#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
+ #:use-module (guix build-system gnu)
#:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages fontutils)
+ #:use-module (gnu packages fribidi)
#:use-module (gnu packages gcc)
#:use-module (gnu packages geo)
#:use-module (gnu packages ghostscript)
(define-public r-brio
(package
(name "r-brio")
- (version "1.1.0")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "brio" version))
(sha256
(base32
- "0f7amcd2cjm09aiq39209cz680l5d2gqpp6wwfhz24zagfsa7cvb"))))
+ "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
(properties `((upstream-name . "brio")))
(build-system r-build-system)
(home-page "https://github.com/r-lib/brio")
files and provide more explicit control over line endings.")
(license license:expat)))
+(define-public r-cachem
+ (package
+ (name "r-cachem")
+ (version "1.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "cachem" version))
+ (sha256
+ (base32
+ "0y3jb96lyn3vc3nq8gs9x669w3xp69vdg5xc69qy0l356r39gp3r"))))
+ (properties `((upstream-name . "cachem")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fastmap" ,r-fastmap)
+ ("r-rlang" ,r-rlang)))
+ (home-page "https://cachem.r-lib.org/")
+ (synopsis "Cache R objects with automatic pruning")
+ (description
+ "This package provides key-value stores with automatic pruning. Caches
+can limit either their total size or the age of the oldest object (or both),
+automatically pruning objects to maintain the constraints.")
+ (license license:expat)))
+
(define-public r-diffobj
(package
(name "r-diffobj")
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
- (version "0.3.7")
+ (version "0.3.8-1")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
- "121s6c9k4fn3rcz2myc1kxczllq2826c8zllaii58q8lica7dsyn"))))
+ "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-broom" ,r-broom)
- ("r-dplyr" ,r-dplyr)
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
("r-glue" ,r-glue)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
(define-public r-reprex
(package
(name "r-reprex")
- (version "0.3.0")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "reprex" version))
(sha256
(base32
- "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
+ "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
+ ("r-cli" ,r-cli)
("r-clipr" ,r-clipr)
("r-fs" ,r-fs)
+ ("r-glue" ,r-glue)
+ ("r-knitr" ,r-knitr)
("r-rlang" ,r-rlang)
("r-rmarkdown" ,r-rmarkdown)
- ("r-whisker" ,r-whisker)
("r-withr" ,r-withr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tidyverse/reprex")
(synopsis "Prepare reproducible R code examples for sharing")
(description
(define-public r-htmltools
(package
(name "r-htmltools")
- (version "0.5.1")
+ (version "0.5.1.1")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
- "01v33zcs9rv16r6v8ckqh92k5axj6skmk9hyakmqqmgra522xj3a"))))
+ "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
(define-public r-fastmap
(package
(name "r-fastmap")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "fastmap" version))
(sha256
(base32
- "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
+ "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
(properties `((upstream-name . "fastmap")))
(build-system r-build-system)
(home-page "https://r-lib.github.io/fastmap/")
data structures in C++.")
(license license:expat)))
+;; This package includes minified JavaScript files. When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-jquerylib
+ (package
+ (name "r-jquerylib")
+ (version "0.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "jquerylib" version))
+ (sha256
+ (base32
+ "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
+ (snippet
+ '(for-each delete-file
+ '("inst/lib/jquery-1.12.4.min.js"
+ "inst/lib/jquery-2.2.4.min.js"
+ "inst/lib/jquery-3.5.1.min.js")))))
+ (properties `((upstream-name . "jquerylib")))
+ (build-system r-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/lib/"
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `(("jquery-1.12.4.js"
+ "jquery-1.12.4.min.js")
+ ("jquery-2.2.4.js"
+ "jquery-2.2.4.min.js")
+ ("jquery-3.5.1.js"
+ "jquery-3.5.1.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #t "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))
+ sources targets)))))))))
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)))
+ (native-inputs
+ `(("esbuild" ,esbuild)))
+ (home-page "https://cran.r-project.org/package=jquerylib")
+ (synopsis "Obtain jQuery as an HTML dependency object")
+ (description
+ "Obtain any major version of jQuery and use it in any webpage generated
+by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
+need to use this package directly, but other R packages (e.g. shiny,
+rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
+jQuery.")
+ (license license:expat)))
+
(define-public r-shiny
(package
(name "r-shiny")
(define-public r-shinythemes
(package
(name "r-shinythemes")
- (version "1.1.2")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinythemes" version))
(sha256
(base32
- "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
+ "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
(properties `((upstream-name . "shinythemes")))
(build-system r-build-system)
(propagated-inputs `(("r-shiny" ,r-shiny)))
;; 3-clause BSD license.
(license (list license:gpl3+ license:bsd-3)))))
+(define-public r-wesanderson
+ (package
+ (name "r-wesanderson")
+ (version "0.3.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "wesanderson" version))
+ (sha256
+ (base32
+ "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
+ (properties `((upstream-name . "wesanderson")))
+ (build-system r-build-system)
+ (home-page "https://github.com/karthik/wesanderson")
+ (synopsis "Wes Anderson color palette generator")
+ (description
+ "This package provides color palettes that have been generated mostly
+from Wes Anderson movies.")
+ (license license:expat)))
+
+(define-public r-tablerdash
+ (package
+ (name "r-tablerdash")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tablerDash" version))
+ (sha256
+ (base32
+ "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
+ (snippet
+ '(begin
+ ;; Delete minified JavaScript
+ (for-each delete-file
+ '("inst/tablerDash-0.1.0/require.min.js"
+ "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
+ #true))))
+ (properties `((upstream-name . "tablerDash")))
+ (build-system r-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst"
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `((,(assoc-ref inputs "js-requirejs")
+ "tablerDash-0.1.0/require.min.js")
+ (,(assoc-ref inputs "js-bootstrap")
+ "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #t "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))
+ sources targets))))
+ #t)))))
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)
+ ("r-knitr" ,r-knitr)
+ ("r-shiny" ,r-shiny)))
+ (native-inputs
+ `(("esbuild" ,esbuild)
+ ("js-requirejs"
+ ,(origin
+ (method url-fetch)
+ (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
+ (sha256
+ (base32
+ "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
+ ("js-bootstrap"
+ ,(origin
+ (method url-fetch)
+ (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
+v4.0.0/dist/js/bootstrap.bundle.js")
+ (sha256
+ (base32
+ "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
+ (home-page "https://rinterface.github.io/tablerDash/")
+ (synopsis "Tabler API for Shiny")
+ (description
+ "This package provides an R interface to the
+@url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
+4 dashboard template. There are different layouts available such as a one
+page dashboard or a multi-page template, where the navigation menu is
+contained in the navigation bar.")
