to be tested again : add -t option to give a folder containing tarballs to check

rtest.sh

@@ -92,6 +92,7 @@ function generate_html_report(){
     # CHECK, for all the downloaded archives
     if [[ "`ls $dir | grep ".tar.gz" | wc -l`" != "0" ]]; then
         for elem in `ls $dir/*.tar.gz`; do
+
             local baselem=`basename $elem`
             local baselem=${baselem/.tar.gz/}
             # split string into array
@@ -100,26 +101,28 @@ function generate_html_report(){
             local package_name=${package[0]}
             local package_version=${package[1]}
 
-            # si CHECKOK
-            if [ -f $dir"/"$package_name".CHECKOK" ]; then
-                local status="ok"
-                local color="#4EE877"
-            # si CHECKPROBLEM
-            else 
-                if [ -f $dir"/"$package_name".CHECKPROBLEM" ]; then
-                    local status="problem"
-                    local color="red"
-                else
-                    local status="running"
-                    local color="yellow"
+            if [ -d $dir"/"$package_name".Rcheck/" ]; then
+                # si CHECKOK
+                if [ -f $dir"/"$package_name".CHECKOK" ]; then
+                    local status="ok"
+                    local color="#4EE877"
+                # si CHECKPROBLEM
+                else 
+                    if [ -f $dir"/"$package_name".CHECKPROBLEM" ]; then
+                        local status="problem"
+                        local color="red"
+                    else
+                        local status="running"
+                        local color="yellow"
+                    fi
                 fi
-            fi
 
-            local log=`cat $dir"/"$package_name".Rcheck/00check.log"`
-            local nlines=`cat $dir"/"$package_name".Rcheck/00check.log" | wc -l`
-            echo "<tr style='background-color:$color' class='title'><td>CHECK $package_name V $package_version</td>" >> $dest_html
-            echo "<td>$status ($nlines lines)</td></tr>" >> $dest_html
-            echo "<tr class='retractable' id='$package_name'><td colspan=3><textarea cols='200' rows='30'>$log</textarea></td></tr>" >> $dest_html
+                local log=`cat $dir"/"$package_name".Rcheck/00check.log"`
+                local nlines=`cat $dir"/"$package_name".Rcheck/00check.log" | wc -l`
+                echo "<tr style='background-color:$color' class='title'><td>CHECK $package_name V $package_version</td>" >> $dest_html
+                echo "<td>$status ($nlines lines)</td></tr>" >> $dest_html
+                echo "<tr class='retractable' id='$package_name'><td colspan=3><textarea cols='200' rows='30'>$log</textarea></td></tr>" >> $dest_html
+            fi
         done
     fi
 
@@ -205,10 +208,11 @@ 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] [-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 || -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]
 
 -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)
+-t | --tarfolder TAR_FOLDER_PATH : path to folder where tarballs of packages can be found. All of these packages are going to be \"R CMD CHECKED\"
 -r | --repo PACKAGE_TO_TEST_REPO : repository of package you want to test (DEFAULT : R-CRAN)
 -l | --libuser R_LIBS_USER : directory where packages depending on PACKAGE_TO_TEST are going to be installed (DEFAULT : R will choose it)
                              This directory can be used several times for several tests. Using same directory several times will save time.
@@ -226,7 +230,7 @@ Don't forget to set JAVA_HOME if some dependencies need java, which is quite pro
 "
 }
 
-ARGS=$(getopt -o c:p:r:d:m:l:x:n:shu: -l "checklist: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: -l "tarfolder:checklist:package:repo:mail:libuser:dest:xvfb:nbcores:skipinstall,html,urlresult:" -n "$0" -- "$@");
 
