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-rw-r--r--gnu/packages/bioinformatics.scm21
-rw-r--r--gnu/packages/python.scm3
-rw-r--r--gnu/packages/statistics.scm83
3 files changed, 81 insertions, 26 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")
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 @@ 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/")
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 @@ 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")