diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 212 |
1 files changed, 144 insertions, 68 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 458b141f91..5bf37e3900 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -53,7 +53,7 @@ #:use-module (gnu packages gnome) #:use-module (gnu packages graph) #:use-module (gnu packages gtk) - #:use-module (gnu packages haskell) + #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) @@ -166,14 +166,14 @@ objects.") (define-public r-sys (package (name "r-sys") - (version "3.2") + (version "3.3") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 - "1k5vk5q9wa5sin0n226i05nymg469s24f6lx64yyhb7yc624j698")))) + "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6")))) (build-system r-build-system) (home-page "https://github.com/jeroen/sys") (synopsis "Powerful and reliable tools for running system commands in R") @@ -212,14 +212,14 @@ read a protected key.") (define-public r-vegan (package (name "r-vegan") - (version "2.5-5") + (version "2.5-6") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0wb90ng02gi13854bjq0b8a2vrknyhb0s0l1v3z38c4zy9k54sw7")))) + "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -872,14 +872,14 @@ well as file saving is available.") (define-public r-d3r (package (name "r-d3r") - (version "0.8.6") + (version "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 - "0vcmiyhd000xyl28k6rm7ba50x5sz5b2cpllxnq36q13qhdnqw6k")))) + "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) @@ -1122,14 +1122,14 @@ coordinates.") (define-public r-rgooglemaps (package (name "r-rgooglemaps") - (version "1.4.3") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 - "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4")))) + "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,r-png))) @@ -1441,14 +1441,14 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 - "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19")))) + "0y4i85axwajrk67h3w6fiqfm6wxmhn3dr240w5l2nvqg3ahpxc8q")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -1649,14 +1649,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f")))) + "07y1bchkslpz2wl43yg5j5h1nl9z0i425a07jdmfd5avrynd8p3m")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -2663,14 +2663,14 @@ Optimization problems by using the simplex algorithm.") (define-public r-geometry (package (name "r-geometry") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 - "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz")))) + "0z4491mhfmrlbb8lazjvq55alrprx7k0abg2d39fj0lsj84cls1r")))) (build-system r-build-system) (propagated-inputs `(("r-magic" ,r-magic) @@ -3476,14 +3476,14 @@ of Eigenmatrices} (JADE).") (define-public r-dtw (package (name "r-dtw") - (version "1.20-1") + (version "1.21-3") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 - "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3")))) + "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s")))) (build-system r-build-system) (propagated-inputs `(("r-proxy" ,r-proxy))) (home-page "http://dtw.r-forge.r-project.org/") @@ -3765,14 +3765,14 @@ Markdown documents.") (define-public r-seriation (package (name "r-seriation") - (version "1.2-7") + (version "1.2-8") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 - "0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6")))) + "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -3799,14 +3799,14 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 - "05jlbi5byqpw0fkhmmxqglnaxh9gwbcigx77kcpw1pkxnpwfry62")))) + "1c3wmy6s4ck821mwl7i2g8cxd31g30llbpivbgq21g1rxs4zwlyl")))) (build-system r-build-system) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") @@ -4699,14 +4699,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.0.0") + (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw")) + "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg")) (modules '((guix build utils))) (snippet '(begin @@ -5064,14 +5064,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-3") + (version "1.6-4") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y")))) + "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -5161,14 +5161,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a")))) + "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") @@ -6921,14 +6921,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "2.9-23") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh")))) + "0z4qh3ag1iyly4zjvzi3x2namkndkqn3cjb3ac22xd11sq5gdgiz")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -7489,14 +7489,14 @@ multiple-imputation datasets.") (define-public r-magick (package (name "r-magick") - (version "2.1") + (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg")))) + "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -7927,14 +7927,14 @@ Cohen (1988).") (define-public r-libcoin (package (name "r-libcoin") - (version "1.0-4") + (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 (base32 - "1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i")))) + "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) (home-page "https://cran.r-project.org/web/packages/libcoin") @@ -7947,14 +7947,14 @@ and permutation inference in the framework of Strasser and Weber (1999).") (define-public r-coin (package (name "r-coin") - (version "1.3-0") + (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 - "1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd")))) + "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin) @@ -8518,14 +8518,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f")))) + "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) @@ -8696,14 +8696,14 @@ analysing multivariate abundance data in community ecology.") (define-public r-afex (package (name "r-afex") - (version "0.24-1") + (version "0.25-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 - "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455")))) + "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) @@ -8930,14 +8930,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.100.26") + (version "0.100.30") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271")))) + "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -9325,6 +9325,51 @@ in-memory raw vectors.") ;; Either of these two license versions. (license (list license:gpl2 license:gpl3)))) +(define-public r-nlp + (package + (name "r-nlp") + (version "0.