 #Bad arguments
 if [ $? -ne 0 ] || [ $# -eq 0 ];
@@ -239,6 +243,7 @@ MAILTOFLAG=0
 DESTINATIONFLAG=0
 PACKAGE_TO_TEST=""
 CHECKLIST_FILE=""
+TAR_FOLDER_PATH=""
 NBCORES=1
 SKIPINSTALLFLAG=0
 HTMLFLAG=0
@@ -362,6 +367,26 @@ while true; do
             fi
             shift;
             ;;
+        -t|--tarfolder)
+            shift;
+            if [ -n "$1" ]; then
+                TAR_FOLDER_PATH="$1"
+                MAIL_SUBJECT_BEGIN="Folder of packages \"$TAR_FOLDER_PATH\""
+                if ! [ -d $TAR_FOLDER_PATH ]; then
+                    echo "Folder $TAR_FOLDER_PATH not found...
+
+                    "
+                    exit
+                fi
+            else
+                echo "You have to set a non-empty TAR_FOLDER_PATH path
+
+                "
+                printUsage
+                exit
+            fi
+            shift;
+            ;;
         -x|--xvfb)
             shift;
             if [ -n "$1" ]; then
@@ -422,21 +447,27 @@ done
 
 if ! [ -n "$PACKAGE_TO_TEST" ]; then
     if ! [ -n "$CHECKLIST_FILE" ]; then
-        echo "
-There must be a package to test OR a CHECKLIST_FILE.
+        if ! [ -n "$TAR_FOLDER_PATH" ]; then
+            echo "
+There must be a package to test OR a CHECKLIST_FILE OR a TAR_FOLDER_PATH.
 
-        "
-        exit
+At least -p or -c or -t option must be set.
+
+"
+            exit
+        fi
     fi
-else
-    if [ -n "$CHECKLIST_FILE" ]; then
-        echo "
+fi
+
+if ([ -n "$CHECKLIST_FILE" ] && [ -n "$TAR_FOLDER_PATH" ]) ||
+   ([ -n "$CHECKLIST_FILE" ] && [ -n "$PACKAGE_TO_TEST" ]) ||
+   ([ -n "$PACKAGE_TO_TEST" ] && [ -n "$TAR_FOLDER_PATH" ]); then
+    echo "
 There must choose between testing a specific package (R CMD CHECK on all packages depending on it) OR checking a given list of packages.
 
-In other words : choose between -p and -c option
+In other words : choose between -p and -c and -t option.
 "
-        exit
-    fi
+    exit
 fi
 
 #### DEFAULT VALUES management
@@ -453,7 +484,11 @@ fi
 if [ -n "$PACKAGE_TO_TEST" ]; then
     echo "PACKAGE TO TEST : $PACKAGE_TO_TEST . Last version of $PACKAGE_TO_TEST and all packages depending on $PACKAGE_TO_TEST will be installed and checked"
 else
-    echo "LIST OF PACKAGES TO INSTALL AND CHECK : $CHECKLIST_FILE"
+    if [ -n "$CHECKLIST_FILE" ]; then
+        echo "LIST OF PACKAGES TO INSTALL AND CHECK : $CHECKLIST_FILE"
+    else
+        echo "FOLDER OF PACKAGES TO INSTALL AND CHECK : $TAR_FOLDER_PATH"
+    fi
 fi
 if [ -n "$R_LIBS_USER" ]; then
     echo "R_LIBS_USER : $R_LIBS_USER"
@@ -501,6 +536,11 @@ fi
 # Destination directory creation
 mkdir $DESTINATION
 cd $DESTINATION
+if [ -n "$TAR_FOLDER_PATH" ]; then
+    for i in $TAR_FOLDER_PATH/*; do
+        cp $i ./
+    done
+fi
 
 if [[ $HTMLFLAG == 1 ]]; then
     echo "Downloading jquery inside result folder..."
@@ -647,42 +687,80 @@ fi
 if [ -n "$PACKAGE_TO_TEST" ]; then
     PACKAGES_TO_CHECK_LIST_FILE="list_dependencies.txt"
 else
-    cp $CHECKLIST_FILE ./list_packages_to_check.txt
-    PACKAGES_TO_CHECK_LIST_FILE=$CHECKLIST_FILE
+    if [ -n "$CHECKLIST_FILE" ]; then
+        cp $CHECKLIST_FILE ./list_packages_to_check.txt
+        PACKAGES_TO_CHECK_LIST_FILE=$CHECKLIST_FILE
+    fi
 fi
 
