diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 357 |
1 files changed, 201 insertions, 156 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5c01a4ae06..cc879be99c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -39,6 +39,7 @@ #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages autotools) #:use-module (gnu packages bash) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -75,7 +76,7 @@ (define-public pspp (package (name "pspp") - (version "1.0.1") + (version "1.2.0") (source (origin (method url-fetch) @@ -83,7 +84,7 @@ version ".tar.gz")) (sha256 (base32 - "1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s")))) + "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5")))) (build-system gnu-build-system) (inputs `(("cairo" ,cairo) @@ -94,11 +95,15 @@ ("readline" ,readline) ("gtk" ,gtk+) ("gtksourceview" ,gtksourceview) + ("spread-sheet-widget" ,spread-sheet-widget) ("zlib" ,zlib))) (native-inputs - `(("glib" ,glib "bin") ;for glib-genmarshal + `(("autoconf" ,autoconf) ;for tests + ("glib" ,glib "bin") ;for glib-genmarshal ("perl" ,perl) - ("pkg-config" ,pkg-config))) + ("pkg-config" ,pkg-config) + ("python" ,python-2) ;for tests + ("texinfo" ,texinfo))) (home-page "https://www.gnu.org/software/pspp/") (synopsis "Statistical analysis") (description @@ -110,13 +115,43 @@ can be imported from spreadsheets, text files and database sources and it can be output in text, PostScript, PDF or HTML.") (license license:gpl3+))) +(define-public jags + (package + (name "jags") + (version "4.3.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/" + (version-major version) ".x/Source/" + "JAGS-" version ".tar.gz")) + (sha256 + (base32 + "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica")))) + (build-system gnu-build-system) + (home-page "http://mcmc-jags.sourceforge.net/") + (native-inputs + `(("gfortran" ,gfortran) + ("lapack" ,lapack))) + (synopsis "Gibbs sampler") + (description "JAGS is Just Another Gibbs Sampler. It is a program for +analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) +simulation not wholly unlike BUGS. JAGS was written with three aims in mind: + +@enumerate +@item To have a cross-platform engine for the BUGS language; +@item To be extensible, allowing users to write their own functions, + distributions and samplers; +@item To be a platform for experimentation with ideas in Bayesian modelling. +@end enumerate\n") + (license license:gpl2))) + ;; Update this package together with the set of recommended packages: r-boot, ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. (define r-with-tests (package (name "r-with-tests") - (version "3.5.0") + (version "3.5.1") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -124,7 +159,7 @@ be output in text, PostScript, PDF or HTML.") version ".tar.gz")) (sha256 (base32 - "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx")))) + "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -339,14 +374,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-50") + (version "7.3-51.1") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "16hasv9k4n773jsyzvh8s3gbga49hwdj8n5hxij6zqisy4i0kxq6")))) + "14907ia8418mp3p1rs1i2f1x5b6kk5z998dk353a29j3xqf3ybyq")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -467,13 +502,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) (define-public r-lattice (package (name "r-lattice") - (version "0.20-35") + (version "0.20-38") (source (origin (method url-fetch) (uri (cran-uri "lattice" version)) (sha256 (base32 - "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88")))) + "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx")))) (build-system r-build-system) (home-page "http://lattice.r-forge.r-project.org/") (synopsis "High-level data visualization system") @@ -487,14 +522,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.2-14") + (version "1.2-15") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "15hknim84nj3f54vkchca5ac0c3ip15v1by18k5parmn8wsl19j9")))) + "1mshhyia6imh939p8labxi0wv21lal7csmccxi42klpgdh1j89kv")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -532,14 +567,14 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-24") + (version "1.8-25") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "15b76m1f0hz8dbmj9shqvslihdx5b7c48vck9grj5xs1z2y45r9c")))) + "1y2rq6v45pr2wcxihhgmingcdvcsilim2cvskrlb7k2n00qg6v2q")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -614,14 +649,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "2.42-6") + (version "2.43-1") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "1bsxc2fir9pbvdzy9n474fkl7har606h9zhspp0z67wnjpp48g73")))) + "0220fjsq4ycx1n5zc5h39wdbj5j6xr8rzqbcixx2p25akzdn7kqk")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -725,13 +760,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.16") + (version "0.6.18") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "1lhs59pdjhpb63jyy98pi1shk9shw044k6vl0mvw0f40v08326ar")))) + (base32 "0k3iv0r8wy8w7zchmgrnrqv3bc149075j4817kf0q521vi4f6vbj")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -960,14 +995,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1sgg4krw03qkz1n4dwiya0djggk7giwd0w21qlp0pfjqi0rxq6qx")))) + "1y46xab7g1lsjmilp4hbl7pjad6pcxp66hdj8wnfdg9518h0lmq1")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -1033,19 +1068,17 @@ using just two functions: melt and dcast (or acast).") (define-public r-scales (package (name "r-scales") - (version "0.5.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 - (base32 "0zg9wfzmsdjxpbld0nzv7hcpq5r0wazqxmn7grvvif2agj0w1z6v")))) + (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc")))) (build-system r-build-system) (propagated-inputs - `(("r-dichromat" ,r-dichromat) - ("r-labeling" ,r-labeling) + `(("r-labeling" ,r-labeling) ("r-munsell" ,r-munsell) - ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-r6" ,r-r6) @@ -1061,13 +1094,13 @@ legends.") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.0.0") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "0kb977hizsvk3b1k3zr717q78bpmbabhl8cj9a3w717nkq1zas67")))) + (base32 "1msy36r21nlmnpyaw2m9k0ykmnd19b9il01b65w457pfw75prrs9")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -1251,16 +1284,14 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.10.1") + (version "0.12") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9")))) + "11rpn40153kcvqqrfhg2ldqfs68frg6yzsl0k3rxnlnv4c0v008g")))) (build-system r-build-system) - (propagated-inputs - `(("r-stringr" ,r-stringr))) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") (description @@ -1312,13 +1343,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw")))) + "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") @@ -1356,13 +1387,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.1.19") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "04bzrnfgbpk0rhkvzwp3k3ip7jpq26bjxz71bx5mwxmcjdb07nz5")))) + "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") @@ -1425,13 +1456,13 @@ from knitr Rmarkdown.") (define-public r-microbenchmark (package (name "r-microbenchmark") - (version "1.4-4") + (version "1.4-6") (source (origin (method url-fetch) (uri (cran-uri "microbenchmark" version)) (sha256 (base32 - "0fv2w2vsiz18imf4115nd9chhmf275w2mb49pn7pkxi6z3bamc9c")))) + "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/microbenchmark/") (synopsis "Accurate timing functions for R") @@ -1528,13 +1559,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "155l53kb69jga5d8c5nvdwqlvlgfmk4vzyyl4d0108j53jnlgh1v")))) + "1cafy5xsjx6m08s45456mjsal7mfxzwpbrds0p4z3gwam948gpzy")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -1555,13 +1586,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.2.2") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8")))) + "1jgshp0x8a65rwyvk31slnfp7l153dk5826y2rxcd5lpclby3d85")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") @@ -1577,13 +1608,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.2.2") + (version "0.3.0.1") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "0cqd894wzi53rs53prg0j7i75h0yzgi0127fzjqbdbhczwh984f9")))) + "0j7kp6h25wbkvpzr7dpc0zgdpjiwsjjlgprj3mv7bgfalfq1si99")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1619,13 +1650,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.7.6") + (version "0.7.8") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0c43h13s5mr0fklikbbm89gs6z5n66rkjzdv6w3w6kl5af5wr2fl")))) + "06p59nhli8c1sarghzxq0y4pk6lyyz3xwkarp55b252dfg2rly9p")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -1656,14 +1687,14 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "1nwrls9c3kc9q7405jp6b9sh23642sz13yw55iikgw134shffj5k")))) + "0j5w6a1qim972kv4vmvinp3j50yr4idmm9cd3w7y3zsz0nq0nhcx")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -1751,13 +1782,13 @@ and density estimation.") (define-public r-chron (package (name "r-chron") - (version "2.3-52") + (version "2.3-53") (source (origin (method url-fetch) (uri (cran-uri "chron" version)) (sha256 (base32 - "185lfp75cv3l4cavg64sccj8lgc5sivch13n6gkannv3pd5cyzy4")))) + "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/chron") (synopsis "Chronological R objects which can handle dates and times") @@ -1769,13 +1800,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.11.4") + (version "1.11.8") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "1mc1drqj5i5ar2za3nkh5j70y37s7z7xwqri2r2b72zkqggg3k7x")))) + "1nb6wngrk1a30m984524gf26fa1nwgyf4y4an94dibcwb5jp8hnw")))) (build-system r-build-system) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") @@ -1789,17 +1820,17 @@ and fast file reading.") (define-public r-xtable (package (name "r-xtable") - (version "1.8-2") + (version "1.8-3") (source (origin (method url-fetch) (uri (cran-uri "xtable" version)) (sha256 (base32 - "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn")))) + "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "http://xtable.r-forge.r-project.org/") (synopsis "Export R tables to LaTeX or HTML") (description @@ -1845,14 +1876,14 @@ building design matrices.") (define-public python-statsmodels (package (name "python-statsmodels") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (pypi-uri "statsmodels" version)) (sha256 (base32 - "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6")))) + "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4")))) (build-system python-build-system) (arguments `(;; The test suite is very large and rather brittle. Tests often fail @@ -1871,18 +1902,7 @@ building design matrices.") (("import matplotlib\\.pyplot as plt" line) (string-append "import matplotlib;matplotlib.use('Agg');" line))) - #t)) - ;; FIXME: This is a bug in version 0.8 since the upgrade to scipy 1.0. - ;; See https://github.com/statsmodels/statsmodels/issues/3931 - ;; This has been fixed in version 0.9. - (add-after 'unpack 'patch-for-scipy - (lambda _ - (substitute* "statsmodels/discrete/discrete_model.py" - (("return stats.chisqprob" match) - (string-append - "stats.chisqprob = lambda chisq, df: stats.chi2.sf(chisq, df);" - match))) - #t))))) + #t))))) (propagated-inputs `(("python-numpy" ,python-numpy) ("python-scipy" ,python-scipy) @@ -1915,13 +1935,13 @@ inference for statistical models.") (define-public r-coda (package (name "r-coda") - (version "0.19-1") + (version "0.19-2") (source (origin (method url-fetch) (uri (cran-uri "coda" version)) (sha256 (base32 - "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl")))) + "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -1936,14 +1956,14 @@ chain.") (define-public r-ade4 (package (name "r-ade4") - (version "1.7-11") + (version "1.7-13") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 - "0wm54wcpn87rdh6vyw04cr8vgba899y6jsl61f22bmlvx6d7kkac")))) + "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -2214,14 +2234,14 @@ other packages.") (define-public r-commonmark (package (name "r-commonmark") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 - "1jwx5rgm0ypd9a3v4jd9za4a644rdzhk1n4dvmgkj9hdpwsida3z")))) + "1xymqncf8byqxzpx64zlp6vbx7gry572jkr2ax0zlavr8bli861x")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") @@ -2237,24 +2257,28 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "6.0.1") + (version "6.1.1") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj")))) + "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd")))) (build-system r-build-system) (propagated-inputs `(("r-brew" ,r-brew) ("r-commonmark" ,r-commonmark) ("r-desc" ,r-desc) ("r-digest" ,r-digest) + ("r-pkgload" ,r-pkgload) + ("r-purrr" ,r-purrr) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/klutometis/roxygen") (synopsis "In-source documentation system for R") (description @@ -2265,14 +2289,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.0.2") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1djfpnphkcxx8idk5rjfzg8r8dnqsgc0shh2pw8lns5hap2wc5rc")))) + "0ldxgcr33lawwr8wp14kdk2678gpkvqkzv6g333bhck1hn6qspzv")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) @@ -2320,13 +2344,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.21.0") + (version "0.23.