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "NLP" version)) + (sha256 + (base32 + "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w")))) + (properties `((upstream-name . "NLP"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/NLP/") + (synopsis "Natural language processing infrastructure") + (description + "This package provides basic classes and methods for Natural Language +Processing.") + (license license:gpl3))) + +(define-public r-tm + (package + (name "r-tm") + (version "0.7-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "tm" version)) + (sha256 + (base32 + "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r")))) + (properties `((upstream-name . "tm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-nlp" ,r-nlp) + ("r-rcpp" ,r-rcpp) + ("r-slam" ,r-slam) + ("r-xml2" ,r-xml2))) + (home-page "http://tm.r-forge.r-project.org/") + (synopsis "Text mining package") + (description + "This package provides a framework for text mining applications within R.") + (license license:gpl3))) + (define-public r-waveslim (package (name "r-waveslim") @@ -9364,7 +9409,10 @@ pairs (Selesnick 2001, 2002).") (build-system r-build-system) (propagated-inputs `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ;; The "tm" package is only "suggested" according to CRAN, but the + ;; wordcloud package cannot be loaded without it. + ("r-tm" ,r-tm))) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description @@ -10749,14 +10797,14 @@ Differences with other sparse matrix packages are: (define-public r-fields (package (name "r-fields") - (version "9.8-3") + (version "9.8-6") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 (base32 - "1q9x68dczjym56v7x90x4x5br59vj3dww6w8v42zd3yl17h7c1h1")))) + "07x95vk1idjfzi5ikn0ijal754mssdmgr1p4nswmx9w3i5ndcqaz")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps) @@ -11786,14 +11834,14 @@ select colors to use in your R code.") (define-public r-ggextra (package (name "r-ggextra") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "ggExtra" version)) (sha256 (base32 - "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b")))) + "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj")))) (properties `((upstream-name . "ggExtra"))) (build-system r-build-system) (propagated-inputs @@ -11801,6 +11849,7 @@ select colors to use in your R code.") ("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-miniui" ,r-miniui) + ("r-r6" ,r-r6) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-shinyjs" ,r-shinyjs))) @@ -11900,14 +11949,14 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-4") + (version "0.6-5") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g")))) + "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -12189,14 +12238,14 @@ network.") (define-public r-apcluster (package (name "r-apcluster") - (version "1.4.7") + (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 - "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s")))) + "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -12347,17 +12396,17 @@ extensions.") (define-public r-wgaim (package (name "r-wgaim") - (version "1.4-11") + (version "2.0-0") (source (origin (method url-fetch) (uri (cran-uri "wgaim" version)) (sha256 (base32 - "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg")))) + "0wnb10vibgq8h1ly6lq8kzymf30vx0j0g8fc2zidblbvwag9ka1g")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) + `(("r-ggplot2" ,r-ggplot2) ("r-qtl" ,r-qtl))) (home-page "https://cran.r-project.org/web/packages/wgaim") (synopsis "Whole genome average interval mapping for QTL detection") @@ -12566,14 +12615,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.6-3") + (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "0kx640h60s3zzkdr302asap7diap6vri6d41scnx507yvkcqiph3")))) + "1jz0mzd78sdfxkhqw041ji50hmhjk2ha55i31yjvz35nsw30lwi5")))) (build-system r-build-system) (inputs `(("udunits" ,udunits))) @@ -13121,14 +13170,14 @@ exact test for Hardy-Weinberg equilibrium.") (define-public r-tdthap (package (name "r-tdthap") - (version "1.1-9") + (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "tdthap" version)) (sha256 (base32 - "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r")))) + "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tdthap/") (synopsis "TDT tests for extended haplotypes") @@ -13164,13 +13213,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.12") + (version "0.13") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq")))) + "15r9scgnq68hmfcfxvjk286hpbr825bib1d2kgh0lv3dgz2i2bg1")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -13764,14 +13813,14 @@ sets of URLs.") (define-public r-ggforce (package (name "r-ggforce") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 - "118qyzy8h9kkkdpjd09667gxgw7xy1kbc8r87pswh54ixn8hymwk")))) + "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -14616,14 +14665,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-dalex (package (name "r-dalex") - (version "0.4.4") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r")))) + "0iiwkf0pfdb90lf1xhv43qd32z3cjmkmf0ly9841n5lldkjazy3h")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) @@ -14642,14 +14691,14 @@ and model output.") (define-public r-enrichr (package (name "r-enrichr") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 - "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz")))) + "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs @@ -14812,17 +14861,18 @@ easily.") (define-public r-umap (package (name "r-umap") - (version "0.2.2.0") + (version "0.2.3.1") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 - "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31")))) + "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) + `(("r-openssl" ,r-openssl) + ("r-rcpp" ,r-rcpp) ("r-reticulate" ,r-reticulate) ("r-rspectra" ,r-rspectra))) (home-page "https://github.com/tkonopka/umap") @@ -14993,6 +15043,32 @@ radius searches and @code{bd} as well as @code{kd} trees. The distance is computed using the L1 (Manhattan, taxicab) metric.") (license license:gpl3+))) +(define-public r-leiden + (package + (name "r-leiden") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "leiden" version)) + (sha256 + (base32 + "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp")))) + (properties `((upstream-name . "leiden"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-reticulate" ,r-reticulate))) + (home-page "https://github.com/TomKellyGenetics/leiden") + (synopsis "R implementation of Leiden clustering algorithm") + (description + "This package implements the Python @code{leidenalg} module to be called +in R. It enables clustering using the Leiden algorithm for partitioning a +graph into communities. See also Traag et al (2018) \"From Louvain to Leiden: +guaranteeing well-connected communities.\" <arXiv:1810.08473>.") + (license license:gpl3))) + (define-public r-patchwork ;; There has been no public release yet. (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242") |