxaahxdl"))))
(build-system r-build-system)
(inputs `(("icu4c" ,icu4c)))
(native-inputs `(("pkg-config" ,pkg-config)))
(define-public r-stringr
(package
(name "r-stringr")
- (version "1.2.0")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringr" version))
(sha256
- (base32 "16hj2rmv8x03lp6cp2jk0k2plibvbggf444kp05przdvd03v7l31"))))
+ (base32 "07dvfbkhv8gk6l32j43jvxpmqlhqp0mdby406h5a3bsc6k94ic13"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-magrittr" ,r-magrittr)
+ `(("r-glue" ,r-glue)
+ ("r-magrittr" ,r-magrittr)
("r-stringi" ,r-stringi)))
(home-page "https://github.com/hadley/stringr")
(synopsis "Simple, consistent wrappers for common string operations")
(define-public r-gdtools
(package
(name "r-gdtools")
- (version "0.1.6")
+ (version "0.1.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "gdtools" version))
(sha256
(base32
- "103wnc8sq0iwcnj4j14hd420d2dqdyf13s3f25icsznrlyzdkhf5"))))
+ "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6"))))
(build-system r-build-system)
(native-inputs
`(("r-rcpp" ,r-rcpp)
("pkg-config" ,pkg-config)))
(inputs
- `(("cairo" ,cairo)))
+ `(("cairo" ,cairo)
+ ("zlib" ,zlib)))
(propagated-inputs
`(("r-withr" ,r-withr)))
(home-page "https://cran.r-project.org/web/packages/gdtools")
(define-public r-dbi
(package
(name "r-dbi")
- (version "0.7")
+ (version "0.8")
(source (origin
(method url-fetch)
(uri (cran-uri "DBI" version))
(sha256
(base32
- "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5"))))
+ "16nf8flxr5vdz8yrpprfbzydy3ajixkp9hc8ibd9n7r9nc29waym"))))
(build-system r-build-system)
(home-page "https://github.com/rstats-db/DBI")
(synopsis "R database interface")
(define-public r-bh
(package
(name "r-bh")
- (version "1.65.0-1")
+ (version "1.66.0-1")
(source (origin
(method url-fetch)
(uri (cran-uri "BH" version))
(sha256
(base32
- "0n6byzrvl1w4hjdxz479q4a7w1118f9ckqc4gqydq7lgzs5agfl2"))))
+ "14kab6wp0c27d8x4jqyf065p4bj210s9b67c0bfsfjnp29aypn8p"))))
(build-system r-build-system)
(home-page "https://github.com/eddelbuettel/bh")
(synopsis "R package providing subset of Boost headers")
(define-public r-yaml
(package
(name "r-yaml")
- (version "2.1.16")
+ (version "2.1.17")
(source (origin
(method url-fetch)
(uri (cran-uri "yaml" version))
(sha256
(base32
- "1xlsmqal607w6c9rx86061y1fwpbyd5lqp9bad5n7cc9a0blpnkm"))))
+ "10y6wnv2v8k396far29haqv2s82p4zm04rrsxk183wg19gb51was"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/yaml/")
(synopsis "Methods to convert R data to YAML and back")
(define-public r-knitr
(package
(name "r-knitr")
- (version "1.17")
+ (version "1.20")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
- "00gljbz57n9lkvbd6az4n37gpbs8vg3fxx5p9biamhmhqyra514l"))))
+ "1408dm25cxahk2clff8hlajaqdj5v1gs40nm3q6rf0ghd82hj93v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-evaluate" ,r-evaluate)
- ("r-digest" ,r-digest)
("r-highr" ,r-highr)
("r-markdown" ,r-markdown)
("r-stringr" ,r-stringr)
(define-public r-microbenchmark
(package
(name "r-microbenchmark")
- (version "1.4-2.1")
+ (version "1.4-4")
(source (origin
(method url-fetch)
(uri (cran-uri "microbenchmark" version))
(sha256
(base32
- "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
+ "0fv2w2vsiz18imf4115nd9chhmf275w2mb49pn7pkxi6z3bamc9c"))))
(build-system r-build-system)
- (propagated-inputs
- `(("r-ggplot2" ,r-ggplot2)))
(home-page "https://cran.r-project.org/web/packages/microbenchmark/")
(synopsis "Accurate timing functions for R")
(description
(define-public r-pryr
(package
(name "r-pryr")
- (version "0.1.3")
+ (version "0.1.4")
(source (origin
(method url-fetch)
(uri (cran-uri "pryr" version))
(sha256
(base32
- "1b1rcywq9sqzgjsnh3ynnx16gp41n94kkzfalm3y4kyy3ls8ikba"))))
+ "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-stringr" ,r-stringr)