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "11xgddmxzh9cy85k8fb90il43qswpvryz0h9r0j1gbclfg2f9004")))) + "01250jz255fnyy2ap90nskvzhd8nhlmbhwgpvb43mk1fax077lrz")))) (build-system r-build-system) ;; This R package contains modified sources of libgit2. This modified ;; version of libgit2 is built as the package is built. Hence libgit2 is @@ -2335,6 +2359,8 @@ functions make it easy to control additional request components.") `(("libssh2" ,libssh2) ("openssl" ,openssl) ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/ropensci/git2r") (synopsis "Access Git repositories with R") (description @@ -2346,13 +2372,13 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5")))) + "0d6r0in13k0rcyr6asanwy0a9dv4lizq6l2w913rr222pq6vrrck")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") @@ -2364,22 +2390,29 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.13.6") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "1d9n49djydywfyp9w3njgxs5lag4ac7719wmxy1lkgcmn3l9sx5r")))) + "1nyspqicn9zd1rgq3k07b3179i8w5ys6jbd65g9q8qczrb7z3x8f")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) + `(("r-callr" ,r-callr) + ("r-cli" ,r-cli) + ("r-digest" ,r-digest) ("r-git2r" ,r-git2r) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-memoise" ,r-memoise) + ("r-pkgbuild" ,r-pkgbuild) + ("r-pkgload" ,r-pkgload) + ("r-rcmdcheck" ,r-rcmdcheck) + ("r-remotes" ,r-remotes) ("r-rstudioapi" ,r-rstudioapi) - ("r-whisker" ,r-whisker) + ("r-sessioninfo" ,r-sessioninfo) + ("r-usethis" ,r-usethis) ("r-withr" ,r-withr))) (home-page "https://github.com/hadley/devtools") (synopsis "Tools to make developing R packages easier") @@ -2455,13 +2488,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.7-2") + (version "3.7-4") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "0hx3xv94gzlyy7ny5k4mzs7w1798h1zka175m5bkzc524493cm88")))) + "1hs0zwaqs34559girinvysjfbvznyn8znp9cwvkqx6k2cqvcjinj")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2514,13 +2547,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.8.500.0") + (version "0.9.200.4.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1sh36dx6inmb56m40nigy94gxlgjva816qnlmjwg7y2bdvqj8vsi")))) + "1ayvpyi4hgaqrhx1kqi640iillc2byj4kam7vydlgqmdrzpgrfvz")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs @@ -2629,11 +2662,7 @@ certain criterion, e.g., it contains a certain regular file.") ("r-stringr" ,r-stringr) ("r-tinytex" ,r-tinytex) ("r-yaml" ,r-yaml) - ;; rmarkdown works with the 2.x release of Pandoc, but with degraded - ;; functionality. For example, tabbed plots do not currently work with - ;; Pandoc 2. The authors of rmarkdown recommend the use of Pandoc 1 - ;; for the time being. - ("ghc-pandoc" ,ghc-pandoc-1))) + ("ghc-pandoc" ,ghc-pandoc))) (home-page "http://rmarkdown.rstudio.com") (synopsis "Convert R Markdown documents into a variety of formats") (description @@ -2799,13 +2828,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.11") + (version "3.98-1.16") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "18izvlg2x9mzr6yb3yf02ghwbyn00frki3av4lpc44r22m4djnsh")))) + "0nl1kk354r8snhj6p9mc74m7awvqc6akmd4y3a46y78yv3g15njp")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -2942,13 +2971,13 @@ multiple breakpoints are allowed.") (define-public r-snow (package (name "r-snow") - (version "0.4-2") + (version "0.4-3") (source (origin (method url-fetch) (uri (cran-uri "snow" version)) (sha256 (base32 - "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf")))) + "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/snow") (synopsis "Support for simple parallel computing in R") @@ -3034,14 +3063,14 @@ parallel.") (define-public r-doparallel (package (name "r-doparallel") - (version "1.0.11") + (version "1.0.14") (source (origin (method url-fetch) (uri (cran-uri "doParallel" version)) (sha256 (base32 - "0sppgxk3d8mfsrb3cjdyn0mv0s4i7pcy8g8c3cjzbr6k8vmx5jsc")))) + "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb")))) (properties `((upstream-name . "doParallel"))) (build-system r-build-system) (propagated-inputs @@ -3080,13 +3109,13 @@ using the multicore functionality of the parallel package.") (define-public r-dt (package (name "r-dt") - (version "0.4") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix")))) + "1s5d3sld4l8zygpkvprvlbqa0pm2cv1bm7h7p999wxlap28vnnqf")))) (properties `((upstream-name . "DT"))) (build-system r-build-system) @@ -3094,7 +3123,8 @@ using the multicore functionality of the parallel package.") `(("r-crosstalk" ,r-crosstalk) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr))) + ("r-magrittr" ,r-magrittr) + ("r-promises" ,r-promises))) (home-page "http://rstudio.github.io/DT") (synopsis "R wrapper of the DataTables JavaScript library") (description @@ -3257,14 +3287,14 @@ the way current RNG settings can be changed.") (define-public r-rtsne (package (name "r-rtsne") - (version "0.13") + (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "Rtsne" version)) (sha256 (base32 - "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw")))) + "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn")))) (properties `((upstream-name . "Rtsne"))) (build-system r-build-system) (propagated-inputs @@ -3281,14 +3311,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.6-8") + (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn")))) + "0fk4pw67cw1663d0n9rf1qfdqzz8k5nqkjgp3hi5jr422qp9lsck")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class))) @@ -3459,13 +3489,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x")))) + "0cxhn14a57x4gcyrwpfz1d6dw4xh0jcpqkb33hx8imnr340blh7n")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs @@ -3507,13 +3537,13 @@ persistent (on the file system).") (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.42.0") + (version "0.43.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "1zcq0hzi0j7fvj2rs796a1i120wbr0387vck17rrd644awwbsbm0")))) + "0ax6781kfylx0acz0i3sqnpkxmrq73x29wwfic59ng7vj0ws0gyd")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (propagated-inputs @@ -3558,13 +3588,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.53.1") + (version "0.54.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0bkiz5fm09d3512mfr2ymj9qsb1b8aic5l5m6fkaf5j7nsgvqw6z")))) + "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (native-inputs @@ -3634,14 +3664,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw")))) + "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw")))) (build-system r-build-system) (propagated-inputs `(("r-glue" ,r-glue) @@ -3660,14 +3690,14 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "0.8.1") + (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "0485f19mkkglc4bv57y6bm6l9rfgd878hsz2xdg1nwgbqchjhgix")))) + "03s9dv6c2dj65a769h8fgy9878y46rdq7x65i53kd44kag80i9cr")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3739,13 +3769,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.7.1") + (version "4.8.0") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w")))) + "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -3761,8 +3791,10 @@ features present in other programming languages.") ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) + ("r-promises" ,r-promises) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) @@ -3844,14 +3876,14 @@ character vector.") (define-public r-googlesheets (package (name "r-googlesheets") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "googlesheets" version)) (sha256 (base32 - "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b")))) + "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) @@ -3861,6 +3893,7 @@ character vector.") ("r-purrr" ,r-purrr) ("r-readr" ,r-readr) ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) (home-page "https://github.com/jennybc/googlesheets") @@ -4023,14 +4056,14 @@ hierarchical clustering dendrograms.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1afar1z7959v7mbzsqa77vqfh0yc7y3nv5ayx71485a8scwsfwbk")))) + "0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -4088,14 +4121,14 @@ Zurich, including many that are related to graphics.") (define-public r-gtools (package (name "r-gtools") - (version "3.5.0") + (version "3.8.1") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 - "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6")))) + "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505")))) (build-system r-build-system) (arguments `(#:phases @@ -4228,13 +4261,13 @@ mechanism.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-2") + (version "1.8-4") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "1lpwigxmi5sc23xrha4gcsccsm4yfsg0sa97y6vac3pg1lliblvx")))) + "1pywcp86kqijdrvl42qwdy75szrag9pzj0p88zbrj2r1klb8rn5i")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -4248,14 +4281,22 @@ series of numeric vectors/matrices and factors.") (define-public r-ztable (package (name "r-ztable") - (version "0.1.8") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "ztable" version)) (sha256 (base32 - "1hk5k9614n52dpfrhdws06w4gvwhnz8q47x4cwxx88qmrzm8z2m3")))) + "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy")))) (build-system r-build-system) + (propagated-inputs + `(("r-flextable" ,r-flextable) + ("r-magrittr" ,r-magrittr) + ("r-moonbook" ,r-moonbook) + ("r-officer" ,r-officer) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) (home-page "https://cran.r-project.org/web/packages/ztable") (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") (description @@ -4350,19 +4391,20 @@ data at that region, and avoids over-plotting.") (define-public r-ggthemes (package (name "r-ggthemes") - (version "3.5.