diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 542 |
1 files changed, 308 insertions, 234 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 41c0668151..ad3032e2ec 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -34,6 +34,7 @@ #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages compression) + #:use-module (gnu packages cran) #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages gtk) @@ -64,7 +65,7 @@ (define-public pspp (package (name "pspp") - (version "0.10.2") + (version "1.0.0") (source (origin (method url-fetch) @@ -72,7 +73,7 @@ version ".tar.gz")) (sha256 (base32 - "1afsq0a3iij64qacczvwhk81qg0q5rfqm055y5h9ls28d6paqz7p")))) + "10yb8nknh33c1y2ji3gww5dcnx9n3nqgsj6yfb4wibdjypa1m68v")))) (build-system gnu-build-system) (inputs `(("cairo" ,cairo) @@ -125,6 +126,13 @@ be output in text, PostScript, PDF or HTML.") "PKG_BUILT_STAMP=1970-01-01") #:phases (modify-phases %standard-phases + (add-before 'configure 'do-not-compress-serialized-files + (lambda* (#:key inputs #:allow-other-keys) + ;; This ensures that Guix can detect embedded store references; + ;; see bug #28157 for details. + (substitute* "src/library/base/makebasedb.R" + (("compress = TRUE") "compress = FALSE")) + #t)) (add-before 'configure 'patch-uname (lambda* (#:key inputs #:allow-other-keys) (let ((uname-bin (string-append (assoc-ref inputs "coreutils") @@ -226,7 +234,6 @@ be output in text, PostScript, PDF or HTML.") ("perl" ,perl) ("pkg-config" ,pkg-config) ("texinfo" ,texinfo) ; for building HTML manuals - ("which" ,which) ; for tests/Examples/base-Ex.R ("tzdata" ,tzdata-2017a) ("xz" ,xz))) (inputs @@ -244,6 +251,7 @@ be output in text, PostScript, PDF or HTML.") ("libxt" ,libxt) ("pcre" ,pcre) ("readline" ,readline) + ("which" ,which) ("zlib" ,zlib))) (native-search-paths (list (search-path-specification @@ -260,17 +268,29 @@ publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.") (license license:gpl3+))) +(define-public rmath-standalone + (package (inherit r-minimal) + (name "rmath-standalone") + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'configure 'chdir + (lambda _ (chdir "src/nmath/standalone/") #t))))) + (synopsis "Standalone R math library") + (description + "This package provides the R math library as an independent package."))) + (define-public r-boot (package (name "r-boot") - (version "1.3-19") + (version "1.3-20") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "16hsw4bw9pkfc2lqxfwycm1sbvbrm4linvm0ci71n8sxc7srvkis")))) + "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -365,14 +385,14 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (define-public r-foreign (package (name "r-foreign") - (version "0.8-67") + (version "0.8-69") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) + "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -427,14 +447,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.2-8") + (version "1.2-10") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "1dyv42d7ranb85y8hvi57hbg5xnvhdzqn56wcq3qmhazqj3s3liw")))) + "0r3qjcz92xwgdzrfz444mqzwnja5sv9abaf252fh6k48qbyahahh")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -472,14 +492,14 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-17") + (version "1.8-18") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "1zj223l4a3j15d3c01wv7dkzn9w6084gxrq5600ck9rvr0lfpwwg")))) + "011mgcypr56xvm9nizsfsb2285kzql93x0d3lzg849g39vbpp4s2")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -621,14 +641,14 @@ binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") (define-public r-bit64 (package (name "r-bit64") - (version "0.9-5") + (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "bit64" version)) (sha256 (base32 - "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg")))) + "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) @@ -644,26 +664,6 @@ interactive data exploration and manipulation and optionally leverage caching.") (license license:gpl2))) -(define-public r-colorspace - (package - (name "r-colorspace") - (version "1.3-2") - (source - (origin - (method url-fetch) - (uri (cran-uri "colorspace" version)) - (sha256 - (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx")))) - (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/colorspace") - (synopsis "Color space manipulation") - (description - "This package carries out a mapping between assorted color spaces -including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar -CIELAB. Qualitative, sequential, and diverging color palettes based on HCL -colors are provided.") - (license license:bsd-3))) - (define-public r-dichromat (package (name "r-dichromat") @@ -812,30 +812,6 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") Munsell colour system.") (license license:expat))) -(define-public r-rcpp - (package - (name "r-rcpp") - (version "0.12.10") - (source - (origin - (method url-fetch) - (uri (cran-uri "Rcpp" version)) - (sha256 - (base32 "108p485agxwgmnl9p54vsyy94w96lcimlk08v71ddm77gfl13y2f")))) - (build-system r-build-system) - (home-page "http://www.rcpp.org") - (synopsis "Seamless R and C++ Integration") - (description - "The Rcpp package provides R functions as well as C++ classes which offer -a seamless integration of R and C++. Many R data types and objects can be -mapped back and forth to C++ equivalents which facilitates both writing of new -code as well as easier integration of third-party libraries. Documentation -about Rcpp is provided by several vignettes included in this package, via the -'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel -and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see -'citation(\"Rcpp\")' for details on these last two.") - (license license:gpl2+))) - (define-public r-permute (package (name "r-permute") @@ -1074,14 +1050,14 @@ aesthetic attributes.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "0l8c4bh6765x9s6rw3mfm1bgicdzdngir1kxh9pxx4sidrdndcip")))) + "09y9x09gri33ghhrvjjnj5k5rk0kdpsk3wq02cln8gmywd6728vk")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -1163,13 +1139,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "0.6-1") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "1fg158k4n6l3rzx9nrwhp4nwkwpbmv1q7z2xz5rw138zws68fkgr")))) + "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") @@ -1201,13 +1177,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.10") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1")))) + "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) @@ -1223,13 +1199,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f")))) + "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47")))) (build-system r-build-system) (home-page "http://yihui.name/formatR") (synopsis "Format R code automatically") @@ -1324,13 +1300,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.15.1") + (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1pbxd3k7kv5sa1a5gxm0zc2bhjxdgx2nfch9xap5k85djmgsfqc1")))) + "02balmhvc955rkqv4v0wkxbw4vjphydajgcpy4ml0s3b4sziyj0h")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) @@ -1352,14 +1328,14 @@ generation in R using Literate Programming techniques.") (define-public r-knitrbootstrap (package (name "r-knitrbootstrap") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "knitrBootstrap" version)) (sha256 (base32 - "0pshn2slzqwpryklslsxwh1dmqcnwv6bwi7yfm6m342wjybpk0wl")))) + "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p")))) (properties `((upstream-name . "knitrBootstrap"))) (build-system r-build-system) (propagated-inputs @@ -1504,13 +1480,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.2.0") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx")))) + "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") @@ -1523,20 +1499,38 @@ private members, and they support inheritance, even when the classes are defined in different packages.") (license license:expat))) +(define-public r-rlang + (package + (name "r-rlang") + (version "0.1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "rlang" version)) + (sha256 + (base32 + "0grwqy3zkvz96mvpwfbfyqid4jkfrqh3ldy2n6dpv2kjd1fzj0ar")))) + (build-system r-build-system) + (home-page "http://rlang.tidyverse.org") + (synopsis "Functions for base types, core R and Tidyverse features") + (description "This package provides a toolbox for working with base types, +core R features like the condition system, and core @code{Tidyverse} features +like tidy evaluation.") + (license license:gpl3))) + (define-public r-tibble (package (name "r-tibble") - (version "1.3.0") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "1q25i1cv3qms6d3lw7jd3z142w188znkcbyam460gn9si8l8g2bk")))) + "1bhq4pm56l7l6s1k44ajrcr7hz56h37m9ck4zji9f8xfdqschbl0")))) (build-system r-build-system) (propagated-inputs - `(("r-lazyeval" ,r-lazyeval) + `(("r-rlang" ,r-rlang) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") @@ -1548,20 +1542,23 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.5.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk")))) + "0jpb32ca1c0mr660igna4yw4fmzydzfhxshd0g8wgmggkynx2qi2")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-r6" ,r-r6) ("r-magrittr" ,r-magrittr) - ("r-lazyeval" ,r-lazyeval) - ("r-dbi" ,r-dbi) + ("r-rlang" ,r-rlang) + ("r-plogr" ,r-plogr) + ("r-glue" ,r-glue) + ("r-pkgconfig" ,r-pkgconfig) + ("r-bindrcpp" ,r-bindrcpp) ("r-tibble" ,r-tibble))) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -1621,37 +1618,17 @@ It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (license license:gpl2+))) -(define-public r-foreign - (package - (name "r-foreign") - (version "0.8-67") - (source - (origin - (method url-fetch) - (uri (cran-uri "foreign" version)) - (sha256 - (base32 - "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) - (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/foreign") - (synopsis "Read data stored by other statistics