diff options
author | Ricardo Wurmus <rekado@elephly.net> | 2018-05-31 13:23:49 +0200 |
---|---|---|
committer | Ricardo Wurmus <rekado@elephly.net> | 2018-05-31 13:23:49 +0200 |
commit | 59f87b44da801a479f38c10f20025586259acf91 (patch) | |
tree | 3929b8095066d0c5cb3841bff6cf2ad575213f9d /gnu/packages | |
parent | 1e341fa50849094fd5c685b6dfb2ee328a2ae44e (diff) | |
parent | 404e5c7d7d2f6fc80eebec831283c2f4161b6582 (diff) | |
download | patches-59f87b44da801a479f38c10f20025586259acf91.tar patches-59f87b44da801a479f38c10f20025586259acf91.tar.gz |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 12 | ||||
-rw-r--r-- | gnu/packages/cran.scm | 255 | ||||
-rw-r--r-- | gnu/packages/databases.scm | 6 | ||||
-rw-r--r-- | gnu/packages/linux.scm | 57 | ||||
-rw-r--r-- | gnu/packages/machine-learning.scm | 6 | ||||
-rw-r--r-- | gnu/packages/statistics.scm | 90 | ||||
-rw-r--r-- | gnu/packages/web.scm | 30 |
7 files changed, 281 insertions, 175 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index abea913723..b4988aeb7b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6134,20 +6134,20 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.5-1") + (version "2.5-2") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r")))) + "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) - ("r-knitr" ,r-knitr) + ("r-knitr" ,r-knitr) ; needed for vignettes ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) @@ -9702,13 +9702,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0")) + "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9752,7 +9752,6 @@ Main-Class: ModularityOptimizer\n"))) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) - ("r-gridextra" ,r-gridextra) ("r-hmisc" ,r-hmisc) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) @@ -9773,6 +9772,7 @@ Main-Class: ModularityOptimizer\n"))) ("r-rcppeigen" ,r-rcppeigen) ("r-rcppprogress" ,r-rcppprogress) ("r-reshape2" ,r-reshape2) + ("r-reticulate" ,r-reticulate) ("r-rocr" ,r-rocr) ("r-rtsne" ,r-rtsne) ("r-sdmtools" ,r-sdmtools) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 96044e114a..fa71035796 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -36,7 +36,9 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) #:use-module (gnu packages statistics) + #:use-module (gnu packages tls) #:use-module (gnu packages web)) (define-public r-tidyverse @@ -167,21 +169,18 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1k3mflgn10hcvy74y4pbigpv74zb66fz1phfd3c8isqmn88xbxzi")))) + "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon) - ("r-debugme" ,r-debugme) - ("r-r6" ,r-r6) - ("r-testthat" ,r-testthat))) + `(("r-r6" ,r-r6) + ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") (description @@ -316,14 +315,14 @@ and several other tools.") (define-public r-abbyyr (package (name "r-abbyyr") - (version "0.5.1") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "abbyyR" version)) (sha256 (base32 - "1s8zf18sh0s89vk3dl09fzrq50csmmfvmsanf5vfkv9n5lx6pklg")))) + "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx")))) (properties `((upstream-name . "abbyyR"))) (build-system r-build-system) (propagated-inputs @@ -427,13 +426,13 @@ error stream.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.16") + (version "0.12.17") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1rm8hcy72p1jvxikvmkwg20pjqmvmfvqb45lfghmddp2adp67qfl")))) + (base32 "08xg8h3w25sdb3xr18g9pa0x8cirkdgljqapxmw56ss1j9fc89s2")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -729,14 +728,14 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "2.2-13") + (version "2.2-14") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb")))) + "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) (home-page "http://ff.r-forge.r-project.org/") @@ -843,23 +842,26 @@ package also provides a C++ API, that works with or without Rcpp.") (define-public r-ggally (package (name "r-ggally") - (version "1.3.