From cddc0300b7fb5fbbc80f45a626073f8372bf491f Mon Sep 17 00:00:00 2001 From: lakshmi Date: Tue, 6 Nov 2018 15:59:01 +0100 Subject: gnu: Add r-weights. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-weights): New variable. Signed-off-by: Gábor Boskovits --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index df869794db..8fed911360 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7225,3 +7225,31 @@ R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et al. (2016)).") (license license:gpl2))) + +(define-public r-weights + (package + (name "r-weights") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "weights" version)) + (sha256 + (base32 + "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdata" ,r-gdata) + ("r-hmisc" ,r-hmisc) + ("r-mice" ,r-mice))) + (home-page + "https://cran.r-project.org/web/packages/weights/") + (synopsis "Weighting and weighted statistics") + (description "This package Provides a variety of functions for producing +simple weighted statistics, such as weighted Pearson's correlations, partial +correlations, Chi-Squared statistics, histograms, and t-tests. Also now +includes some software for quickly recoding survey data and plotting point +estimates from interaction terms in regressions (and multiply imputed +regressions). NOTE: Weighted partial correlation calculations pulled to +address a bug.") + (license license:gpl2+))) -- cgit v1.2.3 From bfa5662e38de7bd02c493e52796c05359a984c66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:27:16 +0100 Subject: gnu: Add r-rcppannoy. * gnu/packages/cran.scm (r-rcppannoy): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8fed911360..43ff292cb2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7253,3 +7253,30 @@ estimates from interaction terms in regressions (and multiply imputed regressions). NOTE: Weighted partial correlation calculations pulled to address a bug.") (license license:gpl2+))) + +(define-public r-rcppannoy + (package + (name "r-rcppannoy") + (version "0.0.11") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppAnnoy" version)) + (sha256 + (base32 + "1ik50ancfgcvh03n4jsqwjk8lf056rbgd70q4l4didmvh5kcyjd1")))) + (properties `((upstream-name . "RcppAnnoy"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") + (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") + (description + "Annoy is a small C++ library for Approximate Nearest Neighbors written +for efficient memory usage as well an ability to load from and save to disk. +This package provides an R interface.") + ;; Annoy is released under ASL 2.0, but this wrapper is released under + ;; GPLv2+. + (license (list license:gpl2+ license:asl2.0)))) -- cgit v1.2.3 From b58940cb0345705a9681f2c47d668f252d00a699 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:27:41 +0100 Subject: gnu: Add r-ncdf4. * gnu/packages/cran.scm (r-ncdf4): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 43ff292cb2..11f7717bd8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7280,3 +7280,30 @@ This package provides an R interface.") ;; Annoy is released under ASL 2.0, but this wrapper is released under ;; GPLv2+. (license (list license:gpl2+ license:asl2.0)))) + +(define-public r-ncdf4 + (package + (name "r-ncdf4") + (version "1.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "ncdf4" version)) + (sha256 + (base32 + "0lwjjis0b83c4l3xvqai4ckzrskd6mychck1iwxcxgjvh0d77mgd")))) + (build-system r-build-system) + (inputs + `(("netcdf" ,netcdf) + ("zlib" ,zlib))) + (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") + (synopsis "R interface to Unidata netCDF format data files") + (description + "This package provides a high-level R interface to data files written +using Unidata's netCDF library (version 4 or earlier), which are binary data +files that are portable across platforms and include metadata information in +addition to the data sets. Using this package, netCDF files can be opened and +data sets read in easily. It is also easy to create new netCDF dimensions, +variables, and files, in either version 3 or 4 format, and manipulate existing +netCDF files.") + (license license:gpl3+))) -- cgit v1.2.3 From 1e605c030feaab4d3c24075f5c5b3783454973f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:28:09 +0100 Subject: gnu: Add r-biocmanager. * gnu/packages/cran.scm (r-biocmanager): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 11f7717bd8..ffad46be01 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7307,3 +7307,23 @@ data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files.") (license license:gpl3+))) + +(define-public r-biocmanager + (package + (name "r-biocmanager") + (version "1.30.