software in R") - (description - "This package provides functions for reading and writing data stored by -some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and -for reading and writing some dBase files.") - (license license:gpl2+))) - (define-public r-formula (package (name "r-formula") - (version "1.2-1") + (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "Formula" version)) (sha256 (base32 - "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax")))) + "0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd")))) (properties `((upstream-name . "Formula"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/Formula") @@ -1976,14 +1953,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.0.5") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "1pn1ii8vbkgxcqvx52kzsbwf9gkn9fp33388087zky2hmdzdirn0")))) + "1kcz6j82by28cjk5wi2j6dfqdin1kib4y7d2r4h3zabcxmk6jly5")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") @@ -1999,14 +1976,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g")))) + "04rxabzamhv6ybynx627sxk02qvq8znkv0y10vmq67xx6pxhqvla")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) @@ -2115,14 +2092,14 @@ module, Java Server Pages, and Python's psp module.") (define-public r-desc (package (name "r-desc") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 - "0mc1jmiwqyj7s6gzxz6fyamzjpmdn3rpfpllby2fq11ml30c6jpr")))) + "0k07qighac1xzmm8k988zi7i88a0yfvia3gk5hbz0fyvb2v9kzrj")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -2249,13 +2226,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "0bgzdsdi9n6l8pchivs6a2g4ksa56qs8hygpyv2c0ndqmx4jxcwi")))) + "0ws6fbndmaafk2am4dwnz24qizxhld0yh54hgx0z6lzv3p1j209q")))) (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 @@ -2293,25 +2270,21 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.13.2") + (version "1.13.3") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "08ajsr12wd31lsx3jv5l9mq4063dc5fpr9lcnzra6kl59vi5pa7v")))) + "146wb09cmfh10vhn1ps2nmzx104zldb3nj9qv2ic0gbcikbbryp6")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-evaluate" ,r-evaluate) + `(("r-digest" ,r-digest) ("r-git2r" ,r-git2r) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-memoise" ,r-memoise) - ("r-roxygen2" ,r-roxygen2) ("r-rstudioapi" ,r-rstudioapi) - ("r-rversions" ,r-rversions) ("r-whisker" ,r-whisker) ("r-withr" ,r-withr))) (home-page "https://github.com/hadley/devtools") @@ -2323,13 +2296,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "1.0.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493")))) + "0ncq9ygx33rx7aazn53p0a0vbr5xv0r6wbkzcwbhbwyd8k55bgin")))) (build-system r-build-system) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") @@ -2361,13 +2334,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1g7g3gdmvq7nj8asw6fi13k38c420sy9696nqgkrhlvv5h13yqs7")))) + "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -2385,13 +2358,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.6-4") + (version "3.6-5") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "1wxzjnzvkl3aga51ad2xhv4s7v46kvnp4z0nz4cb9cn10057sfw8")))) + "01655y3qzy0283ppc85bi0g42g20zrqzcl0qb30cl6rcbflhymlb")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2444,13 +2417,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.7.800.2.0") + (version "0.7.900.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "025lh504nw7ir1f2xsqnvfkq9rg0rb2xzfn3a2s0b2a9snqdzzwr")))) + "01qsff2p1fp5i9lq7rsykrskgr6smz24ddspbl5ad9a8rkmczwyv")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2536,14 +2509,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "1dvs9cq88g61wfimifagq6y98yxavxzjan39jvpdsg98mafckq9g")))) + "0p8ph5z5pifk1nxc1bppkfs1ir5gjc6ap9n64b4255m2fdaqfrc7")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2606,36 +2579,55 @@ variety of formats.") and draw tables.") (license license:gpl2+))) -(define-public r-plogr +(define-public r-pkgconfig (package - (name "r-plogr") - (version "0.1-1") - (source - (origin - (method url-fetch) - (uri (cran-uri "plogr" version)) - (sha256 - (base32 - "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) + (name "r-pkgconfig") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "pkgconfig" version)) + (sha256 + (base32 + "0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb")))) (build-system r-build-system) - (home-page "https://github.com/krlmlr/plogr") - (synopsis "R bindings for the plog C++ logging library") - (description - "This package provides the header files for a stripped-down version of -the plog header-only C++ logging library, and a method to log to R's standard -error stream.") + (home-page "https://github.com/gaborcsardi/pkgconfig") + (synopsis "Private configuration for R packages") + (description "This package provides the functionality to set configuration +options on a per-package basis. Options set by a given package only apply to +that package, other packages are unaffected.") (license