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 - "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l")))) + "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) + (inputs + `(("libressl" ,libressl))) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-plyr" ,r-plyr) ("r-progress" ,r-progress) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape))) + ("r-reshape" ,r-reshape) + ("r-rlang" ,r-rlang))) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description @@ -1077,13 +1079,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.14") + (version "0.3.15") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x")))) + "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -1122,14 +1124,14 @@ classes in the @code{stats4} package.") (define-public r-emdbook (package (name "r-emdbook") - (version "1.3.9") + (version "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 - "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69")))) + "0880cx6rqm9vgd2zxnd2k0igfl80gy7ak15w36clwlzavab59hmv")))) (build-system r-build-system) (propagated-inputs `(("r-bbmle" ,r-bbmle) @@ -1234,14 +1236,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-2") + (version "1.7-4") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p")))) + "12skvlridfq4jd5mh0yxl79ps0zi2xnlh4hsdgxad0gm7qky8awd")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -1315,14 +1317,14 @@ samples.") (define-public r-cvst (package (name "r-cvst") - (version "0.2-1") + (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "CVST" version)) (sha256 (base32 - "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2")))) + "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5")))) (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs @@ -1774,14 +1776,14 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618")))) + "1m3p84d6nh9mzzvxb82vgig3ngcvkz86rjwzl9a66ckdf5p611k3")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -1841,23 +1843,98 @@ can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.") (license license:gpl3+))) +(define-public r-jomo + (package + (name "r-jomo") + (version "2.6-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "jomo" version)) + (sha256 + (base32 + "0zyqwa2y08asj9xqwnngh6da1b9cqcx8pzc9cxwrmgnxd5nnsjb7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lme4" ,r-lme4) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/jomo/") + (synopsis "Multilevel Joint Modelling Multiple Imputation") + (description + "Similarly to Schafer's package pan, jomo is a package for multilevel +joint modelling multiple imputation @url{Carpenter and Kenward (2013), +http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the +possibility of handling binary and categorical data through latent normal +variables, the option to use cluster-specific covariance matrices and to +impute compatibly with the substantive model.") + (license license:gpl2))) + +(define-public r-pan + (package + (name "r-pan") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "pan" version)) + (sha256 + (base32 + "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/pan/") + (synopsis "Multiple imputation for multivariate panel or clustered data") + (description + "This package implements multiple imputation for multivariate panel or +clustered data.") + (license license:gpl3))) + +(define-public r-mitml + (package + (name "r-mitml") + (version "0.3-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "mitml" version)) + (sha256 + (base32 + "1s888r9y2ri39b48h1iypps6lddqkqv3g31l2sjmi2pvyccfpkwb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-haven" ,r-haven) + ("r-jomo" ,r-jomo) + ("r-pan" ,r-pan))) + (home-page "https://cran.r-project.org/web/packages/mitml/") + (synopsis "Tools for multiple imputation in multilevel modeling") + (description + "This package provides tools for multiple imputation of missing data in +multilevel modeling. It includes a user-friendly interface to the packages +pan and jomo, and several functions for visualization, data management and the +analysis of multiply imputed data sets.") + (license license:gpl2+))) + (define-public r-mice (package (name "r-mice") - (version "2.46.