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gnu: r: Do not build recommended packages.

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* 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
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21
gnu/packages/bioinformatics.scm
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@ -108,6 +108,9 @@
(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 @@ information as possible.")
(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 @@ microarrays.")
`(("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 @@ annotation infrastructure.")
("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 @@ functionality.")
(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 @@ files.")
("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 @@ information about the latest version of the Gene Ontologies.")
("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 @@ number detection tools.")
"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 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
(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 @@ analysis.")
`(("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 @@ specific parser.")
(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 @@ operators such as union, intersection, and difference.")
`(("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 @@ can be imported from spreadsheets, text files and database sources and it can
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 @@ be output in text, PostScript, PDF or HTML.")
(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 @@ be output in text, PostScript, PDF or HTML.")
(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 @@ legends.")
("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 @@ side.")
(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 @@ inference for statistical models.")
(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 @@ flexible than the orphaned \"base64\" package.")
(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 @@ analysis of large sparse or dense matrices.")
(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 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
(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 @@ from within R.")
(("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 @@ package instead.")
`(("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 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
(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 @@ letters, as is often required for scientific publications.")
"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 @@ to change in the future.")
"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 @@ and resampling-based inference.")
"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 @@ of the points.")
"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 @@ based on an interface to Fortran implementations by M. J. D. Powell.")
(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 @@ metrics for evaluating models.")
"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 @@ algorithms.")
("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 @@ C++ library for numerical linear algebra and RcppEigen glue.")
"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 @@ bootstrap test for generalized linear mixed models.")
"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 @@ multivariate case.")
"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 @@ empty list when the FIELD cannot be found."
(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"