diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 255 |
1 files changed, 200 insertions, 55 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 96044e114a..fa71035796 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -36,7 +36,9 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) #:use-module (gnu packages statistics) + #:use-module (gnu packages tls) #:use-module (gnu packages web)) (define-public r-tidyverse @@ -167,21 +169,18 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1k3mflgn10hcvy74y4pbigpv74zb66fz1phfd3c8isqmn88xbxzi")))) + "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon) - ("r-debugme" ,r-debugme) - ("r-r6" ,r-r6) - ("r-testthat" ,r-testthat))) + `(("r-r6" ,r-r6) + ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") (description @@ -316,14 +315,14 @@ and several other tools.") (define-public r-abbyyr (package (name "r-abbyyr") - (version "0.5.1") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "abbyyR" version)) (sha256 (base32 - "1s8zf18sh0s89vk3dl09fzrq50csmmfvmsanf5vfkv9n5lx6pklg")))) + "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx")))) (properties `((upstream-name . "abbyyR"))) (build-system r-build-system) (propagated-inputs @@ -427,13 +426,13 @@ error stream.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.16") + (version "0.12.17") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1rm8hcy72p1jvxikvmkwg20pjqmvmfvqb45lfghmddp2adp67qfl")))) + (base32 "08xg8h3w25sdb3xr18g9pa0x8cirkdgljqapxmw56ss1j9fc89s2")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -729,14 +728,14 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "2.2-13") + (version "2.2-14") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb")))) + "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) (home-page "http://ff.r-forge.r-project.org/") @@ -843,23 +842,26 @@ package also provides a C++ API, that works with or without Rcpp.") (define-public r-ggally (package (name "r-ggally") - (version "1.3.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 - "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l")))) + "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) + (inputs + `(("libressl" ,libressl))) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape))) + ("r-reshape" ,r-reshape) + ("r-rlang" ,r-rlang))) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description @@ -1077,13 +1079,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.14") + (version "0.3.15") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x")))) + "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -1122,14 +1124,14 @@ classes in the @code{stats4} package.") (define-public r-emdbook (package (name "r-emdbook") - (version "1.3.9") + (version "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 - "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69")))) + "0880cx6rqm9vgd2zxnd2k0igfl80gy7ak15w36clwlzavab59hmv")))) (build-system r-build-system) (propagated-inputs `(("r-bbmle" ,r-bbmle) @@ -1234,14 +1236,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-2") + (version "1.7-4") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p")))) + "12skvlridfq4jd5mh0yxl79ps0zi2xnlh4hsdgxad0gm7qky8awd")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -1315,14 +1317,14 @@ samples.") (define-public r-cvst (package (name "r-cvst") - (version "0.2-1") + (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "CVST" version)) (sha256 (base32 - "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2")))) + "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5")))) (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs @@ -1774,14 +1776,14 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618")))) + "1m3p84d6nh9mzzvxb82vgig3ngcvkz86rjwzl9a66ckdf5p611k3")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -1841,23 +1843,98 @@ can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.") (license license:gpl3+))) +(define-public r-jomo + (package + (name "r-jomo") + (version "2.6-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "jomo" version)) + (sha256 + (base32 + "0zyqwa2y08asj9xqwnngh6da1b9cqcx8pzc9cxwrmgnxd5nnsjb7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lme4" ,r-lme4) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/jomo/") + (synopsis "Multilevel Joint Modelling Multiple Imputation") + (description + "Similarly to Schafer's package pan, jomo is a package for multilevel +joint modelling multiple imputation @url{Carpenter and Kenward (2013), +http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the +possibility of handling binary and categorical data through latent normal +variables, the option to use cluster-specific covariance matrices and to +impute compatibly with the substantive model.") + (license license:gpl2))) + +(define-public r-pan + (package + (name "r-pan") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "pan" version)) + (sha256 + (base32 + "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/pan/") + (synopsis "Multiple imputation for multivariate panel or clustered data") + (description + "This package implements multiple imputation for multivariate panel or +clustered data.") + (license license:gpl3))) + +(define-public r-mitml + (package + (name "r-mitml") + (version "0.3-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "mitml" version)) + (sha256 + (base32 + "1s888r9y2ri39b48h1iypps6lddqkqv3g31l2sjmi2pvyccfpkwb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-haven" ,r-haven) + ("r-jomo" ,r-jomo) + ("r-pan" ,r-pan))) + (home-page "https://cran.r-project.org/web/packages/mitml/") + (synopsis "Tools for multiple imputation in multilevel modeling") + (description + "This package provides tools for multiple imputation of missing data in +multilevel modeling. It includes a user-friendly interface to the packages +pan and jomo, and several functions for visualization, data management and the +analysis of multiply imputed data sets.") + (license license:gpl2+))) + (define-public r-mice (package (name "r-mice") - (version "2.46.