ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-12-24 21:38:07 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions

gnu: r: Do not build recommended packages.

Browse source 
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
This commit is contained in:
Ricardo Wurmus 2017-03-12 00:21:39 +01:00
parent 6eaa9bfba6
commit aeb64f3cb2
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
4 changed files with 82 additions and 43 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

21
gnu/packages/bioinformatics.scm
View file

@ -108,6 +108,9 @@ (define-public r-ape
(base32
"0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)
("r-nlme" ,r-nlme)))
(home-page "http://ape-package.ird.fr/")
(synopsis "Analyses of phylogenetics and evolution")
(description
@ -5353,6 +5356,7 @@ (define-public r-vegan
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
("r-mgcv" ,r-mgcv)
("r-permute" ,r-permute)))
(home-page "https://cran.r-project.org/web/packages/vegan")
@ -5434,7 +5438,8 @@ (define-public r-genefilter
`(("r-annotate" ,r-annotate)
("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-s4vectors" ,r-s4vectors)))
("r-s4vectors" ,r-s4vectors)
("r-survival" ,r-survival)))
(home-page "http://bioconductor.org/packages/genefilter")
(synopsis "Filter genes from high-throughput experiments")
(description
@ -5732,6 +5737,7 @@ (define-public r-grohmm
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-mass" ,r-mass)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://github.com/Kraus-Lab/groHMM")
@ -6131,7 +6137,8 @@ (define-public r-bioccheck
(native-inputs
`(("which" ,which)))
(propagated-inputs
`(("r-graph" ,r-graph)
`(("r-codetools" ,r-codetools)
("r-graph" ,r-graph)
("r-knitr" ,r-knitr)
("r-httr" ,r-httr)
("r-optparse" ,r-optparse)
@ -6659,6 +6666,7 @@ (define-public r-summarizedexperiment
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/SummarizedExperiment")
(synopsis "Container for representing genomic ranges by sample")
@ -6850,8 +6858,9 @@ (define-public r-topgo
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-go-db" ,r-go-db)
("r-matrixstats" ,r-matrixstats)
("r-graph" ,r-graph)
("r-lattice" ,r-lattice)
("r-matrixstats" ,r-matrixstats)
("r-sparsem" ,r-sparsem)))
(home-page "http://bioconductor.org/packages/topGO")
(synopsis "Enrichment analysis for gene ontology")
@ -8243,7 +8252,8 @@ (define-public r-sva
"1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
(build-system r-build-system)
(propagated-inputs
`(("r-genefilter" ,r-genefilter)))
`(("r-genefilter" ,r-genefilter)
("r-mgcv" ,r-mgcv)))
(home-page "http://bioconductor.org/packages/sva")
(synopsis "Surrogate variable analysis")
(description
@ -8295,6 +8305,7 @@ (define-public r-raremetals2
(propagated-inputs
`(("r-seqminer" ,r-seqminer)
("r-mvtnorm" ,r-mvtnorm)
("r-mass" ,r-mass)
("r-compquadform" ,r-compquadform)
("r-getopt" ,r-getopt)))
(home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
@ -8453,6 +8464,7 @@ (define-public r-vsn
`(("r-affy" ,r-affy)
("r-biobase" ,r-biobase)
("r-ggplot2" ,r-ggplot2)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
(synopsis "Variance stabilization and calibration for microarray data")
@ -8516,6 +8528,7 @@ (define-public r-pcamethods
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-mass" ,r-mass)
("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/hredestig/pcamethods")
(synopsis "Collection of PCA methods")

3
gnu/packages/python.scm
View file

@ -4085,7 +4085,8 @@ (define-public python-rpy2
`(("readline" ,readline)
("icu4c" ,icu4c)
("pcre" ,pcre)
("r" ,r)))
("r" ,r)
("r-survival" ,r-survival)))
(native-inputs
`(("zlib" ,zlib)))
(home-page "http://rpy.sourceforge.net/")

