From aeb64f3cb295f63ecea772716c5576cfd8223dd8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 12 Mar 2017 00:21:39 +0100 Subject: gnu: r: Do not build recommended packages. * 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. --- gnu/packages/bioinformatics.scm | 21 +++++++++-- gnu/packages/python.scm | 3 +- gnu/packages/statistics.scm | 83 ++++++++++++++++++++++++++++++----------- guix/import/cran.scm | 18 +-------- 4 files changed, 82 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 077f9b2885..bd3c97b721 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5706218f15..ba3c7d4c36 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -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/") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c836409b61..b8abbf62db 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -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") diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 40cdea029b..7521a39bc9 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -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" -- cgit v1.2.3