+ (license license:gpl2+)))
+
+(define-public r-spelling
+ (package
+ (name "r-spelling")
+ (version "2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "spelling" version))
+ (sha256
+ (base32
+ "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
+ (properties `((upstream-name . "spelling")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-commonmark" ,r-commonmark)
+ ("r-hunspell" ,r-hunspell)
+ ("r-knitr" ,r-knitr)
+ ("r-xml2" ,r-xml2)))
+ (home-page "https://docs.ropensci.org/spelling/")
+ (synopsis "Tools for spell checking in R")
+ (description
+ "This is an R package for spell checking common document formats
+including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
+utilities to automate checking of documentation and vignettes as a unit test
+during @code{R CMD check}. Both British and American English are supported
+out of the box and other languages can be added. In addition, packages may
+define a wordlist to allow custom terminology without having to abuse
+punctuation.")
+ (license license:expat)))
+
(define-public r-crosstalk
(package
(name "r-crosstalk")
(define-public r-partykit
(package
(name "r-partykit")
- (version "1.2-11")
+ (version "1.2-12")
(source (origin
(method url-fetch)
(uri (cran-uri "partykit" version))
(sha256
(base32
- "00n6a74x257m2jk7jadjfxaclihxqpqwh356bgxmq8rag0nk70rs"))))
+ "15d5g89winndv8cy8jjjxy87fliafp5zyb8b58czrijwcmagg50l"))))
(build-system r-build-system)
(propagated-inputs
`(("r-formula" ,r-formula)
(define-public r-inum
(package
(name "r-inum")
- (version "1.0-1")
+ (version "1.0-3")
(source (origin
(method url-fetch)
(uri (cran-uri "inum" version))
(sha256
(base32
- "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
+ "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)))
(define-public r-broom
(package
(name "r-broom")
- (version "0.7.3")
+ (version "0.7.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "broom" version))
(sha256
(base32
- "0bxwmqj37m06ci378xqlf7kar7pg5g903i1vnrv4i256dkj50mny"))))
+ "1zwdgv59a5c4mdcfn3anvsf83ymi11ij6k9nssw3aqzirp6fwg3w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
(define-public r-mitml
(package
(name "r-mitml")
- (version "0.3-7")
+ (version "0.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "mitml" version))
(sha256
(base32
- "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
+ "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
(build-system r-build-system)
(propagated-inputs
`(("r-haven" ,r-haven)
("r-jomo" ,r-jomo)
("r-pan" ,r-pan)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/mitml/")
(synopsis "Tools for multiple imputation in multilevel modeling")
(description
(define-public r-mice
(package
(name "r-mice")
- (version "3.12.0")
+ (version "3.13.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mice" version))
(sha256
(base32
- "0i7i9r0ipn7fypzp5xv1dnr54l30b7kg38mmq1kcvj2z1mjrwpap"))))
+ "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
(define-public r-cli
(package
(name "r-cli")
- (version "2.2.0")
+ (version "2.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "cli" version))
(sha256
(base32
- "1f20mk9pb9kqn0ni2z0sqsx8qj1apcbiw08pa4gwry142zv7m9rr"))))
+ "128bx3bds0dnkixc4frbky11rz1ilnvdfzz9mggajj690i11b62q"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
- ("r-crayon" ,r-crayon)
- ("r-fansi" ,r-fansi)
("r-glue" ,r-glue)))
(home-page "https://github.com/r-lib/cli#readme")
(synopsis "Helpers for developing command line interfaces")
(define-public r-xfun
(package
(name "r-xfun")
- (version "0.20")
+ (version "0.21")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
- (base32 "043wv9qihs3r29810mf8ajpn2iks1bxq44wbxz8sfpix5b8kjhi8"))))
+ (base32 "18qjs81fn8q2d2drcan8gpgvrbgxgd0b659c92z19kg2h4c1g3k4"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.28")
+ (version "0.29")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "11pa1q7gl17ala74lz10qbghk2yqanl9pylwvi9b4kmhx856b83n"))))
+ "0my1412vn5zri01w2myzn268lfwinbhfgdj4bbcib3s48i9djw0n"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
automatically.")
(license license:expat)))
+(define-public r-tinytest
+ (package
+ (name "r-tinytest")
+ (version "1.2.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tinytest" version))
+ (sha256
+ (base32
+ "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
+ (properties `((upstream-name . "tinytest")))
+ (build-system r-build-system)
+ (home-page "https://github.com/markvanderloo/tinytest")
+ (synopsis "Lightweight unit testing framework")
+ (description
+ "This package provides a lightweight unit testing framework. Main
+features:
+
+@enumerate
+@item install tests with the package;
+@item test results are treated as data that can be stored and manipulated;
+@item test files are R scripts interspersed with test commands, that can be
+ programmed over;
+@item fully automated build-install-test sequence for packages;
+@item skip tests when not run locally (e.g. on CRAN);
+@item flexible and configurable output printing;
+@item compare computed output with output stored with the package;
+@item run tests in parallel;
+@item extensible by other packages;
+@item report side effects.
+@end enumerate
+")
+ (license license:gpl3)))
+
(define-public r-network
(package
(name "r-network")
(define-public r-stabs
(package
- (name "r-stabs")
- (version "0.6-3")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "stabs" version))
- (sha256
+ (name "r-stabs")
+ (version "0.6-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "stabs" version))
+ (sha256
(base32
- "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
- (build-system r-build-system)
- (home-page "https://github.com/hofnerb/stabs")
- (synopsis "Stability selection with error control")
- (description
- "This package provides resampling procedures to assess the stability of
+ "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/hofnerb/stabs")
+ (synopsis "Stability selection with error control")
+ (description
+ "This package provides resampling procedures to assess the stability of
selected variables with additional finite sample error control for
high-dimensional variable selection procedures such as Lasso or boosting.
Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
complementary pairs stability selection with improved error bounds
(Shah & Samworth, 2013) are implemented. The package can be combined with
arbitrary user specified variable selection approaches.")
- (license license:gpl2)))
+ (license license:gpl2)))
(define-public r-rle
(package
(define-public r-splus2r
(package
(name "r-splus2r")
- (version "1.2-2")
+ (version "1.3-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "splus2R" version))
(sha256
(base32
- "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
+ "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
(properties `((upstream-name . "splus2R")))
(build-system r-build-system)
- (native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/splus2R/")
(synopsis "Supplemental S-PLUS functionality in R")
(description
(define-public r-heatmaply
(package
(name "r-heatmaply")
- (version "1.1.1")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "heatmaply" version))
(sha256
(base32
- "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
+ "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
(define-public r-riverplot
(package
(name "r-riverplot")
- (version "0.6")
+ (version "0.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "riverplot" version))
(sha256
(base32
- "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
+ "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
(build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://logfc.wordpress.com")
(synopsis "Sankey or ribbon plots")
(description
using the @code{snow} package.")
