add option to choose R binary path

rtest.sh

@@ -209,7 +209,7 @@ function printUsage(){
 echo "`basename $0` is a tool to test that a R package (PACKAGE_TO_TEST) does not break packages that depend on it by running 'R CMD check' for each of them.
 
 usage :
-$0 [-p|--package NAME_OF_PACKAGE_TO_TEST || -c|--checklist CHECKLIST_FILE || --checklistraw -t|--tarfolder TAR_FOLDER_PATH] [-l|--libuser R_USER_LIB_VALUE] [-d|--dest DESTINATION_DIRECTORY] [-m|--mail MAIL_TO] [-u|--urlresult URL] [-r|--repo PACKAGE_TO_TEST_REPO] [-x|--xvfb XVFB-RUN PATH] [-n|--nbcores NBCORES] [-s|--skipinstall] [-h|--html]
+$0 [-p|--package NAME_OF_PACKAGE_TO_TEST || -c|--checklist CHECKLIST_FILE || --checklistraw -t|--tarfolder TAR_FOLDER_PATH] [-l|--libuser R_USER_LIB_VALUE] [-d|--dest DESTINATION_DIRECTORY] [-m|--mail MAIL_TO] [-u|--urlresult URL] [-r|--repo PACKAGE_TO_TEST_REPO] [-x|--xvfb XVFB-RUN PATH] [-n|--nbcores NBCORES] [-s|--skipinstall] [-h|--html] [--rpath PATH_TO_R_BINARY]
 
 -p | --package NAME_OF_PACKAGE_TO_TEST : name of package to test (case sensible), all packages depending on this package are going to be checked by their R CMD CHECK
 -c | --checklist CHECKLIST_FILE : file listing packages you want to check (each line should look like : PKG_NAME,PKG_VERSION,anything)
@@ -226,13 +226,14 @@ $0 [-p|--package NAME_OF_PACKAGE_TO_TEST || -c|--checklist CHECKLIST_FILE || --c
 -n | --nbcores NBCORES : Number of cores for parallel executions of installations (Ncpu parameter) and number of simultaneous checks (DEFAULT : 1)
 -s | --skipinstall : flag to skip the packages update/installation
 -h | --html : generate html report in DESTINATION_DIRECTORY/index.html . Will download jquery in destination directory
+--rpath PATH_TO_R_BINARY : will use PATH_TO_R_BINARY to call R (default=R)
 
 Don't forget to set JAVA_HOME if some dependencies need java, which is quite probable.
 
 "
 }
 
-ARGS=$(getopt -o t:c:p:r:d:m:l:x:n:shu: --long tarfolder:,checklist:,checklistraw:,package:,repo:,mail:,libuser:,dest:,xvfb:,nbcores:,skipinstall,html,urlresult: -n "$0" -- "$@");
+ARGS=$(getopt -o t:c:p:r:d:m:l:x:n:shu: --long rpath:,tarfolder:,checklist:,checklistraw:,package:,repo:,mail:,libuser:,dest:,xvfb:,nbcores:,skipinstall,html,urlresult: -n "$0" -- "$@");
 
 #Bad arguments
 if [ $? -ne 0 ] || [ $# -eq 0 ];
@@ -250,6 +251,8 @@ NBCORES=1
 SKIPINSTALLFLAG=0
 HTMLFLAG=0
 RESULTURLFLAG=0
+R_LIBS_USER_FLAG=0
+RPATH=R
 eval set -- "$ARGS";
 
 while true; do
@@ -276,6 +279,19 @@ while true; do
             fi
             shift;
             ;;
+        --rpath)
+            shift;
+            if [ -n "$1" ]; then
+                RPATH=$1
+            else
+                echo "You have to set a non-empty R PATH
+
+                "
+                printUsage
+                exit
+            fi
+            shift;
+            ;;
         -l|--libuser)
             shift;
             if [ -n "$1" ]; then
@@ -284,6 +300,7 @@ while true; do
                     echo "CREATING '$1' personnal R library"
                 fi
                 export R_LIBS_USER=$(readlink -f "$1")
+                R_LIBS_USER_FLAG=1
             else
                 echo "You have to set a non-empty R LIB USER directory
 