83
gnu/packages/statistics.scm
View file

@ -99,6 +99,9 @@ (define-public pspp
be output in text, PostScript, PDF or HTML.")
(license license:gpl3+)))
;; 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-public r
(package
(name "r")
@ -128,12 +131,8 @@ (define-public r
(substitute* "src/scripts/R.sh.in"
(("uname") uname-bin)))
#t))
(add-after 'unpack 'build-recommended-packages-reproducibly
(add-after 'unpack 'build-reproducibly
(lambda _
(substitute* "src/library/Recommended/Makefile.in"
(("INSTALL_OPTS =(.*)" line rest )
(string-append "INSTALL_OPTS = --built-timestamp=1970-01-01"
rest)))
;; Ensure that gzipped files are reproducible
(substitute* '("src/library/grDevices/Makefile.in"
"doc/manual/Makefile.in")
@ -162,7 +161,12 @@ (define-public r
(add-after 'build 'install-info
(lambda _ (zero? (system* "make" "install-info")))))
#:configure-flags
'("--with-cairo"
'(;; Do not build the recommended packages. The build system creates
;; random temporary directories and embeds their names in some
;; package files. We build these packages with the r-build-system
;; instead.
"--without-recommended-packages"
"--with-cairo"
"--with-blas=-lopenblas"
"--with-libpng"
"--with-jpeglib"
@ -991,6 +995,7 @@ (define-public r-ggplot2
("r-gtable" ,r-gtable)
("r-plyr" ,r-plyr)
("r-lazyeval" ,r-lazyeval)
("r-mass" ,r-mass)
("r-tibble" ,r-tibble)
("r-reshape2" ,r-reshape2)
("r-scales" ,r-scales)
@ -1611,6 +1616,8 @@ (define-public r-locfit
(base32
"0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(home-page "http://cran.r-project.org/web/packages/locfit")
(synopsis "Local regression, likelihood and density estimation")
(description
@ -1788,6 +1795,8 @@ (define-public r-coda
(base32
"14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(home-page "http://cran.r-project.org/web/packages/coda")
(synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
(description "This package provides functions for summarizing and plotting
@ -2936,6 +2945,8 @@ (define-public r-irlba
(base32
"1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
(home-page "http://cran.r-project.org/web/packages/irlba")
(synopsis "Methods for eigendecomposition of large matrices")
(description
@ -2956,10 +2967,11 @@ (define-public r-glmnet
(base32
"1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)))
(inputs
`(("gfortran" ,gfortran)))
(propagated-inputs
`(("r-foreach" ,r-foreach)))
`(("r-foreach" ,r-foreach)
("r-matrix" ,r-matrix)))
(home-page "http://www.jstatsoft.org/v33/i01")
(synopsis "Lasso and elastic-net regularized generalized linear models")
(description
@ -3077,6 +3089,8 @@ (define-public r-e1071
(base32
"1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)))
(home-page "http://cran.r-project.org/web/packages/e1071")
(synopsis "Miscellaneous functions for probability theory")
(description
@ -3688,6 +3702,9 @@ (define-public r-spams
(("if isnan\\(lambda\\) \\{")
"if (isnan(lambda)) {"))
#t)))))
(propagated-inputs
`(("r-lattice" ,r-lattice)
("r-matrix" ,r-matrix)))
(home-page "http://spams-devel.gforge.inria.fr")
(synopsis "Toolbox for solving sparse estimation problems")
(description "SPAMS (SPArse Modeling Software) is an optimization toolbox
@ -3746,17 +3763,20 @@ (define-public r-hmisc
`(("r-acepack" ,r-acepack)
("r-base64" ,r-base64)
("r-base64enc" ,r-base64enc)
("r-cluster" ,r-cluster)
("r-data-table" ,r-data-table)
("r-foreign" ,r-foreign)
("r-formula" ,r-formula)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-gtable" ,r-gtable)
;; Hmisc needs survival >= 2.40.1, so it cannot use the survival
;; package that comes with R 3.3.2.
("r-survival" ,r-survival)
("r-lattice" ,r-lattice)
("r-latticeextra" ,r-latticeextra)
("r-htmltable" ,r-htmltable)
("r-htmltools" ,r-htmltools)
("r-nnet" ,r-nnet)
("r-rpart" ,r-rpart)
("r-survival" ,r-survival)
("r-viridis" ,r-viridis)))
(home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
(synopsis "Miscellaneous data analysis and graphics functions")
@ -4041,6 +4061,8 @@ (define-public r-zoo
(base32