(license license:gpl2)))
+(define-public r-fst
+ (package
+ (name "r-fst")
+ (version "0.9.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fst" version))
+ (sha256
+ (base32
+ "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
+ (properties `((upstream-name . "fst")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+ (home-page "http://www.fstpackage.org")
+ (synopsis "Fast serialization of data frames")
+ (description
+ "The fst package for R provides a fast, easy and flexible way to
+serialize data frames. With access speeds of multiple GB/s, fst is
+specifically designed to unlock the potential of high speed solid state disks.
+Data frames stored in the fst format have full random access, both in column
+and rows. The fst format allows for random access of stored data and
+compression with the LZ4 and ZSTD compressors.")
+ (license license:agpl3)))
+
(define-public r-snowfall
(package
(name "r-snowfall")
it.")
(license license:gpl2+)))
-(define-public r-rappdirs
+(define-public r-rgexf
(package
- (name "r-rappdirs")
- (version "0.3.1")
+ (name "r-rgexf")
+ (version "0.16.0")
(source
(origin
(method url-fetch)
- (uri (cran-uri "rappdirs" version))
+ (uri (cran-uri "rgexf" version))
(sha256
(base32
- "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
+ "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
+ (snippet
+ '(begin
+ ;; Delete minified JavaScript files
+ (for-each delete-file
+ '("inst/gexf-js/js/jquery-2.0.2.min.js"
+ "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
+ "inst/gexf-js/js/jquery.mousewheel.min.js"))
+ #true))))
+ (properties `((upstream-name . "rgexf")))
(build-system r-build-system)
- (home-page "https://cran.r-project.org/web/packages/rappdirs/")
- (synopsis "Determine where to save data, caches, and logs")
- (description
- "This package provides an easy way to determine which directories on the
-user's computer should be used to save data, caches and logs. It is a port of
-Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1)
+ (ice-9 popen))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
+ (with-directory-excursion "inst/gexf-js/js/"
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `((,(assoc-ref inputs "js-jquery")
+ "jquery-2.0.2.min.js")
+ ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
+ "jquery-ui-1.10.3.custom.min.js")
+ (,(assoc-ref inputs "js-jquery-mousewheel")
+ "jquery.mousewheel.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #true "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))
+ sources targets))))
+ #t)))))
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-servr" ,r-servr)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("esbuild" ,esbuild)
+ ("unzip" ,unzip)
+ ("js-jquery"
+ ,(origin
+ (method url-fetch)
+ (uri "https://code.jquery.com/jquery-2.0.2.js")
+ (sha256
+ (base32
+ "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
+ ("js-jquery-ui"
+ ,(origin
+ (method url-fetch)
+ (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
+ (sha256
+ (base32
+ "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
+ ("js-jquery-mousewheel"
+ ,(origin
+ (method url-fetch)
+ (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
+3.0.6/jquery.mousewheel.js")
+ (sha256
+ (base32
+ "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
+ (home-page "https://gvegayon.github.io/rgexf")
+ (synopsis "Build, import and export GEXF graph files")
+ (description
+ "Create, read and write GEXF (Graph Exchange XML Format) graph
+files (used in Gephi and others). It allows the user to easily build/read
+graph files including attributes, GEXF visual attributes (such as color, size,
+and position), network dynamics (for both edges and nodes) and edge weighting.
+Users can build/handle graphs element-by-element or massively through
+data-frames, visualize the graph on a web browser through gexf-js (a
+JavaScript library) and interact with the igraph package.")
(license license:expat)))
-(define-public r-renv
+(define-public r-data-tree
(package
- (name "r-renv")
- (version "0.12.5")
+ (name "r-data-tree")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
- (uri (cran-uri "renv" version))
+ (uri (cran-uri "data.tree" version))
(sha256
(base32
- "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh"))))
- (properties `((upstream-name . "renv")))
+ "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
+ (properties `((upstream-name . "data.tree")))
(build-system r-build-system)
+ (propagated-inputs
+ `(("r-r6" ,r-r6)
+ ("r-stringi" ,r-stringi)))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "https://rstudio.github.io/renv")
+ (home-page "http://github.com/gluc/data.tree")
+ (synopsis "General purpose hierarchical data structure")
+ (description
+ "Create tree structures from hierarchical data, and traverse the tree in
+various orders. Aggregate, cumulate, print, plot, convert to and from
+data.frame and more. This is useful for decision trees, machine learning,
+finance, conversion from and to JSON, and many other applications.")
+ (license license:gpl2+)))
+
+(define-public r-collapsibletree
+ (package
+ (name "r-collapsibletree")
+ (version "0.1.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "collapsibleTree" version))
+ (sha256
+ (base32
+ "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
+ (snippet
+ '(begin
+ ;; Delete minified JavaScript file
+ (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
+ #true))))
+ (properties
+ `((upstream-name . "collapsibleTree")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
+ (let ((source (assoc-ref inputs "d3.v4.js"))
+ (target "d3.min.js"))
+ (format #t "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))))))))
+ (propagated-inputs
+ `(("r-data-tree" ,r-data-tree)
+ ("r-htmlwidgets" ,r-htmlwidgets)))
+ (native-inputs
+ `(("esbuild" ,esbuild)
+ ("d3.v4.js"
+ ,(origin
+ (method url-fetch)
+ (uri "https://d3js.org/d3.v4.js")
+ (sha256
+ (base32
+ "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
+ (home-page "https://github.com/AdeelK93/collapsibleTree")
+ (synopsis "Interactive collapsible tree diagrams using D3.js")
+ (description
+ "This is a package for interactive Reingold-Tilford tree diagrams created
+using D3.js, where every node can be expanded and collapsed by clicking on it.
+Tooltips and color gradients can be mapped to nodes using a numeric column in
+the source data frame.")
+ (license license:gpl3+)))
+
+(define-public r-rappdirs
+ (package
+ (name "r-rappdirs")
+ (version "0.3.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rappdirs" version))
+ (sha256
+ (base32
+ "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/rappdirs/")
+ (synopsis "Determine where to save data, caches, and logs")
+ (description
+ "This package provides an easy way to determine which directories on the
+user's computer should be used to save data, caches and logs. It is a port of
+Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
+ (license license:expat)))
+
+(define-public r-rastervis
+ (package
+ (name "r-rastervis")
+ (version "0.49")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rasterVis" version))
+ (sha256
+ (base32
+ "0d12h7xqcwy1wps6yya9nzfppbnsxpmbkqmy3a8pvxpg81l632kk"))))
+ (properties `((upstream-name . "rasterVis")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-hexbin" ,r-hexbin)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-raster" ,r-raster)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-sp" ,r-sp)
+ ("r-viridislite" ,r-viridislite)
+ ("r-zoo" ,r-zoo)))
+ (home-page "https://oscarperpinan.github.io/rastervis/")
+ (synopsis "Visualization methods for raster data")
+ (description
+ "This package provides methods for enhanced visualization and interaction
+with raster data. It implements visualization methods for quantitative data
+and categorical data, both for univariate and multivariate rasters. It also
+provides methods to display spatiotemporal rasters, and vector fields.")