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax")))) + "1p8a5ham90iaak4w17114pdnw535r2l9sxr402yrkc4gbwfbpdlq")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) + ("r-mitml" ,r-mitml) ("r-nnet" ,r-nnet) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-rpart" ,r-rpart) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/mice/") @@ -1923,14 +2000,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.5.9") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz")))) + "16n8qanxx0p5ny5zqxafn8hwb1xv94y1wig1iql8as5a5qh8lwcz")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -1955,14 +2032,14 @@ acceptance regions, log-ratio plots and Q-Q plots.") (define-public r-sm (package (name "r-sm") - (version "2.2-5.4") + (version "2.2-5.5") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 - "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9")))) + "1rw2mxygxsmk8mn4wag1ppjgzk0rlvh6zd8q02qrhjrn9jhi5qj3")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") @@ -2146,14 +2223,14 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).") (define-public r-ica (package (name "r-ica") - (version "1.0-1") + (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "ica" version)) (sha256 (base32 - "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq")))) + "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ica/") (synopsis "Independent component analysis") @@ -2166,14 +2243,14 @@ of Eigenmatrices} (JADE).") (define-public r-dtw (package (name "r-dtw") - (version "1.18-1") + (version "1.20-1") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 - "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr")))) + "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3")))) (build-system r-build-system) (propagated-inputs `(("r-proxy" ,r-proxy))) (home-page "http://dtw.r-forge.r-project.org/") @@ -2256,14 +2333,14 @@ plots in @code{ggplot2}.") (define-public r-ggjoy (package (name "r-ggjoy") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggjoy" version)) (sha256 (base32 - "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb")))) + "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2341,20 +2418,20 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "2.0.0.1") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 - "0yw23lp9xjvbpswzghkmjiayw7p19hbvmgv58k3i6b8g5nav4qcg")))) + "0wjr3cqwvnjxbvln25szffmkns5w0xysivdjr6chxap4nh515b0i")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-crayon" ,r-crayon) - ("r-debugme" ,r-debugme) - ("r-r6" ,r-r6))) + ("r-r6" ,r-r6) + ("r-testthat" ,r-testthat))) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description @@ -2551,14 +2628,14 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3")))) + "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) (build-system r-build-system) (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") @@ -2571,14 +2648,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1kmqvny3rw4p5kgxz6mhqfpp7j3nnpp22dfai4kjrr2cfmj6wvb7")))) + "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -3263,18 +3340,19 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.2.1") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9")))) + "1hqgszbiv99dibhwr21v21ll4s2hjn3ccqdicsm0z3gk77bh8iyb")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs - `(("r-shiny" ,r-shiny))) + `(("r-shiny" ,r-shiny) + ("r-jsonlite" ,r-jsonlite))) (home-page "http://cran.r-project.org/web/packages/shinyAce") (synopsis "Ace editor bindings for Shiny") (description @@ -3384,14 +3462,14 @@ It also includes interpolation functions.") (define-public r-psych (package (name "r-psych") - (version "1.8.3.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "1zhp8j81nkzd65168zdw9ylypb9n07ajan21x0wqcn8jdbg970sg")))) + "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -3766,19 +3844,41 @@ measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.") (license license:gpl3+))) +(define-public r-zip + (package + (name "r-zip") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "zip" version)) + (sha256 + (base32 + "0rgr9pcdhdq3k8n29h2ircp3ri1ibhrx81gja1y7331v15xyrabg")))) + (build-system r-build-system) + (home-page "https://github.com/gaborcsardi/zip") + (synopsis "Cross-platform Zip compression") + (description + "This package provides a cross-platform Zip compression library for R. +It