license:expat))) +(define-public r-blob + (package + (name "r-blob") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "blob" version)) + (sha256 + (base32 + "05pazzcyz3c3vd2l70zq9cf172cgjff4dnf419zigfnxycyn1mhn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-tibble" ,r-tibble))) + (home-page "https://github.com/hadley/blob") + (synopsis "Simple S3 Class for representing vectors of binary data") + (description "Raw vectors in R are useful for storing a single binary +object. What if you want to put a vector of them in a data frame? The blob +package provides the blob object, a list of raw vectors, suitable for use as +a column in data frame.") + (license license:gpl3+))) + (define-public r-rsqlite (package (name "r-rsqlite") - (version "1.1-2") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "0mg9yhdvny3vjn72agai5ghqxd3vk8cd4x1lsc0gzc2b2dm2w0p4")))) + "1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2643,13 +2635,16 @@ error stream.") ("r-bh" ,r-bh) ("r-memoise" ,r-memoise) ("r-plogr" ,r-plogr) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-bit64" ,r-bit64) + ("r-blob" ,r-blob) + ("r-pkgconfig" ,r-pkgconfig))) (home-page "https://github.com/rstats-db/RSQLite") (synopsis "SQLite interface for R") (description "This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite -engine (version 3.8.6) is included.") +engine (version 3.8.8.2) is included.") (license license:lgpl2.0+))) (define-public r-rcurl @@ -2686,13 +2681,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.6") + (version "3.98-1.9") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "1amxx7fpik162nimrr7m5lvv6rhx9cwdyg44fxp1i5wm3y4skwnz")))) + "1hzkdkgs0nzmfg9wm7kyh1j9i0i2g7925whzlihqvg9grdlh3dx3")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -2804,14 +2799,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "0.5-1.4") + (version "0.5-2.1") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i")))) + "1i576xksc761nyv2dmq86nwbgqvp0plz6bjcn69nkdwq2wbizmw8")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") @@ -2845,13 +2840,13 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.76") + (version "1.77") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "16xnl9cacim35aawq6bmd2y6rrhnh1kg6dwsy3k5yslkfr1y9j62")))) + "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9")))) (properties `((upstream-name . "SparseM"))) (inputs @@ -3032,14 +3027,14 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.1.2") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) + "0zfb7x1701n6gask0f8y2yq0vmb82xkxf6limp43ivx551hx600s")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -3054,14 +3049,14 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "2.0-5") + (version "2.0-10") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 (base32 - "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) + "07n2hz4fvjyv0siai8z8wqwfj8d58i8n1vzf1ckdfzp4kxa3z08d")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) @@ -3304,36 +3299,6 @@ optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) -(define-public r-igraph - (package - (name "r-igraph") - (version "1.0.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "igraph" version)) - (sha256 - (base32 - "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran))) - (inputs - `(("gmp" ,gmp) - ("libxml2" ,libxml2))) - (propagated-inputs - `(("r-irlba" ,r-irlba) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf))) - (home-page "http://igraph.org") - (synopsis "Network analysis and visualization") - (description - "This package provides routines for simple graphs and network analysis. -It can handle large graphs very well and provides functions for generating -random and regular graphs, graph visualization, centrality methods and much -more.") - (license license:gpl2+))) - (define-public r-r-methodss3 (package (name "r-r-methodss3") @@ -3558,14 +3523,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyr (package (name "r-tidyr") - (version "0.6.1") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "11hs3gqpbaw3w281as4m7j9n594ix5axfpwbyjsd0l62pwnzj217")))) + "14s57zrjm2phiy600z9ivq4az71z0ggmp6nj0js7yrybxf0dlah6")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3614,21 +3579,19 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "0lss8q733nv7s154wargm6vnxq55qygnxakib8xdj4jv0y86sxc3")))) + "0j1y0nbvljcis9hgic4wbbzslcsidhpw0wzs7d2hx7a2ygi6mkma")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-dplyr" ,r-dplyr) - ("r-lazyeval" ,r-lazyeval) + `(("r-tibble" ,r-tibble) ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp))) + ("r-rlang" ,r-rlang))) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") (description @@ -3639,26 +3602,30 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.5.6") + (version "4.7.1") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "09yw977yxlcxv57kni3q899zrxyxa6pznr06cylr9lqkyr7llfhx")))) + "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) + ("r-crosstalk" ,r-crosstalk) ("r-digest" ,r-digest) + ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-hexbin" ,r-hexbin) + ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-scales" ,r-scales) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) @@ -3740,14 +3707,14 @@ character vector.") (define-public r-googlesheets (package (name "r-googlesheets") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "googlesheets" version)) (sha256 (base32 - "0ps13h1cv7fj5dh8s4nvwi64wnnyqdsadcaa4iizq1c5s615cwk3")))) + "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) @@ -3834,21 +3801,20 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.0-2") + (version "4.0-3") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 (base32 - "1lg9k0kj803wsm3h0a991q9l2lrgsqryzfv2z79b88kjbfapqpqr")))) + "1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-acepack" ,r-acepack) - ("r-base64" ,r-base64) ("r-base64enc" ,r-base64enc) ("r-cluster" ,r-cluster) ("r-data-table" ,r-data-table) @@ -3919,14 +3885,14 @@ hierarchical clustering dendrograms.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.38.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1vq8hwxz73j93q0ldw5bnhbas1f2ha5q1lr9pp4l8gp8zdwzfrjn")))) + "1ggvmak13rhxc4ghf16ncjfvgszc8yvza93s2l9kn8yiwr96vp2h")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -3965,14 +3931,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-0") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0580piv4n1nispl3pa8nfjjfnb8iwaqky2dzdy0aqnxrxgrhqhvz")))) + "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -4006,14 +3972,14 @@ tests for whether a value is missing, empty or contains only @code{NA} and (define-public r-gdata (package (name "r-gdata") - (version "2.17.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (cran-uri "gdata" version)) (sha256 (base32 - "0kiy3jbcszlpmarg311spdsfi5pn89wgy742dxsbzxk8907fr5w0")))) + "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b")))) (build-system r-build-system) (inputs `(("perl" ,perl))) @@ -4239,13 +4205,13 @@ representation of R code.") (define-public r-ggbeeswarm (package (name "r-ggbeeswarm") - (version "0.5.3") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ggbeeswarm" version)) (sha256 (base32 - "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd")))) + "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v")))) (build-system r-build-system) (propagated-inputs `(("r-beeswarm" ,r-beeswarm) @@ -4287,13 +4253,13 @@ Wall Street Journal, among others. This package also provides (define-public r-statmod (package (name "r-statmod") - (version "1.4.29") + (version "1.4.30") (source (origin (method url-fetch) (uri (cran-uri "statmod" version)) (sha256 (base32 - "1fgzkwriba39d7946lq892f0si2fjdy37pvxki6ix8xyj8qgnci4")))) + "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/statmod") (native-inputs @@ -4313,13 +4279,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.5") + (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "007cgqg9bybg2zlljbv5m6cmlm3r6i251018rpgjcn0xnm9sjsj7")))) + "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) @@ -4382,14 +4348,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "03iimcsh1pk7iqzjdlfcj43b8khijdk4hg00j4jdllv19xsfb0hx")))) + "03bh0r6ynr95gk4lc8asfi3kpmskm59vfzwn417pdziha3igs5x6")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -4455,14 +4421,14 @@ regression.") (define-public r-fastica (package (name "r-fastica") - (version "1.2-0") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 - "0ykk78fsk5da2g16i4wji85bvji7nayjvkfp07hyaxq9d15jmf0r")))) + "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/fastICA") @@ -4538,14 +4504,14 @@ to change in the future.") (define-public r-flexmix (package (name "r-flexmix") - (version "2.3-13") + (version "2.3-14") (source (origin (method url-fetch) (uri (cran-uri "flexmix" version)) (sha256 (base32 - "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z")))) + "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -4564,14 +4530,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.2.3") + (version "5.3") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0045msdw1xndfmlylbnm1ss716iiqzqwj454a97gmcq5kph86qzz")))) + "0h5syvpg3azrz5d10z2afilaa27jb4azi38idzlv05mfcs16s6rb")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4654,6 +4620,111 @@ can be efficiently implemented directly in the R language.") regression methodology including model selections and multivariate statistics.") (license license:gpl2+))) +(define-public r-pcapp + (package + (name "r-pcapp") + (version "1.9-72") + (source + (origin + (method url-fetch) + (uri (cran-uri "pcaPP" version)) + (sha256 + (base32 + "0i2822bv86dpqmk3q17x61nsp3gjjnn4nr8191rwvbiib7xhpgaq")))) + (properties `((upstream-name . "pcaPP"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mvtnorm" ,r-mvtnorm))) + (home-page "http://cran.r-project.org/web/packages/pcaPP") + (synopsis "Robust PCA by projection pursuit") + (description + "This package provides functions for robust @dfn{principal component +analysis} (PCA) by projection pursuit.") + (license license:gpl3+))) + +(define-public r-rrcov + (package + (name "r-rrcov") + (version "1.