(define-public r-rlang
(package
(name "r-rlang")
- (version "0.1.4")
+ (version "0.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "rlang" version))
(sha256
(base32
- "1x5rwwsx7xrlyspy41yl5nhyvfgzl73195nsdb4rc6z85ab6r6wd"))))
+ "0f87fhw5pj6s2zjdxnpnd7pwn78czdz71b0xhm5adqg1p38sfwj8"))))
(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 "1.3.4")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "tibble" version))
(sha256
(base32
- "02vn6yqzcvmazy5jaqar3wwbrmh83a1bfgsqgk0hgz38i80zgvm7"))))
+ "05svbjkm1xqv56ybjgsqqg2pp8nn6hams1yxcr8aanbhzx9h6rqi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)
- ("r-rcpp" ,r-rcpp)))
+ ("r-cli" ,r-cli)
+ ("r-crayon" ,r-crayon)
+ ("r-pillar" ,r-pillar)))
(home-page "https://github.com/hadley/tibble")
(synopsis "Simple data frames")
(description
(define-public r-dbplyr
(package
(name "r-dbplyr")
- (version "1.1.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dbplyr" version))
(sha256
(base32
- "17gn8vr4a6m9ynarjbm9xsrhcvgn5lnxhb2qhiiglmhh5mm4a7kv"))))
+ "1nwrls9c3kc9q7405jp6b9sh23642sz13yw55iikgw134shffj5k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-purrr" ,r-purrr)
("r-r6" ,r-r6)
("r-rlang" ,r-rlang)
- ("r-tibble" ,r-tibble)))
+ ("r-tibble" ,r-tibble)
+ ("r-tidyselect" ,r-tidyselect)))
(home-page "https://github.com/tidyverse/dbplyr")
(synopsis "Dplyr back end for databases")
(description
(define-public r-chron
(package
(name "r-chron")
- (version "2.3-51")
+ (version "2.3-52")
(source (origin
(method url-fetch)
(uri (cran-uri "chron" version))
(sha256
(base32
- "05aznigw9nwv3hbwjnjbvqhfjqkwsw2csgrjx8500gzr2fvla5w8"))))
+ "185lfp75cv3l4cavg64sccj8lgc5sivch13n6gkannv3pd5cyzy4"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/chron")
(synopsis "Chronological R objects which can handle dates and times")
(define-public r-xml2
(package
(name "r-xml2")
- (version "1.1.1")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "xml2" version))
(sha256
(base32
- "05iifrcgzx53w5ciw8bbm4vdwc3giv4xsvazv8chqxkndfvf7wq0"))))
+ "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
(build-system r-build-system)
(inputs
- `(("libxml2" ,libxml2)))
+ `(("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
(propagated-inputs
- `(("r-rcpp" ,r-rcpp)
- ("r-bh" ,r-bh)))
+ `(("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/hadley/xml2")
(synopsis "Parse XML with R")
(description
(define-public r-openssl
(package
(name "r-openssl")
- (version "0.9.9")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
- "1ir7ggs0rxgn83h40r6jg9dzhb7hbcwhkcj5nsdzj7jz61sfgv77"))))
+ "1qyql5gpwf88bkm1qarjhbqbq4hn6w0d8j4pxb5x7i96is30ap30"))))
(build-system r-build-system)
(inputs
`(("libressl" ,libressl)))
(define-public r-git2r
(package
(name "r-git2r")
- (version "0.20.0")
+ (version "0.21.0")
(source (origin
(method url-fetch)
(uri (cran-uri "git2r" version))
(sha256
(base32
- "1pqggijvsalb5cc2pr5gwfj3s713s63f4xii1xrd0qagfgbgz846"))))
+ "11xgddmxzh9cy85k8fb90il43qswpvryz0h9r0j1gbclfg2f9004"))))
(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
(define-public r-devtools
(package
(name "r-devtools")
- (version "1.13.4")
+ (version "1.13.5")
(source (origin
(method url-fetch)
(uri (cran-uri "devtools" version))
(sha256
(base32
- "1az1qf50vyhm4w6k2a6wqw3pqc8jv2iqzdhs36cg079hx9swm0mb"))))
+ "1x3wsk7dh3yakii61kbfvafx9yz66h40ixiwfkf03dnp2n24hngs"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
(define-public r-withr
(package
(name "r-withr")
- (version "2.1.0")
+ (version "2.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "withr" version))
(sha256
(base32
- "12v263fj6l3ds9nrsj6q7h6zhbivp3w2jk7w9dpk1610d3nx9gf8"))))
+ "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