is a replacement for the @code{zip} function, that does not require any +additional external tools on any platform.") + (license license:cc0))) + (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.0.17") + (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "1mq4lasp12kc30sxcsmz9gskd114l8s7z7wd6svv2nm8qllrhsqi")))) + "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-zip" ,r-zip))) (home-page "https://github.com/awalker89/openxlsx") (synopsis "Read, write and edit XLSX files") (description @@ -4060,3 +4160,48 @@ bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.") (license license:gpl2))) + +(define-public r-reticulate + (package + (name "r-reticulate") + (version "1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "reticulate" version)) + (sha256 + (base32 + "1ghhc4hbmwpp79ilbdbshynhs61i8sv8z6p1al04jy7ij0lcglxy")))) + (build-system r-build-system) + (inputs `(("python" ,python))) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/rstudio/reticulate") + (synopsis "R interface to Python") + (description + "This package provides an interface from R to Python modules, classes, +and functions. When calling into Python, R data types are automatically +converted to their equivalent Python types. When values are returned from +Python to R they are converted back to R types.") + (license license:asl2.0))) + +(define-public r-bibtex + (package + (name "r-bibtex") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bibtex" version)) + (sha256 + (base32 + "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz")))) + (build-system r-build-system) + (propagated-inputs `(("r-stringr" ,r-stringr))) + (home-page "https://github.com/romainfrancois/bibtex") + (synopsis "Bibtex parser") + (description "This package provides a utility for R to parse a bibtex +file.") + (license license:gpl2+))) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 6205df361f..fcf6030752 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -28,7 +28,7 @@ ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2017 Pierre Langlois <pierre.langlois@gmx.com> -;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Kristofer Buffington <kristoferbuffington@gmail.com> ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> @@ -2061,14 +2061,14 @@ and web services platform functionality.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.14") + (version "0.10.15") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "01891kn263b02y6addgpy3gn5axg7m10bqbqv7dg9yx9k85am590")))) + "0bmc7w5fnkjaf333sgc0hskiy332m9gmfaxg0yzkjxscpizdw43n")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (native-inputs diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4100db5d8a..8c12141260 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -404,52 +404,25 @@ It has been modified to remove all non-free binary blobs.") %linux-compatible-systems #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.46") -(define %linux-libre-4.14-hash "17imkhqk3m3djdj0m5h4lqs9cfdh9zq1cz83q8ldyald56rbn622") +(define %linux-libre-4.14-version "4.14.47") +(define %linux-libre-4.14-hash "1hm1vk6cdrwr971g5rcbq425fadn49580xa27zp1h6jz40n119wd") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version %linux-libre-4.14-hash '("x86_64-linux" "i686-linux" "armhf-linux") - #:patches - (list %boot-logo-patch - (origin - ;; The sole fix in the 4.14.47 release. - (method url-fetch) - (uri "https://git.kernel.org/pub/scm/linux/kernel/\ -git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719") - (sha256 - (base32 "1hk1qd6v97zf8an3zww60zhsah1wwax22b3bpdzmfjhhbndyram9")))) #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.104" - "0b6y24vfsjhiv7qq7xqx7h9krc81c49dqh0189nm1lhfwciyir57" + (make-linux-libre "4.9.105" + "0kzznalr69c3z63y4gs38zs6cb0jmn41ggvz4i1gp2sqpmjm6ybb" %intel-compatible-systems - #:patches - (list %boot-logo-patch - (origin - ;; The sole fix in the 4.9.105 release. - (method url-fetch) - (uri "https://git.kernel.org/pub/scm/linux/kernel/\ -git/stable/linux-stable.git/patch/?id=98d69fb3b175855cdd4c37d41a4b477a0860b1a0") - (sha256 - (base32 "1r52fr0w94fgw7nfxrysjk0mljlnqwqsnl0cp84c1sly466i79dv")))) #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.134" - "137mklzyv56yhc48l5h5i0h01gm1q40x2a8nk51lwhbjv592xr8x" + (make-linux-libre "4.4.135" + "0jdf5yx8b6q4zw7q9k8vv0ky8wlvclr9qz70wgrrvmm5dh1662j9" %intel-compatible-systems - #:patches - (list %boot-logo-patch - (origin - ;; The sole fix in the 4.4.135 release. - (method url-fetch) - (uri "https://git.kernel.org/pub/scm/linux/kernel/\ -git/stable/linux-stable.git/patch/?id=393e9b3c30d571c2f655aa24b0dee5be9ce249b5") - (sha256 - (base32 "02wk036v525qwqs42ndqqj4mv8xfkpavibfg5ns6hkg2wc5a1jid")))) #:configuration-file kernel-config)) (define-public linux-libre-4.1 @@ -470,15 +443,6 @@ git/stable/linux-stable.git/patch/?id=393e9b3c30d571c2f655aa24b0dee5be9ce249b5") %linux-libre-4.14-hash '("armhf-linux") #:defconfig "multi_v7_defconfig" - #:patches - (list %boot-logo-patch - (origin - ;; The sole fix in the 4.14.47 release. - (method url-fetch) - (uri "https://git.kernel.org/pub/scm/linux/kernel/\ -git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719") - (sha256 - (base32 "1hk1qd6v97zf8an3zww60zhsah1wwax22b3bpdzmfjhhbndyram9")))) #:extra-version "arm-generic")) (define-public linux-libre-arm-omap2plus @@ -493,15 +457,6 @@ git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719") %linux-libre-4.14-hash '("armhf-linux") #:defconfig "omap2plus_defconfig" - #:patches - (list %boot-logo-patch - (origin - ;; The sole fix in the 4.14.47 release. - (method url-fetch) - (uri "https://git.kernel.org/pub/scm/linux/kernel/\ -git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719") - (sha256 - (base32 "1hk1qd6v97zf8an3zww60zhsah1wwax22b3bpdzmfjhhbndyram9")))) #:extra-version "arm-omap2plus")) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index e6f7a18346..15e4d45749 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> @@ -592,14 +592,14 @@ geometric models.") (define-public r-kernlab (package (name "r-kernlab") - (version "0.9-25") + (version "0.9-26") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 - "0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr")))) + "0xv0slf3ggw3sswsi34416lb1g3h1pqkrr2h7r1n1kvgii3l0jcm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index eb21fcd303..434f26dbe3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -649,14 +649,14 @@ curves, Cox models, and parametric accelerated failure time models.") (define-public r-bit (package (name "r-bit") - (version "1.1-13") + (version "1.1-14") (source (origin (method url-fetch) (uri (cran-uri "bit" version)) (sha256 (base32 - "1yhpwvfkxpb773h8khjzyamqxl2jn7pjjmxjfawq626hhds8fsh6")))) + "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw")))) (build-system r-build-system) (home-page "http://ff.r-forge.r-project.org") (synopsis "Class for vectors of 1-bit booleans") @@ -762,14 +762,14 @@ non-estimable cases correctly.") (define-public r-pheatmap (package (name "r-pheatmap") - (version "1.0.8") + (version "1.0.10") (source (origin (method url-fetch) (uri (cran-uri "pheatmap" version)) (sha256 (base32 - "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji")))) + "1jzxs5hwbz3r0z2pp09i7fd14sndxnrbm3zibaac3kny4nzydzf7")))) (build-system r-build-system) (propagated-inputs `(("r-gtable" ,r-gtable) @@ -1386,19 +1386,20 @@ generation in R using Literate Programming techniques.") (define-public r-knitrbootstrap (package (name "r-knitrbootstrap") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "knitrBootstrap" version)) (sha256 (base32 - "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p")))) + "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3")))) (properties `((upstream-name . "knitrBootstrap"))) (build-system r-build-system) (propagated-inputs `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) + ("r-rmarkdown" ,r-rmarkdown) + ("r-markdown" ,r-markdown))) (home-page "https://github.com/jimhester/knitrBootstrap") (synopsis "Knitr bootstrap framework") (description @@ -1561,13 +1562,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "0f87fhw5pj6s2zjdxnpnd7pwn78czdz71b0xhm5adqg1p38sfwj8")))) + "0ghg66vyri8nck4p6kl1nh47qdppbmxvjiyms69nhvipphk4ifpj")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1753,13 +1754,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.11.0") + (version "1.11.4") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "0n1p35c9sni2272ykxsfbsy7xma62br7v668a5bvc37g75xf10df")))) + "1mc1drqj5i5ar2za3nkh5j70y37s7z7xwqri2r2b72zkqggg3k7x")))) (build-system r-build-system) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") @@ -2438,13 +2439,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.7-1") + (version "3.7-2") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "16p6d2dna6dah7rg2xknhyy65jkfn0zzivx1nnfxhd4f5q0v87w2")))) + "0hx3xv94gzlyy7ny5k4mzs7w1798h1zka175m5bkzc524493cm88")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2835,13 +2836,13 @@ plotted and compared with the asymptotic curve.") (define-public r-lambda-r (package (name "r-lambda-r") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "lambda.r" version)) (sha256 (base32 - "05cfaq9dbgdnmmj3d6ggmsw300qgiw8k7f6h6k0ylv63cf3v6pkq")))) + "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c")))) (properties `((upstream-name . "lambda.r"))) (build-system r-build-system) (propagated-inputs @@ -3164,20 +3165,24 @@ path-wise fashion.") (define-public r-pkgmaker (package (name "r-pkgmaker") - (version "0.22") + (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "pkgmaker" version)) (sha256 (base32 - "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r")))) + "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) + `(("r-bibtex" ,r-bibtex) + ("r-codetools" ,r-codetools) ("r-digest" ,r-digest) + ("r-magrittr" ,r-magrittr) ("r-registry" ,r-registry) + ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) + ("r-withr" ,r-withr) ("r-xtable" ,r-xtable))) (home-page "https://renozao.github.io/pkgmaker") (synopsis "Package development utilities") @@ -3209,14 +3214,14 @@ package registries.") (define-public r-rngtools (package (name "r-rngtools") - (version "1.2.4") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "rngtools" version)) (sha256 (base32 - "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097")))) + "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -3301,14 +3306,14 @@ bigmemory and synchronicity packages.") (define-public r-synchronicity (package (name "r-synchronicity") - (version "1.3.2") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "synchronicity" version)) (sha256 (base32 - "1idrjzl7nkamf1ip55s6qcf64s63xs9j8z9jv3r89p6r5lw7k5mv")))) + "1km5hx82gy71m5nc6pkcksv0dn32fylhg2axpdsnarrxva14mgdg")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -3638,14 +3643,14 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "0.8.0") + (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "1qjpbj1a2vw6nw4hdb6fgassnrxrdpqwf9a8i6wqnv3wxvjb6zqb")))) + "0485f19mkkglc4bv57y6bm6l9rfgd878hsz2xdg1nwgbqchjhgix")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3694,14 +3699,14 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "0wgbnbrqncjpggg8f9bdpcd1gy351s5f0az5k8lc55cvs9lhz3gd")))) + "0dc53zzan3km2l9lzxjixcv6yn7dhw2ppmz8qf2awhak7x2qm9m4")))) (build-system r-build-system) (propagated-inputs `(("r-tibble" ,r-tibble) @@ -3960,14 +3965,14 @@ conversion of R objects to LaTeX code, and recoding variables.") (define-public r-runit (package (name "r-runit") - (version "0.4.31") + (version "0.4.32") (source (origin (method url-fetch) (uri (cran-uri "RUnit" version)) (sha256 (base32 - "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx")))) + "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3")))) (properties `((upstream-name . "RUnit"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RUnit") @@ -4328,13 +4333,13 @@ data at that region, and avoids over-plotting.") (define-public r-ggthemes (package (name "r-ggthemes") - (version "3.4.2") + (version "3.