+ (license license:gpl3)))
+
+(define-public r-rentrez
+ (package
+ (name "r-rentrez")
+ (version "1.2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rentrez" version))
+ (sha256
+ (base32
+ "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
+ (properties `((upstream-name . "rentrez")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-httr" ,r-httr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://docs.ropensci.org/rentrez/")
+ (synopsis "Entrez in R")
+ (description
+ "This package provides an R interface to the NCBI's EUtils API,
+allowing users to search databases like GenBank PubMed, process the results of
+those searches and pull data into their R sessions.")
+ (license license:expat)))
+
+(define-public r-renv
+ (package
+ (name "r-renv")
+ (version "0.12.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "renv" version))
+ (sha256
+ (base32
+ "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh"))))
+ (properties `((upstream-name . "renv")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://rstudio.github.io/renv")
(synopsis "Project environments")
(description
"This package provides a dependency management toolkit for R. Using
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.6.1")
+ (version "0.6.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "06nzyd2a9yaf9hmn740xrgxw0448z5dvlplcj3kizz9sm23aw9li"))))
+ "0as80m19lvajc0vzllq9d9p63zglsm2ph7vdfg3jgk90jp8j76dg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
(define-public r-findpython
(package
(name "r-findpython")
- (version "1.0.5")
+ (version "1.0.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "findpython" version))
(sha256
(base32
- "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
+ "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
(build-system r-build-system)
(home-page "https://github.com/trevorld/findpython")
(synopsis "Functions to find an acceptable Python binary")
(define-public r-furrr
(package
(name "r-furrr")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "furrr" version))
(sha256
(base32
- "16s6sgfgh1ayzhf3kvpy9vhsd5h6p57waj1xgbksgdmf4j1wkcq7"))))
+ "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ellipsis" ,r-ellipsis)
(define-public r-physicalactivity
(package
(name "r-physicalactivity")
- (version "0.2-2")
+ (version "0.2-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "PhysicalActivity" version))
(sha256
- (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
+ (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
(properties
`((upstream-name . "PhysicalActivity")))
(build-system r-build-system)
(define-public r-multcomp
(package
(name "r-multcomp")
- (version "1.4-15")
+ (version "1.4-16")
(source
(origin
(method url-fetch)
(uri (cran-uri "multcomp" version))
(sha256
(base32
- "1klvn4a1rlrzwhy1cjrkbbh6jspgzbrdm0jxsb1lmf1yzdz609wr"))))
+ "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.5.3")
+ (version "1.5.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "11x7bn260v91gb7qri1pq54l339zm4msa5frc8saqb9ykbg4dby5"))))
+ "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
(define-public r-libcoin
(package
(name "r-libcoin")
- (version "1.0-7")
+ (version "1.0-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "libcoin" version))
(sha256
- (base32 "1vb21pw3vpv2pdnfcddw2bax13v0dg656r28j0p8njcyhwk89xln"))))
+ (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
(build-system r-build-system)
(propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
(home-page "https://cran.r-project.org/web/packages/libcoin")
(define-public r-coin
(package
(name "r-coin")
- (version "1.4-0")
+ (version "1.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "coin" version))
(sha256
(base32
- "1n2ad4m3zw8px6yc0h750k59pci3fqpnr742hhvsqirrwcdzp6zv"))))
+ "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)
(define-public r-tmb
(package
(name "r-tmb")
- (version "1.7.18")
+ (version "1.7.19")
(source
(origin
(method url-fetch)
(uri (cran-uri "TMB" version))
(sha256
(base32
- "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
+ "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
(properties `((upstream-name . "TMB")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bayestestr
(package
(name "r-bayestestr")
- (version "0.8.0")
+ (version "0.8.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
- "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw"))))
+ "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-performance
(package
(name "r-performance")
- (version "0.6.1")
+ (version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "0wz2zc98r99pg6r4l09qxxzv1fwxwp1md6wmhay401568kd8h5zn"))))
+ "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
(define-public r-gert
(package
(name "r-gert")
- (version "1.0.2")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gert" version))
(sha256
(base32
- "1lq4hgv2727lwcv8vha5af26nslj99rjxjrgflshmmcihawpls1n"))))
+ "09har6mj7qy813s6dxyzfzmjwg60m8c01yx3q6lfsnvwqzxlqxv8"))))
(properties `((upstream-name . "gert")))
(build-system r-build-system)
(inputs
("r-credentials" ,r-credentials)
("r-openssl" ,r-openssl)
("r-rstudioapi" ,r-rstudioapi)
+ ("r-sys" ,r-sys)
("r-zip" ,r-zip)))
(native-inputs
`(("pkg-config" ,pkg-config)
(define-public r-usethis
(package
(name "r-usethis")
- (version "2.0.0")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "usethis" version))
(sha256
(base32
- "0m4qnnkdiizsdvq33x502zwkn98hw2qcfm45cjj031vaydcjpai2"))))
+ "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
(define-public r-tweedie
(package
(name "r-tweedie")
- (version "2.3.2")
+ (version "2.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "tweedie" version))
(sha256
(base32
- "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
+ "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/tweedie/")
(define-public r-ks
(package
(name "r-ks")
- (version "1.11.7")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ks" version))
(sha256
- (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
+ (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-fnn" ,r-fnn)
("r-mclust" ,r-mclust)
("r-mgcv" ,r-mgcv)
("r-multicool" ,r-multicool)
- ("r-mvtnorm" ,r-mvtnorm)))
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-plot3d" ,r-plot3d)))
(home-page "http://www.mvstat.net/tduong/")
(synopsis "Kernel smoothing")
(description
(define-public r-feature
(package
(name "r-feature")
- (version "1.2.14")
+ (version "1.2.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "feature" version))
(sha256
(base32
- "1c12rny9nx8dynzxbcf49h76a7wlmsk1m131wh0jiyqx3c3y41y1"))))
+ "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-ks" ,r-ks)))
+ `(("r-ks" ,r-ks)
+ ("r-plot3d" ,r-plot3d)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "http://www.mvstat.net/tduong/")
(define-public r-pixmap
(package
(name "r-pixmap")
- (version "0.4-11")
+ (version "0.4-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "pixmap" version))
(sha256
(base32
- "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
+ "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pixmap")
(synopsis "Tools for bitmap images")
(define-public r-ontologyindex
(package
(name "r-ontologyindex")
- (version "2.5")
+ (version "2.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "ontologyIndex" version))
(sha256
(base32
- "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
+ "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
(properties `((upstream-name . "ontologyIndex")))
(build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/ontologyIndex")
(synopsis "Functions for processing ontologies in R")
(description
(define-public r-assertive-base
(package
(name "r-assertive-base")
- (version "0.0-7")
+ (version "0.0-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "assertive.base" version))
(sha256
(base32
- "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
+ "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
(properties
`((upstream-name . "assertive.base")))
(build-system r-build-system)
(define-public r-epi
(package
(name "r-epi")
- (version "2.42")
+ (version "2.43")
(source
(origin
(method url-fetch)
(uri (cran-uri "Epi" version))
(sha256
(base32
- "1vsyxlxl6n5y3wr8w7ji17hnhvbr0xsawqbdl1ajcfg5faizm9sl"))))
+ "0wsjvilcivrhy2kh2dcagkzy7bjmfa0sq9xjpv6qb4b0nc0mv089"))))
(properties `((upstream-name . "Epi")))
(build-system r-build-system)
(propagated-inputs
("r-mgcv" ,r-mgcv)
("r-numderiv" ,r-numderiv)
("r-plyr" ,r-plyr)
+ ("r-purrr" ,r-purrr)
("r-survival" ,r-survival)
("r-zoo" ,r-zoo)))
(home-page "https://BendixCarstensen.com/Epi/")
"This package adds additional Twitter Bootstrap components to Shiny.")