(build-system r-build-system)
- (propagated-inputs
- `(("r-lattice" ,r-lattice)))
(home-page "https://github.com/jimhester/withr")
(synopsis "Run code with temporarily modified global state")
(description
(define-public r-hms
(package
(name "r-hms")
- (version "0.4.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "hms" version))
(sha256
(base32
- "07sh75flp15lx2b00s3nxh04xr9gk4qhlbh125qx25isf71zw6zl"))))
+ "0vr7k3a7k52a5yf67bwzl88lkjz09v1avw5axdk1y9v3nz33zl2h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.8.300.1.0")
+ (version "0.8.400.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "0p6cbnwxgzigf7n5qhqvxdr3nd3pq3c2qq6pskqz7avzf813fy83"))))
+ "11y2ksf46zw6fcz0kk70szyfn7qqxwwd33xylrxvnyb7ldmbc5yr"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(native-inputs
(define-public r-rprojroot
(package
(name "r-rprojroot")
- (version "1.3-1")
+ (version "1.3-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "rprojroot" version))
(sha256
(base32
- "1jigr2jh3hzy35h94im52yq81lyikw7nfvmbxij84a1b9c32r332"))))
+ "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)))
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "1.8")
+ (version "1.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32
- "0q1y1qx87xp6vf9h7mfl77rqhmd01xl53l9ap9qj99bfvpabb572"))))
+ "0wq6kbhrkv3fhcy4hg5yyv9gdvf8gr4nsjwdifs4ih8lnn0dmdyb"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
("r-rprojroot" ,r-rprojroot)
("r-stringr" ,r-stringr)
("r-yaml" ,r-yaml)
- ("ghc-pandoc" ,ghc-pandoc)))
+ ;; rmarkdown works with the 2.x release of Pandoc, but with degraded
+ ;; functionality. For example, tabbed plots do not currently work with
+ ;; Pandoc 2. The authors of rmarkdown recommend the use of Pandoc 1
+ ;; for the time being.
+ ("ghc-pandoc" ,ghc-pandoc-1)))
(home-page "http://rmarkdown.rstudio.com")
(synopsis "Convert R Markdown documents into a variety of formats")
(description
(define-public r-xml
(package
(name "r-xml")
- (version "3.98-1.9")
+ (version "3.98-1.10")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
- "1hzkdkgs0nzmfg9wm7kyh1j9i0i2g7925whzlihqvg9grdlh3dx3"))))
+ "1faza9bbllp67lf1yv1sllxc3iv8llz52m9diazhq322iqbh97m1"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
(inputs
- `(("libxml2" ,libxml2)))
+ `(("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
(home-page "http://www.omegahat.org/RSXML")
(synopsis "Tools for parsing and generating XML within R")
(description
"0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x"))))
(properties `((upstream-name . "lambda.r")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'check 'delete-test-log
+ ;; The test report contains time stamps and is not important for
+ ;; the installed package.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (delete-file-recursively
+ (string-append (assoc-ref outputs "out")
+ "/site-library/lambda.r/unitTests"))
+ #t)))))
+ (native-inputs
+ `(("r-runit" ,r-runit)))
(home-page "https://cran.r-project.org/web/packages/lambda.r")
(synopsis "Functional programming extension for R")
(description
(define-public r-dt
(package
(name "r-dt")
- (version "0.2")
+ (version "0.4")
(source (origin
(method url-fetch)
(uri (cran-uri "DT" version))
(sha256
(base32
- "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
+ "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix"))))
(properties
`((upstream-name . "DT")))
(build-system r-build-system)
(propagated-inputs
- `(("r-htmltools" ,r-htmltools)
+ `(("r-crosstalk" ,r-crosstalk)
+ ("r-htmltools" ,r-htmltools)
("r-htmlwidgets" ,r-htmlwidgets)
("r-magrittr" ,r-magrittr)))
(home-page "http://rstudio.github.io/DT")
(define-public r-irlba
(package
(name "r-irlba")
- (version "2.3.1")