 if [[ "$SKIPINSTALLFLAG" == "0" ]]; then
-    echo "
-    Installing `wc -l $PACKAGES_TO_CHECK_LIST_FILE` packages in R_LIBS_USER (may be long if launched for the first time in this R_LIBS_USER)
-    "
-    while read line; do
-        pname=`echo $line | cut -d ',' -f 1`
-        pversion=`echo $line | cut -d ',' -f 2`
-        printLeftPurple "Installing $pname v $pversion ... started at `date '+%H:%M:%S'` ... "
-        # local install
-        echo 'chooseBioCmirror(ind=3)
-setRepositories(ind=c(1, 2, 5, 6))
-if (!"'$pname'" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
-    install.packages("'$pname'",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus='$NBCORES')
-}
-' > ${pname}_install.R
-
-        $XVFBRUN_PATH -n 222 R 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
-        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
-            printRightGreen "`date '+%H:%M:%S'` : OK"
-        else
-            touch ${pname}_install_problem
-            printRightRed "`date '+%H:%M:%S'` : FAILED"
-        fi
+    if [ -n "$PACKAGE_TO_TEST" ] || [ -n "$CHECKLIST_FILE" ]; then
+        echo "
+Installing `wc -l $PACKAGES_TO_CHECK_LIST_FILE` packages in R_LIBS_USER (may be long if launched for the first time in this R_LIBS_USER)
+        "
+        while read line; do
+            pname=`echo $line | cut -d ',' -f 1`
+            pversion=`echo $line | cut -d ',' -f 2`
+            printLeftPurple "Installing $pname v $pversion ... started at `date '+%H:%M:%S'` ... "
+            # local install
+            echo 'chooseBioCmirror(ind=3)
+    setRepositories(ind=c(1, 2, 5, 6))
+    if (!"'$pname'" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
+        install.packages("'$pname'",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus='$NBCORES')
+    }
+    ' > ${pname}_install.R
+
+            $XVFBRUN_PATH -n 222 R 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
+            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
+                printRightGreen "`date '+%H:%M:%S'` : OK"
+            else
+                touch ${pname}_install_problem
+                printRightRed "`date '+%H:%M:%S'` : FAILED"
+            fi
 
-        if [[ $HTMLFLAG == 1 ]]; then
-            generate_html_report $DESTINATION
-        fi
-    done < $PACKAGES_TO_CHECK_LIST_FILE
+            if [[ $HTMLFLAG == 1 ]]; then
+                generate_html_report $DESTINATION
+            fi
+        done < $PACKAGES_TO_CHECK_LIST_FILE
+    else
+        ######## we have a TAR_FOLDER_PATH ###########
+        echo "
+Installing `ls $TAR_FOLDER_PATH | wc -l` packages in R_LIBS_USER (may be long if launched for the first time in this R_LIBS_USER)
+        "
+        for i in $TAR_FOLDER_PATH/*; do
+            file=`basename $i`
+            pname=`echo $file | cut -d '_' -f 1`
+            pversion=`echo $file | cut -d '_' -f 2`
+            printLeftPurple "Installing $pname v $pversion ... started at `date '+%H:%M:%S'` ... "
+            # local install
+            echo 'chooseBioCmirror(ind=3)
+    setRepositories(ind=c(1, 2, 5, 6))
+    if (!"'$pname'" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
+        install.packages("'$pname'",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus='$NBCORES')
+    }
+    ' > ${pname}_install.R
+
+            $XVFBRUN_PATH -n 222 R CMD INSTALL -l "$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
+            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
+                printRightGreen "`date '+%H:%M:%S'` : OK"
+            else
+                touch ${pname}_install_problem
+                printRightRed "`date '+%H:%M:%S'` : FAILED"
+            fi
+
+            if [[ $HTMLFLAG == 1 ]]; then
+                generate_html_report $DESTINATION
+            fi
+        done
+    fi
 fi
 