(license license:gpl3)))
+(define-public r-shinyjqui
+ (package
+ (name "r-shinyjqui")
+ (version "0.3.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "shinyjqui" version))
+ (sha256
+ (base32
+ "0n4ijxmkp8x6dwrsxwvx0zgd8b5129cmn6q6rrav38v1q5k8889x"))
+ (snippet
+ '(begin
+ (delete-file "inst/www/shinyjqui.min.js")))))
+ (properties `((upstream-name . "shinyjqui")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/www/"
+ (let ((source "shinyjqui.js")
+ (target "shinyjqui.min.js"))
+ (format #true "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))))))))
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-shiny" ,r-shiny)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("esbuild" ,esbuild)))
+ (home-page "https://github.com/yang-tang/shinyjqui")
+ (synopsis "jQuery UI interactions and effects for Shiny")
+ (description
+ "This is an extension to Shiny that brings interactions and animation
+effects from the jQuery UI library.")
+ (license license:expat)))
+
(define-public r-outliers
(package
(name "r-outliers")
(define-public r-pbdzmq
(package
(name "r-pbdzmq")
- (version "0.3-4")
+ (version "0.3-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "pbdZMQ" version))
(sha256
(base32
- "0adiac53yq305ymhrds1gas4jm0rn1ddv7c7df5ky2cfhpb4ny87"))))
+ "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
(properties `((upstream-name . "pbdZMQ")))
(build-system r-build-system)
(inputs
(define-public r-repr
(package
(name "r-repr")
- (version "1.1.0")
+ (version "1.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "repr" version))
(sha256
(base32
- "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
+ "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
(define-public r-irdisplay
(package
(name "r-irdisplay")
- (version "0.7.0")
+ (version "1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "IRdisplay" version))
(sha256
(base32
- "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
+ "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
(properties `((upstream-name . "IRdisplay")))
(build-system r-build-system)
(propagated-inputs
classes.")
(license license:gpl2)))
+(define-public r-udunits2
+ (package
+ (name "r-udunits2")
+ (version "0.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "udunits2" version))
+ (sha256
+ (base32
+ "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
+ (properties `((upstream-name . "udunits2")))
+ (build-system r-build-system)
+ (inputs
+ `(("udunits" ,udunits)))
+ (home-page "https://cran.r-project.org/package=udunits2")
+ (synopsis "Udunits-2 bindings for R")
+ (description
+ "This package provides simple bindings to Unidata's udunits library.")
+ (license license:gpl2)))
+
(define-public r-classint
(package
(name "r-classint")
(define-public r-rms
(package
(name "r-rms")
- (version "6.1-0")
+ (version "6.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rms" version))
(sha256
- (base32 "0llz519rgnc7v2jqhfrjgixkpkmmi5wi1a52hgz3n28s46ww77mq"))))
+ (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
(define-public r-arsenal
(package
(name "r-arsenal")
- (version "3.5.0")
+ (version "3.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "arsenal" version))
(sha256
(base32
- "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
+ "13ql3rb79a764ppsc1sqi8glzzkw79la0j2ahzbxgz7cz879sazy"))))
(properties `((upstream-name . "arsenal")))
(build-system r-build-system)
(propagated-inputs `(("r-knitr" ,r-knitr)))
(define-public r-mlbench
(package
(name "r-mlbench")
- (version "2.1-1")
+ (version "2.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "mlbench" version))
(sha256
(base32
- "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
+ "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/mlbench/")
(synopsis "Machine learning benchmark problems")
(define-public r-ingredients
(package
(name "r-ingredients")
- (version "2.0")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ingredients" version))
(sha256
(base32
- "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
+ "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
(properties `((upstream-name . "ingredients")))
(build-system r-build-system)
(propagated-inputs
(define-public r-enrichr
(package
(name "r-enrichr")
- (version "2.1")
+ (version "3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "enrichR" version))
(sha256
(base32
- "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
+ "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
(properties `((upstream-name . "enrichR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-httr" ,r-httr)
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-httr" ,r-httr)
("r-rjson" ,r-rjson)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/enrichR/")
(synopsis "R Interface to Enrichr database for analyzing gene sets")
(description
(define-public r-leiden
(package
(name "r-leiden")
- (version "0.3.6")
+ (version "0.3.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "leiden" version))
(sha256
(base32
- "1k1250bjgf2cb1whp2sl1r6b88156qwi2zkamw5iy2q1qhw6w2d7"))))
+ "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
(properties `((upstream-name . "leiden")))
(build-system r-build-system)
(propagated-inputs
(define-public r-systemfonts
(package
(name "r-systemfonts")
- (version "0.3.2")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
- "12hdvv66kkd3b4rs82blc3c4ifz2dw1048sqpkbz6vkk1zqpc53x"))))
+ "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
(propagated-inputs
(define-public r-assertr
(package
(name "r-assertr")
- (version "2.7")
+ (version "2.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "assertr" version))
(sha256
(base32
- "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
+ "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
(define-public r-rgdal
(package
(name "r-rgdal")
- (version "1.5-19")
+ (version "1.5-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgdal" version))
(sha256
- (base32 "1cii2azm3zv5l6fn33xzwahp8349z3pb2769vpdxkf7734dxggvg"))))
+ (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
(properties `((upstream-name . "rgdal")))
(build-system r-build-system)
(inputs
(define-public r-insol
(package
(name "r-insol")
- (version "1.2.1")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "insol" version))
(sha256
(base32
- "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