+ (version "2.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "irlba" version))
(sha256
(base32
- "1dclzzkm75sbbqda5scj2hlqnw2sksgxbiqagxs4359fwfszi0k0"))))
+ "0f7wb12wa0zbyllk5adcf4f517wgjpkhsx4j176i9ax6xy7jvprz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
(define-public r-synchronicity
(package
(name "r-synchronicity")
- (version "1.1.9.1")
+ (version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "synchronicity" version))
(sha256
(base32
- "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
+ "1idrjzl7nkamf1ip55s6qcf64s63xs9j8z9jv3r89p6r5lw7k5mv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
("r-bigmemory-sri" ,r-bigmemory-sri)
- ("r-rcpp" ,r-rcpp)))
+ ("r-rcpp" ,r-rcpp)
+ ("r-uuid" ,r-uuid)))
(home-page "http://www.bigmemory.org")
(synopsis "Boost mutex functionality in R")
(description "This package provides support for synchronization
(define-public r-bigmemory
(package
(name "r-bigmemory")
- (version "4.5.31")
+ (version "4.5.33")
(source
(origin
(method url-fetch)
(uri (cran-uri "bigmemory" version))
(sha256
(base32
- "0wv0p746zz5a6r1yd0fgpj2kfcyzk2f4rxqz92p6lp9jzakv4lfs"))))
+ "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
(define-public r-nmf
(package
(name "r-nmf")
- (version "0.20.6")
+ (version "0.21.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "NMF" version))
(sha256
(base32
- "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
+ "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
(properties `((upstream-name . "NMF")))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
- ("r-bigmemory" ,r-bigmemory)
- ("r-synchronicity" ,r-synchronicity)
+ ("r-bigmemory" ,r-bigmemory) ; suggested
+ ("r-synchronicity" ,r-synchronicity) ; suggested
("r-colorspace" ,r-colorspace)
("r-digest" ,r-digest)
("r-doparallel" ,r-doparallel)
(define-public r-r-cache
(package
(name "r-r-cache")
- (version "0.12.0")
+ (version "0.13.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.cache" version))
(sha256
(base32
- "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
+ "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
(properties `((upstream-name . "R.cache")))
(build-system r-build-system)
(propagated-inputs
(define-public r-r-rsp
(package
(name "r-r-rsp")
- (version "0.41.0")
+ (version "0.42.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.rsp" version))
(sha256
(base32
- "01l430avj5ggmdsla2kiriix72g0dlzx9klniq321bs0za808v3c"))))
+ "1zcq0hzi0j7fvj2rs796a1i120wbr0387vck17rrd644awwbsbm0"))))
(properties `((upstream-name . "R.rsp")))
(build-system r-build-system)
(propagated-inputs
- `(("r-r-cache" ,r-r-cache)
+ `(("r-digest" ,r-digest)
+ ("r-r-cache" ,r-r-cache)
("r-r-methodss3" ,r-r-methodss3)
("r-r-oo" ,r-r-oo)
("r-r-utils" ,r-r-utils)))
(define-public r-mvtnorm
(package
(name "r-mvtnorm")
- (version "1.0-6")
+ (version "1.0-7")
(source (origin
(method url-fetch)
(uri (cran-uri "mvtnorm" version))
(sha256
(base32
- "0i74s9dl4jf1gln6agra8h38qn9ifd5v0gi13caj1da5nrbmn0aa"))))
+ "0f7hzflygdnbwvzadr3knhybhanwg7agqddclj6mhbvwqpgb0qyh"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)))
(define-public r-matrixstats
(package
(name "r-matrixstats")
- (version "0.52.2")
+ (version "0.53.1")
(source (origin
(method url-fetch)
(uri (cran-uri "matrixStats" version))
(sha256
(base32
- "19fjf19cr0p3j9pj17myz39zpi5bh7ci72db3la9my09n6k6mnir"))))
+ "0bkiz5fm09d3512mfr2ymj9qsb1b8aic5l5m6fkaf5j7nsgvqw6z"))))
(properties `((upstream-name . "matrixStats")))
(build-system r-build-system)
(native-inputs
(define-public r-viridis
(package
(name "r-viridis")
- (version "0.4.0")
+ (version "0.5.0")
(source (origin
(method url-fetch)
(uri (cran-uri "viridis" version))
(sha256
(base32
- "03mha2935k1mw7mjjkq7mrx185hl0m3vq3967iiwbknpivbdxllk"))))
