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.

1 files changed, 17 insertions, 4 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 @@
         (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")