+ "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
(properties `((upstream-name . "insol")))
(build-system r-build-system)
(propagated-inputs
(define-public r-assertable
(package
(name "r-assertable")
- (version "0.2.7")
+ (version "0.2.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "assertable" version))
(sha256
(base32
- "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
+ "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/assertable/")
(synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
(description "This package provides simple, flexible assertions on
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.2.9")
+ (version "2.3.3")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
+ (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pracma/")
(synopsis "Practical numerical math functions")
(define-public r-actuar
(package
(name "r-actuar")
- (version "3.1-0")
+ (version "3.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
- "15a8axb2ym46j8vlm7icwnsc950p8m66hp0armha7drk0725y77k"))))
+ "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs `(("r-expint" ,r-expint)))
(define-public r-archivist
(package
(name "r-archivist")
- (version "2.3.4")
+ (version "2.3.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "archivist" version))
(sha256
(base32
- "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
+ "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
(properties `((upstream-name . "archivist")))
(build-system r-build-system)
(propagated-inputs
("r-magrittr" ,r-magrittr)
("r-rcurl" ,r-rcurl)
("r-rsqlite" ,r-rsqlite)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://pbiecek.github.io/archivist/")
(synopsis "Tools for storing, restoring and searching for R objects")
(description
(define-public r-stopwords
(package
(name "r-stopwords")
- (version "2.1")
+ (version "2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "stopwords" version))
(sha256
(base32
- "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8"))))
+ "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
(properties `((upstream-name . "stopwords")))
(build-system r-build-system)
(propagated-inputs
- `(("r-desc" ,r-desc)
- ("r-isocodes" ,r-isocodes)
- ("r-usethis" ,r-usethis)))
+ `(("r-isocodes" ,r-isocodes)))
(home-page "https://github.com/quanteda/stopwords")
(synopsis "Multilingual stopword lists")
(description
(define-public r-topicmodels
(package
(name "r-topicmodels")
- (version "0.2-11")
+ (version "0.2-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "topicmodels" version))
(sha256
(base32
- "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
+ "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
(properties `((upstream-name . "topicmodels")))
(build-system r-build-system)
- (native-inputs
+ (inputs
`(("gsl" ,gsl)))
(propagated-inputs
`(("r-modeltools" ,r-modeltools)
(define-public r-qgraph
(package
(name "r-qgraph")
- (version "1.6.5")
+ (version "1.6.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "qgraph" version))
(sha256
(base32
- "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
+ "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
(properties `((upstream-name . "qgraph")))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
- ("r-bdgraph" ,r-bdgraph)
("r-colorspace" ,r-colorspace)
("r-corpcor" ,r-corpcor)
- ("r-d3network" ,r-d3network)
("r-dplyr" ,r-dplyr)
("r-fdrtool" ,r-fdrtool)
("r-ggplot2" ,r-ggplot2)
- ("r-ggraph" ,r-ggraph)
("r-glasso" ,r-glasso)
("r-gtools" ,r-gtools)
("r-hmisc" ,r-hmisc)
- ("r-huge" ,r-huge)
("r-igraph" ,r-igraph)
("r-jpeg" ,r-jpeg)
("r-lavaan" ,r-lavaan)
("r-png" ,r-png)
("r-psych" ,r-psych)
("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ("r-tidygraph" ,r-tidygraph)))
+ ("r-reshape2" ,r-reshape2)))
(home-page "http://sachaepskamp.com/qgraph/")
(synopsis "Weighted network visualization and analysis")
(description
(base32
"017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'install 'install-server-binary
+ ;; Makevars tries to install to R's store directory.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (substitute* "src/Makevars.in"
+ (("\\$\\(R_HOME\\)") out))
+ (mkdir-p bin)))))))
(propagated-inputs
`(("r-checkmate" ,r-checkmate)
("r-mime" ,r-mime)
(define-public r-spatstat-utils
(package
(name "r-spatstat-utils")
- (version "1.20-2")
+ (version "2.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.utils" version))
(sha256
(base32
- "066f35017wpbz9plwc14gji3ddq4a1h2lx4mcgxajrcrk0zl3hk2"))))
+ "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
(properties
`((upstream-name . "spatstat.utils")))
(build-system r-build-system)
(define-public r-spatstat-data
(package
(name "r-spatstat-data")
- (version "1.7-0")
+ (version "2.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.data" version))
(sha256
(base32
- "0by10dx72jjn6rvgrdj4xwh4zg6vxi4cp536aq4b6drb7za95hdv"))))
+ "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
(properties `((upstream-name . "spatstat.data")))
(build-system r-build-system)
(propagated-inputs
(define-public r-cpp11
(package
(name "r-cpp11")
- (version "0.2.5")
+ (version "0.2.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "cpp11" version))
(sha256
(base32
- "081f3b98mcxyilqsxbzzdnj2x6v7xycprrw7r5934163q0397vvg"))))
+ "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
(properties `((upstream-name . "cpp11")))
(build-system r-build-system)
(native-inputs `(("r-knitr" ,r-knitr)))
data to rasters. It speeds up plotting of data with millions of points.")
(license license:gpl3+)))
+(define-public r-seuratobject
+ (package
+ (name "r-seuratobject")
+ (version "4.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "SeuratObject" version))
+ (sha256
+ (base32
+ "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
+ (properties `((upstream-name . "SeuratObject")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rlang" ,r-rlang)
+ ("r-sctransform" ,r-sctransform)))
+ (home-page "https://satijalab.org/seurat")
+ (synopsis "Data structures for single cell data")
+ (description
+ "This package defines S4 classes for single-cell genomic data and
+associated information, such as dimensionality reduction embeddings,
+nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
+access methods and R-native hooks to ensure the Seurat object is familiar to
+other R users.")