+ "1ka6amybgzqkg3cbwfxwwqzzzpfn6q5jcia5am0bw48y5hbpg97y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
(define-public r-viridislite
(package
(name "r-viridislite")
- (version "0.2.0")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "viridisLite" version))
(sha256
(base32
- "1546h44ng4dxs130jkh6lkh990hmp90m1w45sq5p47n546gr0k9d"))))
+ "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
(properties `((upstream-name . "viridisLite")))
(build-system r-build-system)
(home-page "https://github.com/sjmgarnier/viridisLite")
(define-public r-tidyselect
(package
(name "r-tidyselect")
- (version "0.2.3")
+ (version "0.2.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyselect" version))
(sha256
(base32
- "0b0w30yq30c7bwpaghp3hp0nncqwcmvrra9j58fhx9jihay3l68c"))))
+ "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-glue" ,r-glue)
(define-public r-tidyr
(package
(name "r-tidyr")
- (version "0.7.2")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
(base32
- "1700fry2b3d3ksj7x2f09xl6agjrdnx1rqsc1r8gvzsp5cpflb06"))))
+ "1qjpbj1a2vw6nw4hdb6fgassnrxrdpqwf9a8i6wqnv3wxvjb6zqb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
(define-public r-hexbin
(package
(name "r-hexbin")
- ;; The package tarball was updated in place, resulting in a change in the
- ;; hash value. We decided to bump the version to 1.27.1-1 instead of
- ;; keeping the version at upstream's 1.27.1.
- (version "1.27.1-1")
+ (version "1.27.2")
(source
(origin
(method url-fetch)
- (uri (cran-uri "hexbin" "1.27.1"))
+ (uri (cran-uri "hexbin" version))
(sha256
(base32
- "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
+ "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(define-public r-hmisc
(package
(name "r-hmisc")
- (version "4.0-3")
+ (version "4.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Hmisc" version))
(sha256
(base32
- "1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w"))))
+ "160l50ppjs69ipcaya1mlcz29zbn5rmqg91r09dvzzvkvwfb47cr"))))
(properties `((upstream-name . "Hmisc")))
(build-system r-build-system)
(native-inputs
(define-public r-sfsmisc
(package
(name "r-sfsmisc")
- (version "1.1-1")
+ (version "1.1-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sfsmisc" version))
(sha256
(base32
- "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf"))))
+ "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/sfsmisc")
(synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
(base32
"1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'make-deterministic
+ (lambda _
+ (substitute* "R/checkReverseDependencies.R"
+ (("tempdir\\(\\)") "\"/tmp\""))
+ #t)))))
(home-page "https://cran.r-project.org/web/packages/gtools")
(synopsis "Various R programming tools")
(description
(define-public r-zoo
(package
(name "r-zoo")
- (version "1.8-0")
+ (version "1.8-1")
(source (origin
(method url-fetch)
(uri (cran-uri "zoo" version))
(sha256
(base32
- "0mqklbx92ifwa0awm7gpm4r9dvwa09p55zjxjnypiqsxy532r4h9"))))
+ "16nc5jnpkf5j9vgq3pzssv7knj30mi055wj7q3sygz3l0d88hgfr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(define-public r-pcapp
(package
(name "r-pcapp")
- (version "1.9-72")
+ (version "1.9-73")
(source
(origin
(method url-fetch)
(uri (cran-uri "pcaPP" version))
(sha256
(base32
- "0i2822bv86dpqmk3q17x61nsp3gjjnn4nr8191rwvbiib7xhpgaq"))))
+ "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
(properties `((upstream-name . "pcaPP")))
(build-system r-build-system)
(propagated-inputs
(define-public r-fpc
(package
(name "r-fpc")
- (version "2.1-10")
+ (version "2.1-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "fpc" version))
(sha256
(base32
- "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
+ "04alsqb5gbhsjg1000d8w52pmpnlwca29r0s12f7n7mdccdv6xar"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)