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggthemes" version)) (sha256 (base32 - "0i7ygpizs00acizixc29bhbrci523ys7vzxbii9b3bcmfa3pj7i3")))) + "0drbzzb4i5jq1579fx1wmgh87ybnswjn7srak2l8g771ip49xwb8")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -4746,14 +4751,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.4-3") + (version "1.4-4") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "0kagqggi634mvrhd67ia7mpjrj5v6w2wq0z3kyppg5xkvzh335nq")))) + "0wn5h8vi0zyk5ah898m37ysz4kiih6y792nb9zdvhvd8r07f0sc5")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -5021,14 +5026,14 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.35") + (version "5.36") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 (base32 - "18f3qxv1j1bqmq55hzssz8mnp5ww4flhy80rm2v1rk0mmg9paz7m")))) + "023gdzahxp582rpabilpxbl3wyjrgjjnnrhcv9xhrqdfiq5l2yza")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5181,14 +5186,14 @@ to Applied regression, Second Edition, Sage, 2011.") (define-public r-caret (package (name "r-caret") - (version "6.0-79") + (version "6.0-80") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "1i6sjw279g6mj83vz5gv99x0nljcbpy7v0nbl72lmd80sf7rjshl")))) + "0xhdhazzfh0hiqv2hgxglj9ffd2p4ls8acqn2sjn0ndx6158f187")))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) @@ -5302,15 +5307,16 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.3-1") + (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "1li62wynv81kb17fx7nk63a26qlb78l8fdf63in8yzcl7fkpji7y")))) + "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb")))) (build-system r-build-system) + ;; These are all suggested packages, not build dependencies. (propagated-inputs `(("r-cluster" ,r-cluster) ("r-mclust" ,r-mclust) @@ -5327,14 +5333,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "1pilj5pxl8jl0gsy9vsyqxqdqfcxzvphbgvrlp4hf7r9mrfw9v0p")))) + "1yl833cm2jpfy9j7zchkq4mm5x1av70w89zrhpwdn8nq2npxxzf0")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -5546,14 +5552,14 @@ parameters.") (define-public r-directlabels (package (name "r-directlabels") - (version "2017.03.31") + (version "2018.05.22") (source (origin (method url-fetch) (uri (cran-uri "directlabels" version)) (sha256 (base32 - "01ahw0c56mnzwl611s8hnghicww4c4dgf5v2wv6bl1s1pramw9pr")))) + "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog))) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index c5547ec2df..d9ce68ba51 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3824,21 +3824,19 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "0bs0i5mjfzxfshqz8i30nhn7kvgwly4fqn5bfq6dqfdrn7biai2x")))) + "0yz3igqsiyqnjj1ngh199zicg3spx4kbmvl0wc8i8xahk6l9g06v")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) ("r-jsonlite" ,r-jsonlite) ("r-mime" ,r-mime) ("r-xfun" ,r-xfun))) - (native-inputs - `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/yihui/servr") (synopsis "Simple HTTP server to serve static files or dynamic documents") (description @@ -3907,14 +3905,14 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "1.11.2") + (version "1.12") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 - "1lbpi0kkk8b41w10scmlf27dg5azcv51a4q3p5bpqyphrnqp78k4")))) + "1n5136vb7mi4rxl5jgwdmdhn4mwv2pcqyw2mrj406ih4hy6hpxa2")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs @@ -3998,14 +3996,14 @@ objects in HTML format.") (define-public r-rjson (package (name "r-rjson") - (version "0.2.18") + (version "0.2.19") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 - "18myz05ana8zlyqxi6i4xjs5vmafxln8459ab3ws5kk59c1ardfn")))) + "1g29vp3gfbh73a5br68jydsrigia4vnr5avc84avgwl6353749jw")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rjson") (synopsis "JSON library for R") @@ -5322,16 +5320,17 @@ snippets on @url{https://commandlinefu.com}.") (define-public r-shiny (package (name "r-shiny") - (version "1.0.3") + (version "1.1.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/rstudio/shiny/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/rstudio/shiny.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0z2v2s4hd44mvzjn7r70549kdzkrrch9nxhp27r6x2cy6micizm3")))) + "041q2gzvzs13syfhbirmkik96asdji8dxnnbs63j7v1ks97hrvvz")))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) @@ -5396,7 +5395,8 @@ snippets on @url{https://commandlinefu.com}.") "jquery.min.js"))))) #t))))) (propagated-inputs - `(("r-httpuv" ,r-httpuv) + `(("r-crayon" ,r-crayon) + ("r-httpuv" ,r-httpuv) ("r-mime" ,r-mime) ("r-jsonlite" ,r-jsonlite) ("r-xtable" ,r-xtable) |