bug#26095: [PATCH 16/17] gnu: r: Do not build recommended packages.

[Ricardo Wurmus]

* 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/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/statistics.scm     | 83 ++++++++++++++++++++++++++++++-----------
 guix/import/cran.scm            | 18 +--------
 3 files changed, 80 insertions(+), 42 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 770bea7e3..daef0f6de 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
@@ -5344,6 +5347,7 @@ 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";)
@@ -5425,7 +5429,8 @@ 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
@@ -5723,6 +5728,7 @@ 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";)
@@ -6122,7 +6128,8 @@ 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)
@@ -6650,6 +6657,7 @@ 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")
@@ -6841,8 +6849,9 @@ 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")
@@ -8234,7 +8243,8 @@ 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
@@ -8286,6 +8296,7 @@ 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";)
@@ -8444,6 +8455,7 @@ 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")
@@ -8507,6 +8519,7 @@ 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")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c836409b6..b8abbf62d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -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";)
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 40cdea029..7521a39bc 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -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"
-- 
2.12.0