diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1401 |
1 files changed, 1235 insertions, 166 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 874a77c552..1fe90619cd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -55,6 +55,7 @@ #: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) @@ -63,9 +64,11 @@ #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) #:use-module (gnu packages compression) + #:use-module (gnu packages crypto) #: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) @@ -105,14 +108,14 @@ (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") @@ -123,6 +126,30 @@ functions always read and write UTF-8 (8-bit Unicode Transformation Format) 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") @@ -363,17 +390,17 @@ variables.") (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) @@ -894,23 +921,27 @@ package is a port of the Python package @code{cssselect}.") (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 @@ -1128,13 +1159,13 @@ directory.") (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) @@ -1292,14 +1323,14 @@ and vice-versa.") (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/") @@ -1579,14 +1610,14 @@ well as file saving is available.") (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))) @@ -1723,6 +1754,131 @@ in R and Shiny via the D3 visualization library.") ;; 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") @@ -2141,13 +2297,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (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) @@ -3076,13 +3232,13 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and (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))) @@ -3819,14 +3975,14 @@ by base R methods related to model fitting.") (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) @@ -4124,19 +4280,21 @@ clustered data.") (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 @@ -4149,14 +4307,14 @@ analysis of multiply imputed data sets.") (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) @@ -4590,19 +4748,17 @@ plots in @code{ggplot2}.") (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") @@ -4802,13 +4958,13 @@ iVAT).") (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 #; @@ -4952,14 +5108,14 @@ terminals.") (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))) @@ -4973,6 +5129,41 @@ functions to compile LaTeX documents, and install missing LaTeX packages 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") @@ -4998,27 +5189,29 @@ supports arbitrary vertex/edge/graph attributes.") (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 @@ -5188,17 +5381,16 @@ exhaustive search.") (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 @@ -5642,14 +5834,14 @@ functions to enforce symmetric scales or add tags to facetted plots.") (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) @@ -6134,15 +6326,19 @@ are included.") (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 @@ -6489,6 +6685,31 @@ promises, but with a syntax that is idiomatic R.") 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") @@ -6511,17 +6732,187 @@ to the cluster management tool @code{sfCluster}, but can also used without it.") (license license:gpl2+))) +(define-public r-rgexf + (package + (name "r-rgexf") + (version "0.16.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rgexf" version)) + (sha256 + (base32 + "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) + (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-data-tree + (package + (name "r-data-tree") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "data.tree" version)) + (sha256 + (base32 + "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 "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 "0.3.1") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rappdirs" version)) (sha256 (base32 - "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g")))) + "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") @@ -6531,6 +6922,64 @@ 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") @@ -7551,14 +8000,14 @@ functions.") (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) @@ -7683,14 +8132,14 @@ support for default values, positional argument support, etc.") (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") @@ -8519,14 +8968,14 @@ genotypes as \"graphical genotypes\".") (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) @@ -8771,13 +9220,13 @@ singular or ill-conditioned Jacobian.") (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) @@ -9326,14 +9775,14 @@ packages maintained by Torsten Hothorn.") (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) @@ -9354,14 +9803,14 @@ Hothorn, Westfall, 2010, CRC Press).") (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) @@ -9405,13 +9854,13 @@ Cohen (1988).") (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") @@ -9424,14 +9873,14 @@ and permutation inference in the framework of Strasser and Weber (1999).") (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) @@ -9487,14 +9936,14 @@ Bayesian modeling.") (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 @@ -9590,14 +10039,14 @@ differentiation.") (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 @@ -9617,14 +10066,14 @@ ROPE percentage and pd).") (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) @@ -9902,14 +10351,14 @@ user credentials.") (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 @@ -9920,6 +10369,7 @@ user credentials.") ("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) @@ -9937,14 +10387,14 @@ User credentials are shared with command line git through the (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) @@ -10230,14 +10680,14 @@ algorithms, clusterings, and individual clusters.") (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/") @@ -10621,13 +11071,13 @@ isosurfaces.") (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) @@ -10637,7 +11087,8 @@ isosurfaces.") ("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 @@ -10651,17 +11102,18 @@ hypothesis testing.") (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/") @@ -10857,6 +11309,33 @@ Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) +(define-public r-sodium + (package + (name "r-sodium") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sodium" version)) + (sha256 + (base32 + "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w")))) + (properties `((upstream-name . "sodium"))) + (build-system r-build-system) + (inputs + `(("libsodium" ,libsodium))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/jeroen/sodium") + (synopsis "R bindings to the libsodium crypto library") + (description + "This package provides bindings to libsodium: a library for encryption, +decryption, signatures, password hashing and more. Sodium uses curve25519, a +Diffie-Hellman function by Daniel Bernstein, which has become very popular +after it was discovered that the NSA had backdoored Dual EC DRBG.") + (license license:expat))) + (define-public r-softimpute (package (name "r-softimpute") @@ -11766,14 +12245,14 @@ Emphasis is always given to methods for visualizing the data.") (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") @@ -11804,16 +12283,18 @@ library.") (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 @@ -11942,14 +12423,14 @@ Precision Floating-Point Reliable} (MPFR) library.") (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) @@ -12704,14 +13185,14 @@ model