@@ -392,7 +409,7 @@ ff <- file("/tmp/Rversions.txt", open = "w")
 cat( paste(sep=",",a[,1],sub("\n","",a[,2]),sub("\n"," ",a[,3]), collapse = "\n"), "\n", file=ff)
 close(ff)
                     ' > /tmp/getVersions.R
-                    R CMD BATCH /tmp/getVersions.R > /dev/null 2>&1
+                    $RPATH CMD BATCH /tmp/getVersions.R > /dev/null 2>&1
                     cat /tmp/Rversions.txt | sort -t , -k 1,1 > /tmp/join1
                     cat $CHECKLIST_RAW_FILE | sort -t , -k 1,1 > /tmp/join2
                     join /tmp/join1 /tmp/join2 -j 1 -t ',' > /tmp/list_with_versions.txt
@@ -485,6 +502,12 @@ done
 #    shift
 #done
 
+if [ $DESTINATIONFLAG == 1 ]; then
+    RVERSION=`$RPATH --version | head -n 1 | awk '{print $3}'`
+    mkdir "$R_LIBS_USER/$RVERSION"
+    export R_LIBS_USER=$R_LIBS_USER/$RVERSION
+fi
+
 if ! [ -n "$PACKAGE_TO_TEST" ]; then
     if ! [ -n "$CHECKLIST_FILE" ]; then
         if ! [ -n "$TAR_FOLDER_PATH" ]; then
@@ -657,7 +680,7 @@ if [ -n "$PACKAGE_TO_TEST" ]; then
     cat( paste(sep=",",packageVersion("'$PACKAGE_TO_TEST'")), file=ff)
     close(ff)
     ' > $DESTINATION/install_pkg.R
-    R CMD BATCH install_pkg.R
+    $RPATH CMD BATCH install_pkg.R
 
     if [[ $HTMLFLAG == 1 ]]; then
         generate_html_report $DESTINATION
@@ -674,7 +697,7 @@ if [ -n "$PACKAGE_TO_TEST" ]; then
     ############### GENERATION OF DEPENDENCY LIST ###################
 
     printLeftPurple "Generating dependency list (should take less than a minute)... started at `date '+%H:%M:%S'` ... "
-    R CMD BATCH --no-timing depends.R
+    $RPATH CMD BATCH --no-timing depends.R
     #cat depends.txt | grep -v structSSI | grep -v SigTree | grep -v SeqFeatR | grep -v gWidgetsRGtk2 | grep -v GrammR | grep -v RADami > list_dependencies.txt
     cat depends.txt > list_dependencies.txt
     printRightGreen "`date '+%H:%M:%S'` : OK"
@@ -705,7 +728,7 @@ if [[ "$SKIPINSTALLFLAG" == "0" ]]; then
     biocLite("supraHex", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
     install.packages("mpoly",lib=Sys.getenv("R_LIBS_USER"),repos="http://cran.irsn.fr/")
     ' > $DESTINATION/update.R
-    $XVFBRUN_PATH -n 222 R CMD BATCH --slave --vanilla --quiet update.R
+    $XVFBRUN_PATH -n 222 $RPATH CMD BATCH --slave --vanilla --quiet update.R
 
     ret_upd=$?
     non_zero=`grep -i "non-zero exit status" update.Rout | wc -l`
@@ -750,9 +773,9 @@ Installing `wc -l $PACKAGES_TO_CHECK_LIST_FILE` packages in R_LIBS_USER (may be
     }
     ' > ${pname}_install.R
 
-            $XVFBRUN_PATH -n 222 R CMD BATCH --slave --vanilla --quiet ${pname}_install.R
+            $XVFBRUN_PATH -n 222 $RPATH CMD BATCH --slave --vanilla --quiet ${pname}_install.R
             # we do it twice to be sure...
-            $XVFBRUN_PATH -n 222 R CMD BATCH --slave --vanilla --quiet ${pname}_install.R
+            $XVFBRUN_PATH -n 222 $RPATH CMD BATCH --slave --vanilla --quiet ${pname}_install.R
             ret=`grep -i "non-zero exit status|statut de sortie non nul" ${pname}_install.Rout | wc -l`
             if [[ $ret == '0' ]]; then
                 touch ${pname}_install_ok
@@ -784,9 +807,9 @@ Installing `ls $TAR_FOLDER_PATH | wc -l` packages in R_LIBS_USER (may be long if
     }
     ' > ${pname}_install.R
 
