diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 12 | ||||
| -rw-r--r-- | gn/packages/statistics.scm | 85 |
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") |