(define-public r-vgam
(package
(name "r-vgam")
- (version "1.0-4")
+ (version "1.0-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "VGAM" version))
(sha256
(base32
- "0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5"))))
+ "0ik3wyv6jj54bg34z0fzzk4xg0h6x98jqx4q2r7g1f0in0qgbb01"))))
(properties `((upstream-name . "VGAM")))
(build-system r-build-system)
(inputs
(define-public r-pbapply
(package
(name "r-pbapply")
- (version "1.3-3")
+ (version "1.3-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "pbapply" version))
(sha256
(base32
- "0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk"))))
+ "0lk5kxac09xzdv6vf7ix6r5bfrm7cnpyr2l5mkd4igpciadszzfd"))))
(build-system r-build-system)
(home-page "https://github.com/psolymos/pbapply")
(synopsis "Adding progress bar to apply functions")
showing the progress is useful e.g. bootstrap.")
(license license:gpl2)))
-(define-public r-fnn
- (package
- (name "r-fnn")
- (version "1.1")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "FNN" version))
- (sha256
- (base32
- "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
- (properties `((upstream-name . "FNN")))
- (build-system r-build-system)
- (home-page "https://cran.r-project.org/web/packages/FNN")
- (synopsis "Fast nearest neighbor search algorithms and applications")
- (description
- "This package provides cover-tree and kd-tree fast k-nearest neighbor
-search algorithms and related applications including KNN classification,
-regression and information measures.")
- (license license:gpl2+)))
-
(define-public r-minqa
(package
(name "r-minqa")
(define-public r-rcppeigen
(package
(name "r-rcppeigen")
- (version "0.3.3.3.1")
+ (version "0.3.3.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppEigen" version))
(sha256
(base32
- "093g2wmqyk86693l0lzh2va8119w3k7rvw5q24p842jdfv5x5z8l"))))
+ "1m6ssq6lvi36ggf26y4hhq996583pxxdb978jnn1x6r9gdb0q0hi"))))
(properties `((upstream-name . "RcppEigen")))
(build-system r-build-system)
(propagated-inputs
(define-public r-quantreg
(package
(name "r-quantreg")
- (version "5.34")
+ (version "5.35")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantreg" version))
(sha256
(base32
- "0bmgfgnmzqwmwwaraliry682yb8kcr396q3rlzrd2qzaa9sgxxh4"))))
+ "18f3qxv1j1bqmq55hzssz8mnp5ww4flhy80rm2v1rk0mmg9paz7m"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
`(("r-matrix" ,r-matrix)
("r-matrixmodels" ,r-matrixmodels)
("r-sparsem" ,r-sparsem)))
- (home-page "http://www.r-project.org")
+ (home-page "https://www.r-project.org")
(synopsis "Quantile regression")
(description
"This package provides an estimation and inference methods for models
(define-public r-lme4
(package
(name "r-lme4")
- (version "1.1-14")
+ (version "1.1-15")
(source
(origin
(method url-fetch)
(uri (cran-uri "lme4" version))
(sha256
(base32
- "1vars93604q7kyz6y1f8f886l05jkgj8bs78033l2czypvzki5la"))))
+ "0sc6rvhiizxxpkdc3wps200wg3pqc0d89crn29lzm75fk8qdd7vx"))))
(build-system r-build-system)
(native-inputs
`(("r-rcpp" ,r-rcpp)
(define-public r-ranger
(package
(name "r-ranger")
- (version "0.8.0")
+ (version "0.9.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ranger" version))
(sha256
(base32
- "1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz"))))
+ "1pilj5pxl8jl0gsy9vsyqxqdqfcxzvphbgvrlp4hf7r9mrfw9v0p"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
(define-public r-lubridate
(package
(name "r-lubridate")
- (version "1.7.1")
+ (version "1.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "lubridate" version))
(sha256
(base32
- "0pzvazzybzvln3y676yims7whsc74g8i7kgf2nsfbxdq5943z349"))))
+ "1pzkqfiahnsdm3zx46asgn8fw43vlxvbh7r4cn70c7ffmxabzzrc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