 ###################### R CMD check #############################
@@ -696,25 +774,48 @@ export _R_CHECK_FORCE_SUGGESTS_=FALSE
 # SIMPLE CORE PROCESSING
 
 if [[ $NBCORES == 1 ]]; then
-    while read line; do
-        pname=`echo $line | cut -d ',' -f 1`
-        pversion=`echo $line | cut -d ',' -f 2`
-        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
-        if [[ $? == 0 ]]; then
-            touch ${pname}.CHECKOK
-            printRightGreen "`date '+%H:%M:%S'` : OK"
-        else
-            touch ${pname}.CHECKPROBLEM
-            printRightRed "`date '+%H:%M:%S'` : FAILED"
-        fi
+    if [ -n "$PACKAGE_TO_TEST" ] || [ -n "$CHECKLIST_FILE" ]; then
+        while read line; do
+            pname=`echo $line | cut -d ',' -f 1`
+            pversion=`echo $line | cut -d ',' -f 2`
+            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
+            if [[ $? == 0 ]]; then
+                touch ${pname}.CHECKOK
+                printRightGreen "`date '+%H:%M:%S'` : OK"
+            else
+                touch ${pname}.CHECKPROBLEM
+                printRightRed "`date '+%H:%M:%S'` : FAILED"
+            fi
 
-        if [[ $HTMLFLAG == 1 ]]; then
-            generate_html_report $DESTINATION
-        fi
-    done < $PACKAGES_TO_CHECK_LIST_FILE
+            if [[ $HTMLFLAG == 1 ]]; then
+                generate_html_report $DESTINATION
+            fi
+        done < $PACKAGES_TO_CHECK_LIST_FILE
+    else
+        # TAR_FOLDER_PATH
+        for i in $TAR_FOLDER_PATH/*; do
+            file=`basename $i`
+            pname=`echo $file | cut -d '_' -f 1`
+            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
+            if [[ $? == 0 ]]; then
+                touch ${pname}.CHECKOK
+                printRightGreen "`date '+%H:%M:%S'` : OK"
+            else
+                touch ${pname}.CHECKPROBLEM
+                printRightRed "`date '+%H:%M:%S'` : FAILED"
+            fi
+
+            if [[ $HTMLFLAG == 1 ]]; then
+                generate_html_report $DESTINATION
+            fi
+        done
+    fi
 else
     # MULTICORE PROCESSING
 
@@ -780,14 +881,28 @@ else
 
     # INITIALISATION of variables
     i=0
-    while read line; do
-        pname=`echo $line | cut -d ',' -f 1`
-        pversion=`echo $line | cut -d ',' -f 2`
-        names[$i]=$pname
-        versions[$i]=$pversion
-        status[$i]="tocheck"
-        let "i = $i + 1"
-    done < $PACKAGES_TO_CHECK_LIST_FILE
+    if [ -n "$PACKAGE_TO_TEST" ] || [ -n "$CHECKLIST_FILE" ]; then
+        while read line; do
+            pname=`echo $line | cut -d ',' -f 1`
+            pversion=`echo $line | cut -d ',' -f 2`
+            names[$i]=$pname
+            versions[$i]=$pversion
+            status[$i]="tocheck"
+            let "i = $i + 1"
+        done < $PACKAGES_TO_CHECK_LIST_FILE
+    else
+        # TAR_FOLDER_PATH
+        for j in $TAR_FOLDER_PATH/*; do
+            file=`basename $j`
+            pname=`echo $file | cut -d '_' -f 1`
+            pversion=`echo $file | cut -d '_' -f 2`
+            names[$i]=$pname
+            versions[$i]=$pversion
+            files[$i]=$file
+            status[$i]="tocheck"
+            let "i = $i + 1"
+        done
+    fi
     NB_PKG=$i
     echo "Number of packages : $NB_PKG"
     echo
@@ -796,6 +911,7 @@ else
         p_pid[$i]=0
         p_pkgname[$i]=0
         p_pkgversion[$i]=0
+        p_pkgfile[$i]=0
     done
 
     ## CHECK LOOP
@@ -838,12 +954,22 @@ else
                     status[$ftc]="running"
                     pname=${names[$ftc]}
                     pversion=${versions[$ftc]}
-                    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
                     mkdir $DESTINATION/${pname}.rlib
-                    $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 &
-                    p_pid[$j]=$!
+                    if [ -n "$PACKAGE_TO_TEST" ] || [ -n "$CHECKLIST_FILE" ]; then
+                        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 &
+                        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" $pfile  > /dev/null 2>&1 &
+                        p_pid[$j]=$!
+                        p_pkgfile[$j]=$pfile
+                    fi
                     p_num[$j]=$ftc
                     p_pkgname[$j]=$pname
                     p_pkgversion[$j]=$pversion