-            $XVFBRUN_PATH -n 222 R CMD INSTALL -l "$R_LIBS_USER" $file > ${pname}_install.Rout 2>&1
+            $XVFBRUN_PATH -n 222 $RPATH CMD INSTALL -l "$R_LIBS_USER" $file > ${pname}_install.Rout 2>&1
             # we do it twice to be sure...
-            $XVFBRUN_PATH -n 222 R CMD INSTALL -l "$R_LIBS_USER" $file > ${pname}_install.Rout 2>&1
+            $XVFBRUN_PATH -n 222 $RPATH CMD INSTALL -l "$R_LIBS_USER" $file > ${pname}_install.Rout 2>&1
             ret=`grep -i "non-zero exit status|statut de sortie non nul" ${pname}_install.Rout | wc -l`
             if [[ $ret == '0' ]]; then
                 touch ${pname}_install_ok
@@ -821,7 +844,7 @@ if [[ $NBCORES == 1 ]]; then
             printLeftPurple "R CMD check ${pname}_${pversion}.tar.gz ... started at `date '+%H:%M:%S'` ... "
 
             wget $DEFAULT_REPOSITORY/src/contrib/${pname}_${pversion}.tar.gz > ${pname}_${pversion}_download.log 2>&1
-            $XVFBRUN_PATH -n $RANDOM R CMD check --no-manual --no-vignettes --no-build-vignettes -l "$R_LIBS_USER" ${pname}_${pversion}.tar.gz  > /dev/null 2>&1
+            $XVFBRUN_PATH -n $RANDOM $RPATH CMD check --no-manual --no-vignettes --no-build-vignettes -l "$R_LIBS_USER" ${pname}_${pversion}.tar.gz  > /dev/null 2>&1
             if [[ $? == 0 ]]; then
                 touch ${pname}.CHECKOK
                 printRightGreen "`date '+%H:%M:%S'` : OK"
@@ -842,7 +865,7 @@ if [[ $NBCORES == 1 ]]; then
             pversion=`echo $file | cut -d '_' -f 2`
             printLeftPurple "R CMD check ${pname}_${pversion} ... started at `date '+%H:%M:%S'` ... "
 
-            $XVFBRUN_PATH -n $RANDOM R CMD check --no-manual --no-vignettes --no-build-vignettes -l "$R_LIBS_USER" $file  > /dev/null 2>&1
+            $XVFBRUN_PATH -n $RANDOM $RPATH CMD check --no-manual --no-vignettes --no-build-vignettes -l "$R_LIBS_USER" $file  > /dev/null 2>&1
             if [[ $? == 0 ]]; then
                 touch ${pname}.CHECKOK
                 printRightGreen "`date '+%H:%M:%S'` : OK"
@@ -1000,13 +1023,13 @@ else
                         echo "R CMD check ${pname}_${pversion}.tar.gz ... STARTED on slot $j at `date '+%H:%M:%S'` ... "
 
                         wget $DEFAULT_REPOSITORY/src/contrib/${pname}_${pversion}.tar.gz > ${pname}_${pversion}_download.log 2>&1
-                        $XVFBRUN_PATH -n $RANDOM R CMD check --no-manual --no-vignettes --no-build-vignettes -l "$DESTINATION/${pname}.rlib" ${pname}_${pversion}.tar.gz  > /dev/null 2>&1 &
+                        $XVFBRUN_PATH -n $RANDOM $RPATH CMD check --no-manual --no-vignettes --no-build-vignettes -l "$DESTINATION/${pname}.rlib" ${pname}_${pversion}.tar.gz  > /dev/null 2>&1 &
                         p_pid[$j]=$!
                     else
                         pfile=${files[$ftc]}
                         echo "R CMD check $pfile ... STARTED on slot $j at `date '+%H:%M:%S'` ... "
-                        echo "$XVFBRUN_PATH -n $RANDOM R CMD check --no-manual --no-vignettes --no-build-vignettes -l \"$DESTINATION/${pname}.rlib\" $pfile  > /dev/null 2>&1 &"
-                        $XVFBRUN_PATH -n $RANDOM R CMD check --no-manual --no-vignettes --no-build-vignettes -l "$DESTINATION/${pname}.rlib" $pfile  > /dev/null 2>&1 &
+                        echo "$XVFBRUN_PATH -n $RANDOM $RPATH CMD check --no-manual --no-vignettes --no-build-vignettes -l \"$DESTINATION/${pname}.rlib\" $pfile  > /dev/null 2>&1 &"
+                        $XVFBRUN_PATH -n $RANDOM $RPATH CMD check --no-manual --no-vignettes --no-build-vignettes -l "$DESTINATION/${pname}.rlib" $pfile  > /dev/null 2>&1 &
                         p_pid[$j]=$!
                         p_pkgfile[$j]=$pfile
                     fi