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggthemes" version)) (sha256 (base32 - "0drbzzb4i5jq1579fx1wmgh87ybnswjn7srak2l8g771ip49xwb8")))) + "0y6570wv135sf7pv57l7bqilzw47rziaqx4vsk45pf1w4lmj0w8b")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-colorspace" ,r-colorspace) - ("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + `(("r-ggplot2" ,r-ggplot2) + ("r-purrr" ,r-purrr) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble))) (home-page "https://cran.rstudio.com/web/packages/ggthemes") (synopsis "Extra themes, scales and geoms for @code{ggplot2}") (description "This package provides extra themes and scales for @@ -4401,13 +4443,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.5.1") + (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm")))) + "1r6rivh9ba4gwnzryip0aiwsbm46zma7nvd9z5y456p2dgzp9lii")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) @@ -4653,14 +4695,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.1") + (version "5.4.2") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "1vcl4nl8by2vj2k9k84imy5m850khkgd8q02a8ica1h8vz9ijgn4")))) + "09152swfpa3fzhmrq5cwb5kxgvrxvigv1m4v6rhcibrdhfd1x8x4")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4723,14 +4765,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.93-0") + (version "0.93-3") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "130pzibn5cb8mycv8byc6npzcpddghz8m7jqwk15qmx4g3cj8zgy")))) + "1nqh1qg1qd1qrxl1w585dqx7ql55qzjny1r4f9hqxpwd7lml07cc")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) @@ -4999,18 +5041,19 @@ decompositions of such matrices, and solutions of linear systems.") (define-public r-modelmetrics (package (name "r-modelmetrics") - (version "1.1.0") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "ModelMetrics" version)) (sha256 (base32 - "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8")))) + "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6")))) (properties `((upstream-name . "ModelMetrics"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-rcpp" ,r-rcpp) + ("r-data-table" ,r-data-table))) (home-page "https://cran.r-project.org/web/packages/ModelMetrics") (synopsis "Rapid calculation of model metrics") (description @@ -5071,17 +5114,19 @@ expected shortfall risk are also included.") (define-public r-nloptr (package (name "r-nloptr") - (version "1.0.4") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 - "1sz1xj3785x4vsm4nd6in298bk32hs2jk5nsxma7ivxi7jcmn8l4")))) + "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz")))) (build-system r-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("r-knitr" ,r-knitr) ; for building vignettes + ("pkg-config" ,pkg-config) + ("gfortran" ,gfortran))) (inputs `(("nlopt" ,nlopt))) (home-page "https://cran.r-project.org/web/packages/nloptr") @@ -5097,14 +5142,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-18-1") + (version "1.1-19") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "01ar4fak8zj7c1vmh9m576wchxj5qzpfqn637s7fh3fl6cpz0alq")))) + "0j8xhkkcdv45ilab960s9jrcjk6jbzvd7w7myswv5fmalrpq52pf")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -5152,14 +5197,14 @@ bootstrap test for generalized linear mixed models.") (define-public r-cardata (package (name "r-cardata") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "carData" version)) (sha256 (base32 - "193pdwgw6gk19v7swk1kwphg3vqdmpsgi555g9nyz93sa39j7r8j")))) + "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v")))) (properties `((upstream-name . "carData"))) (build-system r-build-system) (home-page "https://r-forge.r-project.org/projects/car/") @@ -5172,14 +5217,14 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 (base32 - "0rdk7hgahs38j6yv861i31wpmsmyvksxcv8jarvvcjl60whizhb2")))) + "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) @@ -5299,14 +5344,14 @@ first and second order derivatives.") (define-public r-sn (package (name "r-sn") - (version "1.5-2") + (version "1.5-3") (source (origin (method url-fetch) (uri (cran-uri "sn" version)) (sha256 (base32 - "16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig")))) + "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc")))) (build-system r-build-system) (propagated-inputs `(("r-mnormt" ,r-mnormt) |