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rrcov" version)) + (sha256 + (base32 + "0kagqggi634mvrhd67ia7mpjrj5v6w2wq0z3kyppg5xkvzh335nq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice) + ("r-mvtnorm" ,r-mvtnorm) + ("r-pcapp" ,r-pcapp) + ("r-robustbase" ,r-robustbase))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/rrcov") + (synopsis "Scalable robust estimators with high breakdown Point") + (description + "This package provides an implementation of robust location and scatter +estimation and robust multivariate analysis with high breakdown point.") + (license license:gpl2+))) + +(define-public r-fit-models + (package + (name "r-fit-models") + (version "0.5-14") + (source + (origin + (method url-fetch) + (uri (cran-uri "fit.models" version)) + (sha256 + (base32 + "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck")))) + (properties `((upstream-name . "fit.models"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "http://cran.r-project.org/web/packages/fit.models") + (synopsis "Compare fitted models") + (description + "The @code{fit.models} function and its associated methods (coefficients, print, +summary, plot, etc.) were originally provided in the @code{robust} package to +compare robustly and classically fitted model objects. The aim of the +@code{fit.models} package is to separate this fitted model object comparison +functionality from the robust package and to extend it to support fitting +methods (e.g., classical, robust, Bayesian, regularized, etc.) more +generally.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-robust + (package + (name "r-robust") + (version "0.4-18") + (source + (origin + (method url-fetch) + (uri (cran-uri "robust" version)) + (sha256 + (base32 + "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fit-models" ,r-fit-models) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-robustbase" ,r-robustbase) + ("r-rrcov" ,r-rrcov))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/robust") + (synopsis "Port of the S+ \"Robust Library\"") + (description + "This package is a port of the S+ \"Robust Library\". It provides +methods for robust statistics, notably for robust regression and robust +multivariate analysis.") + (license license:gpl2))) + (define-public r-trimcluster (package (name "r-trimcluster") @@ -4672,7 +4743,8 @@ regression methodology including model selections and multivariate statistics.") "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and Matran (1997). This optimizes the k-means criterion under trimming a portion of the points.") - (license license:gpl2+))) + ;; Any GPL version + (license (list license:gpl2+ license:gpl3+)))) (define-public r-fpc (package @@ -4711,14 +4783,14 @@ groupings.") (define-public r-vgam (package (name "r-vgam") - (version "1.0-3") + (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 (base32 - "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3")))) + "0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (inputs @@ -4736,14 +4808,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (define-public r-pbapply (package (name "r-pbapply") - (version "1.3-2") + (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 - "1sdmjlnwxb99f95g5v8k8mirrkzw99yig377v0qi9lzwjgd6fqqr")))) + "0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") @@ -4800,14 +4872,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.2.9.1") + (version "0.3.3.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "1ih940yjbc530cmpl6kx1jic7pz2ps1w5vrvy32qizh6m5s3lk7x")))) + "0zz9v0f8nnlvhhqv91lkyfblvjnmav84l89mr6vmbqjc2hzqd3n8")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs @@ -4978,14 +5050,14 @@ bootstrap test for generalized linear mixed models.") (define-public r-car (package (name "r-car") - (version "2.1-4") + (version "2.1-5") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 (base32 - "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx")))) + "1bm0ks9ga60z3izgq0d4kvirr9v4yf1820d1wznkihnbb55bc3m6")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -5122,14 +5194,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.2-3") + (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp")))) + "1mvqr280c6kwpg98byd0r1y0qf238xn2x15y8npqch6lpcszlb3x")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -5147,17 +5219,19 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "0g1rnpk4c06lmy0r5n0j7i2xna190kqalmxp42d9gnk3drnb1x43")))) + "1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-rcpp" ,r-rcpp) + ("r-matrix" ,r-matrix) + ("r-rcppeigen" ,r-rcppeigen))) (home-page "https://github.com/imbs-hl/ranger") (synopsis "Fast implementation of random forests") (description |