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Merge branch 'master' into core-updates

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Ricardo Wurmus 2018-05-31 13:23:49 +02:00
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7 changed files with 281 additions and 175 deletions
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12
gnu/packages/bioinformatics.scm
View file

@ -6134,20 +6134,20 @@ (define-public r-centipede
(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 @@ (define-public r-msnid
(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 @@ (define-public r-seurat
("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 @@ (define-public r-seurat
("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)

255
gnu/packages/cran.scm
View file

@ -36,7 +36,9 @@ (define-module (gnu packages cran)
#: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 @@ (define-public r-reprex
(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 @@ (define-public r-ape
(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 @@ (define-public r-plogr
(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 @@ (define-public r-fastmatch
(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 @@ (define-public r-progress
(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 @@ (define-public r-idr
(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 @@ (define-public r-bbmle
(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 @@ (define-public r-fitdistrplus
(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 @@ (define-public r-ksamples
(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 @@ (define-public r-pdist
(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 @@ (define-public r-stringdist
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 @@ (define-public r-rsolnp
(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 @@ (define-public r-hardyweinberg
(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 @@ (define-public r-vcd
(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 @@ (define-public r-ica
(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 @@ (define-public r-ggridges
(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 @@ (define-public r-debugme
(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 @@ (define-public r-xfun
(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 @@ (define-public r-utf8
(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 @@ (define-public r-import
(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 @@ (define-public r-signal
(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 @@ (define-public r-abc
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 @@ (define-public r-analytics
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+)))

6
gnu/packages/databases.scm
View file

@ -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 @@ (define-public virtuoso-ose
(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

57
gnu/packages/linux.scm
View file

@ -404,52 +404,25 @@ (define-public linux-libre
%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 @@ (define-public linux-libre-arm-generic-4.14
%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 @@ (define-public linux-libre-arm-omap2plus-4.14
%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"))

6
gnu/packages/machine-learning.scm
View file

@ -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 @@ (define-public r-adaptivesparsity
(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")

90
gnu/packages/statistics.scm
View file

@ -649,14 +649,14 @@ (define-public r
(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 @@ (define-public r-estimability
(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 @@ (define-public r-knitr
(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 @@ (define-public r-r6
(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 @@ (define-public r-chron
(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 @@ (define-public r-readr
(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 @@ (define-public r-xnomial
(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 @@ (define-public r-glmnet
(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 @@ (define-public r-registry
(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 @@ (define-public r-bigmemory-sri
(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 @@ (define-public r-tidyselect
(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 @@ (define-public r-hexbin
(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 @@ (define-public r-hmisc
(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 @@ (define-public r-ggbeeswarm
(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 @@ (define-public r-pcapp
(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 @@ (define-public r-matrixmodels
(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 @@ (define-public r-car
(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 @@ (define-public r-sn
(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 @@ (define-public r-tclust
(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 @@ (define-public r-tgconfig
(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)))

30
gnu/packages/web.scm
View file

@ -3824,21 +3824,19 @@ (define-public r-jsonlite
(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 @@ (define-public r-htmlwidgets
(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 @@ (define-public r-hwriter
(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 @@ (define-public python2-clf
(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 @@ (define-public r-shiny
"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)