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "BiocManager" version)) + (sha256 + (base32 + "0mfvx1xzsgiag9p42kdyqg8fvajyakrdy3z2smhdlaawzbi0qmax")))) + (properties `((upstream-name . "BiocManager"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/BiocManager/") + (synopsis "Access the Bioconductor project package repository") + (description + "This package provides a convenient tool to install and update +Bioconductor packages.") + (license license:artistic2.0))) -- cgit v1.2.3 From 0dd84df1210250631554361f735db79f3fa93669 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:52:45 +0100 Subject: gnu: r-ps: Update to 1.2.1. * gnu/packages/cran.scm (r-ps): Update to 1.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ffad46be01..28fa6adc6f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -492,13 +492,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "0ai8igdkysmks1ihbp3h3s552da2hskxqwrvp4cx7vwn91x9f3wd")))) + (base32 "1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx")))) (build-system r-build-system) (home-page "http://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") -- cgit v1.2.3 From 65dd0e67483e79fb4511646ce727f22ebf65a347 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:53:00 +0100 Subject: gnu: r-pkgload: Update to 1.0.2. * gnu/packages/cran.scm (r-pkgload): Update to 1.0.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 28fa6adc6f..dc5e0123ad 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -539,14 +539,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "0mm0avvan528zbrcrxigl5fkd7za01fb0qhlqrqvm3ar0115cqa8")))) + "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii")))) (build-system r-build-system) (propagated-inputs `(("r-desc" ,r-desc) -- cgit v1.2.3 From ec0ee08576d3b4bee4e1b55b481356439e42b699 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:53:09 +0100 Subject: gnu: r-ffbase: Update to 0.12.7. * gnu/packages/cran.scm (r-ffbase): Update to 0.12.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dc5e0123ad..7e604ee197 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -891,14 +891,14 @@ in main memory.") (define-public r-ffbase (package (name "r-ffbase") - (version "0.12.5") + (version "0.12.7") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 - "1h5x6rbb1nrpzf4ywkizn8ij0bz3mlz46byh46ylxhicg1ribi24")))) + "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) -- cgit v1.2.3 From 56af171ffd965c179b2516b1e311a3bfb3f3de4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:53:20 +0100 Subject: gnu: r-ipred: Update to 0.9-8. * gnu/packages/cran.scm (r-ipred): Update to 0.9-8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7e604ee197..9af9fc9df7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1762,14 +1762,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-7") + (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "0q53cqs46501wsd4cmfsmr78l8nv1hkbamk9m0ns5qy02df5r254")))) + "01xcg3c121ndfpz9dirqxszknh4yb1p222p7f1wbwwhdrg1i27cw")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) -- cgit v1.2.3 From 5d986a3b418a29d83dd6d3ddc1556694bc10e9eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:53:30 +0100 Subject: gnu: r-psych: Update to 1.8.10. * gnu/packages/cran.scm (r-psych): Update to 1.8.10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9af9fc9df7..5dc45a8b72 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1789,14 +1789,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "1.8.4") + (version "1.8.10") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf")))) + "0n3frgzsfmnan6cp3yyq5h6c28v5pd7q5a42pp6byaa7n7d1v478")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) -- cgit v1.2.3 From cea8a6074766de4228e75c3d6d5985a20fbe48cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:53:39 +0100 Subject: gnu: r-xts: Update to 0.11-2. * gnu/packages/cran.scm (r-xts): Update to 0.11-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5dc45a8b72..a29117b433 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2319,14 +2319,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.11-1") + (version "0.11-2") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "17d3g14xkxa1a5z5gd3gk1xjqfkjg1ik3i12q0arina8frql3jhd")))) + "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://github.com/joshuaulrich/xts") -- cgit v1.2.3 From 84d0d860e1113bb1e0c2be88a5d03be252de8b28 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:53:51 +0100 Subject: gnu: r-sjmisc: Update to 2.7.6. * gnu/packages/cran.scm (r-sjmisc): Update to 2.7.6. [propagated-inputs]: Remove r-pillar, r-tibble, and r-tidyselect. --- gnu/packages/cran.