"167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
(home-page "http://zoo.R-Forge.R-project.org/")
(synopsis "S3 infrastructure for regular and irregular time series")
(description "This package contains an S3 class with methods for totally
@ -4307,7 +4329,9 @@ (define-public r-mixtools
"133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32"))))
(build-system r-build-system)
(propagated-inputs
`(("r-segmented" ,r-segmented)))
`(("r-boot" ,r-boot)
("r-mass" ,r-mass)
("r-segmented" ,r-segmented)))
(home-page "http://cran.r-project.org/web/packages/mixtools")
(synopsis "Tools for analyzing finite mixture models")
(description
@ -4437,7 +4461,9 @@ (define-public r-flexmix
"1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-modeltools" ,r-modeltools)))
`(("r-lattice" ,r-lattice)
("r-modeltools" ,r-modeltools)
("r-nnet" ,r-nnet)))
(home-page "http://cran.r-project.org/web/packages/flexmix")
(synopsis "Flexible mixture modeling")
(description
@ -4484,7 +4510,8 @@ (define-public r-prabclus
"0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mclust" ,r-mclust)))
`(("r-mass" ,r-mass)
("r-mclust" ,r-mclust)))
(home-page "https://cran.r-project.org/web/packages/prabclus")
(synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
(description
@ -4573,9 +4600,12 @@ (define-public r-fpc
"15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-diptest" ,r-diptest)
`(("r-class" ,r-class)
("r-cluster" ,r-cluster)
("r-diptest" ,r-diptest)
("r-flexmix" ,r-flexmix)
("r-kernlab" ,r-kernlab)
("r-mass" ,r-mass)
("r-mclust" ,r-mclust)
("r-mvtnorm" ,r-mvtnorm)
("r-prabclus" ,r-prabclus)
@ -4694,7 +4724,8 @@ (define-public r-rcppeigen
(properties `((upstream-name . "RcppEigen")))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)))
`(("r-rcpp" ,r-rcpp)
("r-matrix" ,r-matrix)))
(home-page "http://eigen.tuxfamily.org")
(synopsis "Rcpp integration for the Eigen templated linear algebra library")
(description
@ -4739,6 +4770,8 @@ (define-public r-matrixmodels
"0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
(properties `((upstream-name . "MatrixModels")))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
(home-page "https://cran.r-project.org/web/packages/MatrixModels")
(synopsis "Modelling with sparse and dense matrices")
(description
@ -4816,7 +4849,9 @@ (define-public r-lme4
("r-rcppeigen" ,r-rcppeigen)))
(propagated-inputs
`(("r-minqa" ,r-minqa)
("r-nloptr" ,r-nloptr)))
("r-nloptr" ,r-nloptr)
("r-mass" ,r-mass)
("r-nlme" ,r-nlme)))
(home-page "http://cran.r-project.org/web/packages/lme4")
(synopsis "Linear mixed-effects models using eigen and S4")
(description
@ -4839,7 +4874,9 @@ (define-public r-pbkrtest
"00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lme4" ,r-lme4)))
`(("r-lme4" ,r-lme4)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)))
(home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
(synopsis "Methods for linear mixed model comparison")
(description
@ -4861,7 +4898,10 @@ (define-public r-car
"0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-pbkrtest" ,r-pbkrtest)
`(("r-mass" ,r-mass)
("r-mgcv" ,r-mgcv)
("r-nnet" ,r-nnet)
("r-pbkrtest" ,r-pbkrtest)
("r-quantreg" ,r-quantreg)))
(home-page "https://r-forge.r-project.org/projects/car/")
(synopsis "Companion to applied regression")
@ -5000,7 +5040,8 @@ (define-public r-tclust
"0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mclust" ,r-mclust)
`(("r-cluster" ,r-cluster)
("r-mclust" ,r-mclust)
("r-mvtnorm" ,r-mvtnorm)
("r-sn" ,r-sn)))
(home-page "http://cran.r-project.org/web/packages/tclust")

18
guix/import/cran.scm
View file

@ -164,32 +164,16 @@ (define (listify meta field)
(map string-trim-both items))))))
(define default-r-packages
(list "KernSmooth"
"MASS"
"Matrix"
"base"
"boot"
"class"
"cluster"
"codetools"
(list "base"
"compiler"
"datasets"
"foreign"
"grDevices"
"graphics"
"grid"
"lattice"
"methods"
"mgcv"
"nlme"
"nnet"
"parallel"
"rpart"
"spatial"
"splines"
"stats"
"stats4"
"survival"
"tcltk"
"tools"
"translations"