+ (license license:gpl3)))
+
(define-public r-seurat
(package
(name "r-seurat")
- (version "3.2.3")
+ (version "4.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "11rzc7h2ad8z8k5r1sbz4d7y4rl3080qp2hh7vibwmipbkvlial3"))))
+ "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
("r-reticulate" ,r-reticulate)
("r-rlang" ,r-rlang)
("r-rocr" ,r-rocr)
- ("r-rsvd" ,r-rsvd)
("r-rtsne" ,r-rtsne)
("r-scales" ,r-scales)
("r-scattermore" ,r-scattermore)
("r-sctransform" ,r-sctransform)
+ ("r-seuratobject" ,r-seuratobject)
("r-shiny" ,r-shiny)
("r-spatstat" ,r-spatstat)
("r-tibble" ,r-tibble)
(define-public r-paradox
(package
(name "r-paradox")
- (version "0.6.0")
+ (version "0.7.0")
(source (origin
(method url-fetch)
(uri (cran-uri "paradox" version))
(sha256
(base32
- "1zv0q411wcwigkf4yggs3w2gz48lvv3jhnrddrv40qih8b70ywi3"))))
+ "1fz6sdwvvifm4qbmwgm27dil278mswvcfw8bbsvli5v4l1ghw8kj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
(define-public r-mlr3
(package
(name "r-mlr3")
- (version "0.9.0")
+ (version "0.10.0")
(source (origin
(method url-fetch)
(uri (cran-uri "mlr3" version))
(sha256
(base32
- "0gg7rrzxwrnpg6sgm0aa6bmfwmqv3d3za0ghnqrnibg33p9ynpgb"))))
+ "1arqijbbmhv57mj8kyq30zxykah83ab1d1c7gs0cxs0xhfwln66g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
(define-public r-bbotk
(package
(name "r-bbotk")
- (version "0.2.2")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bbotk" version))
(sha256
(base32
- "06iz6gyymcxkbjiw049v1dk3vjfni646z247q08i2s0x59sqfqxv"))))
+ "0kbjbwwq1fdfpl4xzy08hz4qvhjjchvz58icxq0dlbsmdyqwhwv0"))))
(properties `((upstream-name . "bbotk")))
(build-system r-build-system)
(propagated-inputs
("r-mlr3misc" ,r-mlr3misc)
("r-paradox" ,r-paradox)
("r-r6" ,r-r6)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bbotk.mlr-org.com")
(synopsis "Black-Box Optimization Toolkit")
(description "This package provides a common framework for optimization of
(define-public r-mlr3tuning
(package
(name "r-mlr3tuning")
- (version "0.5.0")
+ (version "0.6.0")
(source (origin
(method url-fetch)
(uri (cran-uri "mlr3tuning" version))
(sha256
(base32
- "1pn80qjxzj2pivgs6qgairci6yh1bdnl2zbgl9ykdip2rqzv6r6m"))))
+ "0kxf9wl1jnwyrj2zfmiz12w2594407y44m0xxwp9b2lrwxk31wm7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bbotk" ,r-bbotk)
termination criteria can be set and combined. The class @code{AutoTuner} provides a
convenient way to perform nested resampling in combination with @code{mlr3}.")
(license license:lgpl3)))
+
+(define-public r-fontliberation
+ (package
+ (name "r-fontliberation")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fontLiberation" version))
+ (sha256
+ (base32
+ "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
+ (properties
+ `((upstream-name . "fontLiberation")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/package=fontLiberation")
+ (synopsis "Liberation fonts")
+ (description
+ "This package provides a placeholder for the Liberation fontset intended
+for the fontquiver package. This fontset covers the 12 combinations of
+families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
+supported in R graphics devices.")
+ (license license:silofl1.1)))
+
+(define-public r-fontbitstreamvera
+ (package
+ (name "r-fontbitstreamvera")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fontBitstreamVera" version))
+ (sha256
+ (base32
+ "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
+ (properties
+ `((upstream-name . "fontBitstreamVera")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/package=fontBitstreamVera")
+ (synopsis "Fonts for fontquiver")
+ (description
+ "This package is a placeholder for the Bitstream Vera font. It is
+intended for the fontquiver package.")
+ (license
+ (license:fsdg-compatible
+ "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
+ "The Font Software may be sold as part of a larger software package but
+no copy of one or more of the Font Software typefaces may be sold by
+itself."))))
+
+(define-public r-fontquiver
+ (package
+ (name "r-fontquiver")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fontquiver" version))
+ (sha256
+ (base32
+ "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
+ (properties `((upstream-name . "fontquiver")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
+ ("r-fontliberation" ,r-fontliberation)))
+ (home-page "https://cran.r-project.org/package=fontquiver")
+ (synopsis "Set of installed fonts")
+ (description
+ "This package provides a set of fonts. This is useful when you want to
+avoid system fonts to make sure your outputs are reproducible.")
+ (license license:gpl3)))
+
+(define-public r-freetypeharfbuzz
+ (package
+ (name "r-freetypeharfbuzz")
+ (version "0.2.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "freetypeharfbuzz" version))
+ (sha256
+ (base32
+ "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
+ (properties
+ `((upstream-name . "freetypeharfbuzz")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'prepare-static-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir-p "src/target/include")
+ (let ((freetype (assoc-ref inputs "static-freetype"))
+ (harfbuzz (assoc-ref inputs "static-harfbuzz")))
+ (substitute* "src/Makevars.in"
+ (("include @MK_FILE@") "") ; do not build static libs
+ (("^HB_STATIC_LIB =.*")
+ (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
+ (("^FT_STATIC_LIB =.*")
+ (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
+ (copy-recursively (string-append freetype "/include")
+ "src/target/include")
+ (copy-recursively (string-append harfbuzz "/include")
+ "src/target/include")))))))
+ (propagated-inputs
+ `(("r-fontquiver" ,r-fontquiver)))
+ ;; This may defeat the purpose of this package as our versions of freetype
+ ;; and harfbuzz obviously differ from the tarballs offered by this
+ ;; project. On the other hand, Guix arguably does a better job at
+ ;; "ensur[ing] deterministic computation".
+ (native-inputs
+ `(("static-freetype"
+ ,(package
+ (inherit (static-package freetype))
+ (arguments
+ `(#:configure-flags
+ (list "--enable-static=yes"
+ "--with-pic=yes"
+ "--without-zlib"
+ "--without-bzip2"
+ "--without-png"
+ "--without-harfbuzz")))))
+ ("static-harfbuzz"
+ ,(package
+ (inherit (static-package harfbuzz))
+ (arguments
+ `(#:tests? #false ; fail because shared library is disabled
+ #:configure-flags
+ (list "--enable-static=yes"
+ "--enable-shared=no"
+ "--with-pic=yes"
+ "--with-freetype=yes"
+ "--without-icu"
+ "--without-cairo"
+ "--without-fontconfig"
+ "--without-glib")))))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
+ (synopsis "Deterministic computation of text box metrics")
+ (description
+ "Unlike other tools that dynamically link to the Cairo stack,
+freetypeharfbuzz is statically linked to specific versions of the FreeType and
+harfbuzz libraries. This ensures deterministic computation of text box
+extents for situations where reproducible results are crucial (for instance
+unit tests of graphics).")
