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 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') 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 @@ (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") -- cgit v1.2.3