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax")))) + "1p8a5ham90iaak4w17114pdnw535r2l9sxr402yrkc4gbwfbpdlq")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) + ("r-mitml" ,r-mitml) ("r-nnet" ,r-nnet) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-rpart" ,r-rpart) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/mice/") @@ -1923,14 +2000,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.5.9") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz")))) + "16n8qanxx0p5ny5zqxafn8hwb1xv94y1wig1iql8as5a5qh8lwcz")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -1955,14 +2032,14 @@ acceptance regions, log-ratio plots and Q-Q plots.") (define-public r-sm (package (name "r-sm") - (version "2.2-5.4") + (version "2.2-5.5") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 - "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9")))) + "1rw2mxygxsmk8mn4wag1ppjgzk0rlvh6zd8q02qrhjrn9jhi5qj3")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") @@ -2146,14 +2223,14 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).") (define-public r-ica (package (name "r-ica") - (version "1.0-1") + (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "ica" version)) (sha256 (base32 - "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq")))) + "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ica/") (synopsis "Independent component analysis") @@ -2166,14 +2243,14 @@ of Eigenmatrices} (JADE).") (define-public r-dtw (package (name "r-dtw") - (version "1.18-1") + (version "1.20-1") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 - "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr")))) + "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3")))) (build-system r-build-system) (propagated-inputs `(("r-proxy" ,r-proxy))) (home-page "http://dtw.r-forge.r-project.org/") @@ -2256,14 +2333,14 @@ plots in @code{ggplot2}.") (define-public r-ggjoy (package (name "r-ggjoy") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggjoy" version)) (sha256 (base32 - "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb")))) + "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2341,20 +2418,20 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "2.0.0.1") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 - "0yw23lp9xjvbpswzghkmjiayw7p19hbvmgv58k3i6b8g5nav4qcg")))) + "0wjr3cqwvnjxbvln25szffmkns5w0xysivdjr6chxap4nh515b0i")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-crayon" ,r-crayon) - ("r-debugme" ,r-debugme) - ("r-r6" ,r-r6))) + ("r-r6" ,r-r6) + ("r-testthat" ,r-testthat))) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description @@ -2551,14 +2628,14 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3")))) + "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) (build-system r-build-system) (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") @@ -2571,14 +2648,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1kmqvny3rw4p5kgxz6mhqfpp7j3nnpp22dfai4kjrr2cfmj6wvb7")))) + "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -3263,18 +3340,19 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.2.1") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9")))) + "1hqgszbiv99dibhwr21v21ll4s2hjn3ccqdicsm0z3gk77bh8iyb")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs - `(("r-shiny" ,r-shiny))) + `(("r-shiny" ,r-shiny) + ("r-jsonlite" ,r-jsonlite))) (home-page "http://cran.r-project.org/web/packages/shinyAce") (synopsis "Ace editor bindings for Shiny") (description @@ -3384,14 +3462,14 @@ It also includes interpolation functions.") (define-public r-psych (package (name "r-psych") - (version "1.8.3.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "1zhp8j81nkzd65168zdw9ylypb9n07ajan21x0wqcn8jdbg970sg")))) + "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -3766,19 +3844,41 @@ measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.") (license license:gpl3+))) +(define-public r-zip + (package + (name "r-zip") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "zip" version)) + (sha256 + (base32 + "0rgr9pcdhdq3k8n29h2ircp3ri1ibhrx81gja1y7331v15xyrabg")))) + (build-system r-build-system) + (home-page "https://github.com/gaborcsardi/zip") + (synopsis "Cross-platform Zip compression") + (description + "This package provides a cross-platform Zip compression library for R. +It is a replacement for the @code{zip} function, that does not require any +additional external tools on any platform.") + (license license:cc0))) + (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.0.17") + (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "1mq4lasp12kc30sxcsmz9gskd114l8s7z7wd6svv2nm8qllrhsqi")))) + "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-zip" ,r-zip))) (home-page "https://github.com/awalker89/openxlsx") (synopsis "Read, write and edit XLSX files") (description @@ -4060,3 +4160,48 @@ bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.") (license license:gpl2))) + +(define-public r-reticulate + (package + (name "r-reticulate") + (version "1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "reticulate" version)) + (sha256 + (base32 + "1ghhc4hbmwpp79ilbdbshynhs61i8sv8z6p1al04jy7ij0lcglxy")))) + (build-system r-build-system) + (inputs `(("python" ,python))) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/rstudio/reticulate") + (synopsis "R interface to Python") + (description + "This package provides an interface from R to Python modules, classes, +and functions. When calling into Python, R data types are automatically +converted to their equivalent Python types. When values are returned from +Python to R they are converted back to R types.") + (license license:asl2.0))) + +(define-public r-bibtex + (package + (name "r-bibtex") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bibtex" version)) + (sha256 + (base32 + "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz")))) + (build-system r-build-system) + (propagated-inputs `(("r-stringr" ,r-stringr))) + (home-page "https://github.com/romainfrancois/bibtex") + (synopsis "Bibtex parser") + (description "This package provides a utility for R to parse a bibtex +file.") + (license license:gpl2+))) |