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authorpjotrp2016-02-28 12:45:40 +0000
committerpjotrp2016-02-28 12:45:40 +0000
commit71684ab0577b60b53d4a459e97bb5540952ea4d9 (patch)
tree0fe8aa87c40f567213feaca19284e2a9fa75e8c5 /gn/packages
parentd5a9e7dd0616461ec9960b9e57665dcc766d9b33 (diff)
downloadguix-bioinformatics-71684ab0577b60b53d4a459e97bb5540952ea4d9.tar.gz
r-wgcna deps
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm12
-rw-r--r--gn/packages/statistics.scm85
2 files changed, 93 insertions, 4 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index dd7e77e..92be2b4 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -49,7 +49,7 @@
#:use-module (srfi srfi-1))
(define-public r-wgcna
- (let ((commit "41b24edb522a200b671e8e25f6ffb67769113a49"))
+ (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb"))
(package
(name "r-wgcna")
(version (string-append "1.49-" commit))
@@ -62,18 +62,19 @@
(file-name (string-append name "-" commit))
(sha256
(base32
- "1ad2lgdz8dy8imn4my83jz4xqp4m3phyakfssmdjcp362g739p2w"))))
+ "1zqnsb8s3065rq1y2y3l79zi8wmdwjkcjls96ypycrb7pmdil58j"))))
(properties `((upstream-name . "WGCNA")))
(build-system r-build-system)
(propagated-inputs
`( ;; ("r-annotationdbi" ,r-annotationdbi)
; ("r-biocparallel" ,r-biocparallel)
("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-doparallel" ,r-doparallel)
("r-fastcluster" ,r-fastcluster)
("r-foreach" ,r-foreach)
- ; ("r-go-db" ,r-go-db)
+ ("r-go-db" ,r-go-db)
; ("r-grdevices" ,r-grdevices)
- ; ("r-hmisc" ,r-hmisc)
+ ("r-hmisc" ,r-hmisc)
("r-impute" ,r-impute)
("r-matrixstats" ,r-matrixstats)
; ("r-parallel" ,r-parallel)
@@ -83,6 +84,9 @@
; ("r-survival" ,r-survival)
; ("r-utils" ,r-utils)
))
+ (arguments
+ `(
+ #:tests? #f)) ; no 'setup.py test'
(home-page
"http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
(synopsis
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 57ddfe6..cc2726c 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -18,6 +18,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages file)
+ #:use-module (gnu packages gcc)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
@@ -39,6 +40,90 @@
#:use-module (gnu packages bootstrap)
#:use-module (srfi srfi-1))
+(define-public r-acepack
+(package
+ (name "r-acepack")
+ (version "1.3-3.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acepack" version))
+ (sha256
+ (base32
+ "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y"))))
+ (build-system r-build-system)
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (home-page
+ "http://cran.r-project.org/web/packages/acepack")
+ (synopsis
+ "ace() and avas() for selecting regression transformations")
+ (description
+ "ACE and AVAS methods for choosing regression transformations.")
+ (license license:x11)))
+
+(define-public r-hmisc
+(package
+ (name "r-hmisc")
+ (version "3.17-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Hmisc" version))
+ (sha256
+ (base32
+ "110w5hbrl10isslqs0iq6w2ll0dafqyqznb50cdcallnlnvbvxrg"))))
+ (properties `((upstream-name . "Hmisc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-acepack" ,r-acepack)
+ ; ("r-cluster" ,r-cluster)
+ ; ("r-foreign" ,r-foreign)
+ ; ("r-formula" ,r-formula)
+ ("r-ggplot2" ,r-ggplot2)
+ ; ("r-grid" ,r-grid)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gtable" ,r-gtable)
+ ("r-lattice" ,r-lattice)
+ ; ("r-latticeextra" ,r-latticeextra)
+ ; ("r-methods" ,r-methods)
+ ; ("r-nnet" ,r-nnet)
+ ; ("r-rpart" ,r-rpart)
+ ; ("r-survival" ,r-survival)))
+ ))
+ (home-page
+ "http://biostat.mc.vanderbilt.edu/Hmisc")
+ (synopsis "Harrell Miscellaneous")
+ (description
+ "Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.")
+ (license license:gpl2+)))
+
+(define-public r-doparallel
+(package
+ (name "r-doparallel")
+ (version "1.0.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "doParallel" version))
+ (sha256
+ (base32
+ "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh"))))
+ (properties `((upstream-name . "doParallel")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-foreach" ,r-foreach)
+ ("r-iterators" ,r-iterators)
+ ;; ("r-parallel" ,r-parallel)
+ ))
+ (home-page
+ "http://cran.r-project.org/web/packages/doParallel")
+ (synopsis
+ "Foreach Parallel Adaptor for the 'parallel' Package")
+ (description
+ "Provides a parallel backend for the %dopar% function using the parallel package.")
+ (license license:gpl2+)))
+
(define-public r-iterators
(package
(name "r-iterators")