From 71684ab0577b60b53d4a459e97bb5540952ea4d9 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 12:45:40 +0000
Subject: r-wgcna deps

---
 gn/packages/bioinformatics.scm | 12 ++++--
 gn/packages/statistics.scm     | 85 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+), 4 deletions(-)

(limited to 'gn/packages')

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")
-- 
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