(define-public r-forcats
(package
(name "r-forcats")
- (version "0.2.0")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "forcats" version))
(sha256
(base32
- "1mvwkynvvgz2vi8dyz11x7xrp53kadjawjcja34hwk1d89qf7g5m"))))
+ "0mxn1hng43zdjh1v8shd80hrszrqahcpaqxs1s1sif0qxh84d0cm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magrittr" ,r-magrittr)
- ("r-tibble" ,r-tibble)))
+ ("r-tibble" ,r-tibble)
+ ("r-rlang" ,r-rlang)))
(home-page "http://forcats.tidyverse.org")
(synopsis "Tools for working with factors")
(description "This package provides helpers for reordering factor
(uri (hg-reference
(url "https://bitbucket.org/tanaylab/tgstat")
(changeset changeset)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
(uri (hg-reference
(url "https://bitbucket.org/tanaylab/tgconfig")
(changeset changeset)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
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 "40063ec57f9515d231508f135ca0ec769614efb9")
+ (revision "2"))
+ (package
+ (name "r-catterplots")
+ (version (string-append "0-" revision "." (string-take commit 9)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Gibbsdavidl/CatterPlots.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-png" ,r-png)))
+ (home-page "https://github.com/Gibbsdavidl/CatterPlots")
+ (synopsis "Scatter plots with cat shaped points")
+ (description "Did you ever wish you could make scatter plots with cat
+shaped points? Now you can!")
+ (license license:asl2.0))))
+
+(define-public r-colorout
+ (package
+ (name "r-colorout")
+ (version "1.2-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
+ "v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/jalvesaq/colorout")
+ (synopsis "Colorize output in the R REPL")
+ (description "@code{colorout} is an R package that colorizes R output when
+running in terminal emulator.
+
+R STDOUT is parsed and numbers, negative numbers, dates in the standard
+format, strings, and R constants are identified and wrapped by special ANSI
+scape codes that are interpreted by terminal emulators as commands to colorize
+the output. R STDERR is also parsed to identify the expressions warning and
+error and their translations to many languages. If these expressions are
+found, the output is colorized accordingly; otherwise, it is colorized as
+STDERROR (blue, by default).
+
+You can customize the colors according to your taste, guided by the color
+table made by the command @code{show256Colors()}. You can also set the colors
+to any arbitrary string. In this case, it is up to you to set valid values.")
+ (license license:gpl3+)))
+
+(define-public java-jdistlib
+ (package
+ (name "java-jdistlib")
+ (version "0.4.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
+ version "-src.jar"))
+ (sha256
+ (base32
+ "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:jar-name "jdistlib.jar"
+ #:jdk ,icedtea-8
+ #:tests? #f ; no dedicated test directory
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-broken-encoding
+ (lambda _
+ (with-fluids ((%default-port-encoding "ISO-8859-1"))
+ (substitute* "src/jdistlib/Beta.java"
+ (("Scheff.+-Tukey") "Scheffe-Tukey")))
+ #t)))))
+ (propagated-inputs
+ `(("java-jtransforms" ,java-jtransforms)))
+ (native-inputs
+ `(("java-junit" ,java-junit)))
+ (home-page "http://jdistlib.sourceforge.net/")
+ (synopsis "Java library of statistical distributions")
+ (description "JDistlib is the Java Statistical Distribution Library, a
+Java package that provides routines for various statistical distributions.")
+ ;; The files that were translated from R code are under GPLv2+; some files
+ ;; 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+)))
HCoop / jackhill / guix / guix.git / blobdiff