[Genabel-commits] r1782 - pkg/GenABEL-general/distrib_scripts

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

Author: lckarssen
Date: 2014-07-30 23:24:10 +0200 (Wed, 30 Jul 2014)
New Revision: 1782

Modified:
   pkg/GenABEL-general/distrib_scripts/makedistrib_DatABEL.sh
   pkg/GenABEL-general/distrib_scripts/makedistrib_VariABEL.sh
Log:
- makedistrib_VariABEL.sh: Minor improvement (use of a variable instead of repeating the SVNBASE 3x)
- makedistrib_DatABEL.sh: Updated the script to use functions in distrib_support_functions.sh


Modified: pkg/GenABEL-general/distrib_scripts/makedistrib_DatABEL.sh
===================================================================
--- pkg/GenABEL-general/distrib_scripts/makedistrib_DatABEL.sh	2014-07-30 21:13:06 UTC (rev 1781)
+++ pkg/GenABEL-general/distrib_scripts/makedistrib_DatABEL.sh	2014-07-30 21:24:10 UTC (rev 1782)
@@ -13,15 +13,18 @@
 #   time if you're expecting trouble)
 
 PKG=DatABEL
-CRAN_repo='"http://cran-mirror.cs.uu.nl"'
 
-# Exit on errors
+# Exit on errors and when encountering uninitialised variables
 set -e
+set -u
 
 # Find the directory where this script (and others it depends on) are
 # located
 scriptdir=$(dirname $0)
 
+source $scriptdir/distrib_support_functions.sh
+init_buildenv
+
 # Parse command line options
 NOCHECKOUT=false
 CRANCHECK=true
@@ -63,7 +66,7 @@
     svn export $SVNBASE/pkg/$PKG
     svn export $SVNBASE/pkg/filevector
 
-    cd DatABEL
+    cd $PKG
     rm -f cleanup* configure* *.R
     cd src
     cp DAlib/*.c* .
@@ -96,64 +99,5 @@
 fi
 
 
-# In order not to mess with the current user's R library directory we
-# set one in /tmp. Most Linux distributions will remove the
-# directories in /tmp on reboot or after several days.
-export R_LIBS=/tmp/Rlibs-$PKG-build
-mkdir -p $R_LIBS
-
-echo
-echo "--------------------------------------------------"
-echo "Installing missing R packages from CRAN and Bioconductor" \
-     "into the directory $R_LIBS"
-echo "--------------------------------------------------"
-
-deps=$($scriptdir/getdeps.awk $PKG/DESCRIPTION)
-
-R --vanilla --no-save --slave <<EOF
-deplist=c($deps)
-
-new.packages <- deplist[!(deplist %in% installed.packages()[,"Package"])]
-
-if (length(new.packages)) {
-    install.packages(new.packages, repos=$CRAN_repo)
-}
-EOF
-
-errwarn=0
-echo
-echo "--------------------------------------------------"
-echo "Building the package..."
-echo "--------------------------------------------------"
-R --vanilla CMD build $PKG
-PKGFILE=${PKG}_${DESCVERSION}.tar.gz
-
-echo
-echo "--------------------------------------------------"
-echo "Running normal R check on $PKGFILEs..."
-echo "--------------------------------------------------"
-R --vanilla CMD check $PKGFILE
-if grep -qE "NOTE|WARNING|ERROR" $PKG.Rcheck/00check.log; then
-    errwarn=1
-fi
-
-if [ $CRANCHECK == true ]; then
-    echo
-    echo "--------------------------------------------------"
-    echo "Check $PKGFILE with --as-cran..."
-    echo "--------------------------------------------------"
-    R --vanilla CMD check --as-cran $PKGFILE
-    if sed -e 's/feasibility ... WARNING/feasibility ... WRNNG/' \
-        -e 's/^WARNING/WRNNG/' $PKG.Rcheck/00check.log | \
-        grep -qE "NOTE|WARNING|ERROR"; then
-        errwarn=1
-    fi
-fi
-
-## Report whether warnings, errors, notes where found
-if [ $errwarn -eq 1 ]; then
-    echo
-    echo "NOTEs, WARNINGs or ERRORs found!" 1>&2
-    echo "Please fix before uploading to CRAN" 1>&2
-    exit 1
-fi
+install_deps
+run_checks_build

Modified: pkg/GenABEL-general/distrib_scripts/makedistrib_VariABEL.sh
===================================================================
--- pkg/GenABEL-general/distrib_scripts/makedistrib_VariABEL.sh	2014-07-30 21:13:06 UTC (rev 1781)
+++ pkg/GenABEL-general/distrib_scripts/makedistrib_VariABEL.sh	2014-07-30 21:24:10 UTC (rev 1782)
@@ -62,9 +62,11 @@
     echo "--------------------------------------------------"
     echo "Checking out source code from SVN..."
     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/${PKG}
+    SVNBASE=svn://svn.r-forge.r-project.org/svnroot/genabel/
+    svn export $SVNBASE/pkg/filevector
+    svn export $SVNBASE/pkg/DatABEL
+    svn export $SVNBASE/pkg/${PKG}
+
     cd ${PKG}
     rm -f cleanup* configure* *.R
     cd src