[Genabel-commits] r1485 - pkg/GenABEL-general/scripts

[noreply at r-forge.r-project.org]

Author: maksim
Date: 2013-12-19 11:47:49 +0100 (Thu, 19 Dec 2013)
New Revision: 1485

Modified:
   pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
Log:
Automatic installation of GenABEL. Create directory, extract all neccassary packages from r-forge and crab, build and install them, install tutorial and GenABEL itself at the end

Modified: pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
===================================================================
--- pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-18 23:05:50 UTC (rev 1484)
+++ pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-19 10:47:49 UTC (rev 1485)
@@ -1,14 +1,80 @@
 #!/bin/bash
-rm -rf GenABEL*
-rm -rf DatABEL DatABEL.*
-rm -rf filevector*
+
+installation_dir="GenABEL_version_for_submission"
+
+
+
+echo
+echo Remove GenABEL_version_for_submission...
+echo
+rm -rf $installation_dir
+echo
+echo Create GenABEL_version_for_submission...
+echo
+mkdir GenABEL_version_for_submission
+cd GenABEL_version_for_submission
+
+echo
+echo Extract packages from r-forge...
+echo
 svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/filevector
 svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/DatABEL
+svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/MetABEL
+svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/ProbABEL
+svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/MixABEL
+svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/GenABEL.data
 svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/GenABEL
-svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/GenABEL.data
 svn export svn://svn.r-forge.r-project.org/svnroot/genabel/tutorials/GenABEL_general
 
 
+echo
+echo Install the freshest R packages from CRAN repository...
+echo
+
+echo "install.packages(\"roxygen2\", repos='http://cran.us.r-project.org')" > install_roxygen_file.R
+echo "install.packages(\"mvtnorm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"methods\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"MASS\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"utils\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"qvalue\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"genetics\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"haplo.stats\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"hglm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"PredictABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"VariABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+echo "install.packages(\"bigRR\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
+R -f install_roxygen_file.R
+rm -rf install_roxygen_file.R
+
+
+
+
+
+
+echo
+echo Build and install packages...
+echo
+
+R CMD build DatABEL
+R CMD INSTALL DatABEL_*
+
+R CMD build MetABEL
+R CMD INSTALL MetABEL_*
+
+
+cd ProbABEL
+autoreconf -i
+./configure --without-eigen
+make
+cd ..
+
+probabel_src_location="$(pwd)/ProbABEL/src"
+PATH="$PATH:$probabel_src_location"
+echo Search ProbABEL executive files in $probabel_src_location
+
+R CMD build MixABEL
+R CMD INSTALL MixABEL_*
+
 cd GenABEL.data
 rm -rf inst R
 cd ../
@@ -18,6 +84,9 @@
 
 
 
+echo
+echo Build, check and install GenABEL...
+echo
 # clean up the dev-version for distrib
 cd GenABEL
 rm cleanup* configure* *.R
@@ -43,6 +112,9 @@
 R CMD check GenABEL
 R CMD INSTALL GenABEL
 
+echo
+echo Build the tutorial...
+echo
 # build the tutorial
 cd GenABEL_general
 make
@@ -50,6 +122,9 @@
 cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/.
 # end build the tutorial
 
+echo
+echo Build the working version of GenABEL...
+echo
 R CMD build GenABEL
 
 # and do not forget to run R CMD check --as-cran!