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a29117b433..5afad23dd4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4814,14 +4814,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.7.5") + (version "2.7.6") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "05fjqfr2rfk11065zqkzb9mbqd6mgdkw9jdhq3by425a7f8m2dcg")))) + "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -4829,15 +4829,12 @@ vice versa), or to deal with multiple declared missing values.") ("r-dplyr" ,r-dplyr) ("r-haven" ,r-haven) ("r-magrittr" ,r-magrittr) - ("r-pillar" ,r-pillar) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-stringdist" ,r-stringdist) ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) + ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/strengejacke/sjmisc") (synopsis "Data and variable transformation functions") (description -- cgit v1.2.3 From 244a5c43ec0a140a7c06cde36af11c821e0f9dee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:54:23 +0100 Subject: gnu: r-flextable: Update to 0.4.6. * gnu/packages/cran.scm (r-flextable): Update to 0.4.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5afad23dd4..9f195cf416 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4896,14 +4896,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "09j2y0z7rkc0w1cl9pp1cpk6fnzzfr6245mxa3ca42z9k2cy2jfl")))) + "0fa42dvf0wyl91w4v0rywm3xgw9n03cfyl28ficrv8iabz4k4382")))) (build-system r-build-system) (propagated-inputs `(("r-gdtools" ,r-gdtools) -- cgit v1.2.3 From 3d6fa1a3ad2f7c5d473b45ad478e213c399f9f00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:54:34 +0100 Subject: gnu: r-sessioninfo: Update to 1.1.1. * gnu/packages/cran.scm (r-sessioninfo): Update to 1.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9f195cf416..e24adb496f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6820,14 +6820,14 @@ Rcpp, RStudio projects, and more.") (define-public r-sessioninfo (package (name "r-sessioninfo") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "sessioninfo" version)) (sha256 (base32 - "01c0m8yzadpwd825hky6as0f8ka4xyz7zfy0ih2iy7qqw11w6qn5")))) + "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) -- cgit v1.2.3 From fc532b452f1cc23fe74749f9f6e1e3ed014e15f0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:54:42 +0100 Subject: gnu: r-remotes: Update to 2.0.2. * gnu/packages/cran.scm (r-remotes): Update to 2.0.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e24adb496f..dc7162beab 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6843,14 +6843,14 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "1xkzlciv68jyf4j8hads0i47nxbgsy1kv7258c6zzyq66z0amhss")))) + "0rsjxmhwpr51ilsdjfqn06mj8yr2d7nckcn3arv1ljn23qfkpcxa")))) (build-system r-build-system) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") -- cgit v1.2.3 From 7466c3bb06c2e1162fe352815c26a5c2e514029b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:54:53 +0100 Subject: gnu: r-rcmdcheck: Update to 1.3.1. * gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.1. [propagated-inputs]: Add r-sessioninfo. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dc7162beab..2521651bd1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6885,14 +6885,14 @@ directories or URLs with their associated programs.") (define-public r-rcmdcheck (package (name "r-rcmdcheck") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 - "13liz9lmx9xgc0f7pjiz3sp8ygvazx2zslbiwz3p9fimfsx1yfsg")))) + "1ga19jqix0zs7xyz2j155zyagwbv22r6dgv55g6wdjigc67qfsix")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -6904,6 +6904,7 @@ directories or URLs with their associated programs.") ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot) + ("r-sessioninfo" ,r-sessioninfo) ("r-withr" ,r-withr) ("r-xopen" ,r-xopen))) (home-page "https://github.com/r-Lib/rcmdcheck#readme") -- cgit v1.2.3 From a44f8b00fe0d0e1dd88c1d2f2f3e54bb04788b10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:55:11 +0100 Subject: gnu: r-pander: Update to 0.6.3. * gnu/packages/cran.scm (r-pander): Update to 0.6.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2521651bd1..ec950ce0ac 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6941,14 +6941,14 @@ quick reporting.") (define-public r-pander (package (name "r-pander") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "pander" version)) (sha256 (base32 - "0gd7rqkpbraznip8jmri9lqa8ajg1sryyplhd6m633wg91whiipi")))) + "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) -- cgit v1.2.3