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-rw-r--r--gnu/packages/statistics.scm357
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)
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-17 07:06:55 +0000