+ (license license:gpl3)))
+
+(define-public r-vdiffr
+ (package
+ (name "r-vdiffr")
+ (version "0.3.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "vdiffr" version))
+ (sha256
+ (base32
+ "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
+ (snippet
+ '(begin
+ (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
+ (properties `((upstream-name . "vdiffr")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/htmlwidgets/lib/"
+ (let ((source (assoc-ref inputs "js-jquery"))
+ (target "jquery.min.js"))
+ (format #true "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))))))))
+ (inputs
+ `(("freetype" ,freetype)
+ ("harfbuzz" ,harfbuzz)))
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-devtools" ,r-devtools)
+ ("r-diffobj" ,r-diffobj)
+ ("r-fontquiver" ,r-fontquiver)
+ ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
+ ("r-gdtools" ,r-gdtools)
+ ("r-glue" ,r-glue)
+ ("r-htmltools" ,r-htmltools)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-purrr" ,r-purrr)
+ ("r-r6" ,r-r6)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
+ ("r-shiny" ,r-shiny)
+ ("r-testthat" ,r-testthat)
+ ("r-usethis" ,r-usethis)
+ ("r-xml2" ,r-xml2)))
+ (native-inputs
+ `(("esbuild" ,esbuild)
+ ("js-jquery"
+ ,(origin
+ (method url-fetch)
+ (uri "https://code.jquery.com/jquery-1.12.4.js")
+ (sha256
+ (base32
+ "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
+ (home-page "https://github.com/r-lib/vdiffr")
+ (synopsis "Visual regression testing and graphical diffing")
+ (description
+ "This package is an extension to the testthat package that makes it easy
+to add graphical unit tests. It provides a Shiny application to manage the
+test cases.")
+ (license license:gpl3)))
+
+(define-public r-highlight
+ (package
+ (name "r-highlight")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "highlight" version))
+ (sha256
+ (base32
+ "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
+ (properties `((upstream-name . "highlight")))
+ (build-system r-build-system)
+ (home-page "https://github.com/hadley/highlight")
+ (synopsis "Syntax highlighter for R code")
+ (description
+ "This package provides a syntax highlighter for R code based on the
+results of the R parser. It supports rendering in HTML and LaTeX markup. It
+includes a custom Sweave driver performing syntax highlighting of R code
+chunks.")
+ (license license:gpl3+)))
+
+(define-public r-clustree
+ (package
+ (name "r-clustree")
+ (version "0.4.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "clustree" version))
+ (sha256
+ (base32
+ "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
+ (properties `((upstream-name . "clustree")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-checkmate" ,r-checkmate)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggraph" ,r-ggraph)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-igraph" ,r-igraph)
+ ("r-rlang" ,r-rlang)
+ ("r-tidygraph" ,r-tidygraph)
+ ("r-viridis" ,r-viridis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/lazappi/clustree")
+ (synopsis "Visualize clusterings at different resolutions")
+ (description
+ "Deciding what resolution to use can be a difficult question when
+approaching a clustering analysis. One way to approach this problem is to
+look at how samples move as the number of clusters increases. This package
+allows you to produce clustering trees, a visualization for interrogating
+clusterings as resolution increases.")
+ (license license:gpl3)))
+
+(define-public r-textshaping
+ (package
+ (name "r-textshaping")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "textshaping" version))
+ (sha256
+ (base32
+ "053pbw45by96q62kjfnyc3d0ssar9svssrdqy6a09kdmdh75xdar"))))
+ (properties `((upstream-name . "textshaping")))
+ (build-system r-build-system)
+ (inputs
+ `(("freetype" ,freetype)
+ ("fribidi" ,fribidi)
+ ("harfbuzz" ,harfbuzz)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-cpp11" ,r-cpp11)
+ ("r-systemfonts" ,r-systemfonts)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/r-lib/textshaping")
+ (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
+ (description
+ "This package provides access to the text shaping functionality in the
+HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
+is a low-level utility package mainly for graphic devices that expands upon
+the font tool-set provided by the @code{systemfonts} package.")
+ (license license:expat)))
+
+(define-public r-ragg
+ (package
+ (name "r-ragg")
+ (version "0.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ragg" version))
+ (sha256
+ (base32
+ "0443dhfi7bjfpap041vrnslw3ql3vpsxx18raz2w9nfdb7id8lsc"))))
+ (properties `((upstream-name . "ragg")))
+ (build-system r-build-system)
+ (inputs
+ `(("freetype" ,freetype)
+ ("libjpeg" ,libjpeg-turbo)
+ ("libpng" ,libpng)
+ ("libtiff" ,libtiff)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-systemfonts" ,r-systemfonts)
+ ("r-textshaping" ,r-textshaping)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "https://ragg.r-lib.org")
+ (synopsis "Graphic devices based on AGG")
+ (description
+ "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
+drawing library. The ragg package provides a set of graphic devices based on
+AGG to use as alternative to the raster devices provided through the
+@code{grDevices} package.")
+ (license license:expat)))
+
+(define-public r-downlit
+ (package
+ (name "r-downlit")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "downlit" version))
+ (sha256
+ (base32
+ "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
+ (properties `((upstream-name . "downlit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-brio" ,r-brio)
+ ("r-digest" ,r-digest)
+ ("r-evaluate" ,r-evaluate)
+ ("r-fansi" ,r-fansi)
+ ("r-rlang" ,r-rlang)
+ ("r-vctrs" ,r-vctrs)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://downlit.r-lib.org/")
+ (synopsis "Syntax highlighting and automatic linking")
+ (description
+ "This package provides syntax highlighting of R code, specifically
+designed for the needs of RMarkdown packages like @code{pkgdown},
+@code{hugodown}, and @code{bookdown}. It includes linking of function calls
+to their documentation on the web, and automatic translation of ANSI escapes
+in output to the equivalent HTML.")
+ (license license:expat)))
+
+(define-public r-pkgdown
+ (package
+ (name "r-pkgdown")
+ (version "1.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pkgdown" version))
+ (sha256
+ (base32
+ "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
+ (properties `((upstream-name . "pkgdown")))
+ (build-system r-build-system)
+ (inputs `(("pandoc" ,pandoc)))
+ (propagated-inputs
+ `(("r-callr" ,r-callr)
+ ("r-crayon" ,r-crayon)
+ ("r-desc" ,r-desc)
+ ("r-digest" ,r-digest)
+ ("r-downlit" ,r-downlit)
+ ("r-fs" ,r-fs)
+ ("r-httr" ,r-httr)
+ ("r-magrittr" ,r-magrittr)
+ ("r-memoise" ,r-memoise)
+ ("r-openssl" ,r-openssl)
+ ("r-purrr" ,r-purrr)
+ ("r-ragg" ,r-ragg)
+ ("r-rematch2" ,r-rematch2)
+ ("r-rlang" ,r-rlang)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-tibble" ,r-tibble)
+ ("r-whisker" ,r-whisker)
+ ("r-withr" ,r-withr)
+ ("r-xml2" ,r-xml2)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://pkgdown.r-lib.org")
+ (synopsis "Make static HTML documentation for an R package")
+ (description
+ "The goal of this package is to generate an attractive and useful website
+from a source package. @code{pkgdown} converts your documentation, vignettes,
+README file, and more to HTML making it easy to share information about your
+package online.")
+ (license license:expat)))
HCoop / jackhill / guix / guix.git / blobdiff