with finite state space using the Aalen-Johansen estimator.") (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 @@ -12724,6 +13205,7 @@ model with finite state space using the Aalen-Johansen estimator.") ("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/") @@ -13158,6 +13640,49 @@ several common set, element and attribute related tasks.") "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") @@ -13743,14 +14268,14 @@ graphs.") (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 @@ -13771,14 +14296,14 @@ compatible with @code{rzmq} are also provided.") (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) @@ -13795,14 +14320,14 @@ several formats and MIME types.") (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 @@ -14319,6 +14844,27 @@ is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} 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") @@ -14666,13 +15212,13 @@ lspec, polyclass, and polymars.") (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) @@ -14712,14 +15258,14 @@ generalized linear models, and quantile regression.") (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))) @@ -15795,14 +16341,14 @@ using the three.js visualization library.") (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") @@ -16448,14 +16994,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (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 @@ -16582,19 +17128,22 @@ and model output.") (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 @@ -16942,14 +17491,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (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 @@ -17147,14 +17696,14 @@ both R code and compiled C/C++/FORTRAN code.") (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 @@ -17268,14 +17817,14 @@ cell RNA-seq experiments.") (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) @@ -17324,13 +17873,13 @@ effect size.") (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 @@ -17353,14 +17902,14 @@ PROJ.4 library.") (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 @@ -17410,17 +17959,19 @@ signalled with increasing levels of non-invasive verbosity.") (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 @@ -17486,12 +18037,12 @@ to ODEs by numerical differencing.") (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") @@ -18694,6 +19245,26 @@ the align-and-count method.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-filelock + (package + (name "r-filelock") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "filelock" version)) + (sha256 + (base32 + "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc")))) + (properties `((upstream-name . "filelock"))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/filelock") + (synopsis "Portable file locking") + (description + "This library lets you place an exclusive or shared lock on a file using +the appropriate system call provided by the underlying operating system.") + (license license:expat))) + (define-public r-filematrix (package (name "r-filematrix") @@ -19804,14 +20375,14 @@ API; see the package vignette for details.") (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))) @@ -20697,14 +21268,14 @@ both exclusive and shared locking.") (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 @@ -20716,6 +21287,8 @@ both exclusive and shared locking.") ("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 @@ -20975,20 +21548,18 @@ character codes as well as the UN M.49 area codes.") (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 @@ -21093,17 +21664,17 @@ machine learning, visually representing text and text analyses, and more.") (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) @@ -21592,30 +22163,26 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (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) @@ -21625,8 +22192,7 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") ("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 @@ -22198,6 +22764,39 @@ a formula and @code{data.frame} plus some additional arguments for priors.") trend test.") (license license:gpl2+))) +(define-public r-keyring + (package + (name "r-keyring") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "keyring" version)) + (sha256 + (base32 + "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq")))) + (properties `((upstream-name . "keyring"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-filelock" ,r-filelock) + ("r-getpass" ,r-getpass) + ("r-openssl" ,r-openssl) + ("r-r6" ,r-r6) + ("r-rappdirs" ,r-rappdirs) + ("r-sodium" ,r-sodium) + ("r-yaml" ,r-yaml))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/r-lib/keyring") + (synopsis "Access the system credential store from R") + (description + "This package provides a platform-independent API to access the operating +system's credential store. It currently supports Keychain on macOS, +Credential Store on Windows, the Secret Service API on GNU/Linux, and a +simple, platform independent store implemented with environment variables. +Additional storage back-ends can be added easily.") + (license license:expat))) + (define-public r-zyp (package (name "r-zyp") @@ -23169,6 +23768,31 @@ multi-state models.") pies on a map.") (license license:artistic2.0))) +(define-public r-scrypt + (package + (name "r-scrypt") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "scrypt" version)) + (sha256 + (base32 + "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm")))) + (properties `((upstream-name . "scrypt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/rstudio/rscrypt") + (synopsis "Key derivation functions for R based on Scrypt") + (description + "This package provides functions for working with the scrypt key +derivation functions. Scrypt is a password-based key derivation function +created by Colin Percival. The algorithm was specifically designed to make it +costly to perform large-scale custom hardware attacks by requiring large +amounts of memory.") + (license license:bsd-2))) + (define-public r-boruta (package (name "r-boruta") @@ -23711,14 +24335,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (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) @@ -23732,14 +24356,14 @@ which may also be useful for other purposes.") (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 @@ -23822,14 +24446,14 @@ for linear mixed models (AIREML).") (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))) @@ -25248,16 +25872,45 @@ as allowing spectra with different resolutions.") 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 @@ -25294,11 +25947,11 @@ data to rasters. It speeds up plotting of data with millions of points.") ("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) @@ -25645,13 +26298,13 @@ package also supersedes the package @code{BBmisc}.") (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) @@ -25670,13 +26323,13 @@ implemented as @code{R6} classes.") (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) @@ -25730,14 +26383,14 @@ vector machines, and gradient boosting.") (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 @@ -25747,6 +26400,8 @@ vector machines, and gradient boosting.") ("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 @@ -25758,13 +26413,13 @@ annealing.") (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) @@ -25782,3 +26437,417 @@ tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various 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))) |