" > $dest_html
# show install log of package to test
if [ -f $dir"/install_pkg.Rout" ]; then
if [ -f $dir"/install_pkg_ok" ]; then
local version=`cat $dir"/pkg.version"`
local status="ok, version $version"
local color="#4EE877"
else
if [ -f $dir"/install_pkg_problem" ]; then
local status="problem"
local color="red"
else
local status="running"
local color="yellow"
fi
fi
echo "| $PACKAGE_TO_TEST INSTALL PROCESS | " >> $dest_html
echo "$status |
" >> $dest_html
echo " |
" >> $dest_html
fi
# show update log
if [ -f $dir/update.Rout ]; then
if [ -f $dir/update_ok ]; then
local status="ok"
local color="#4EE877"
else
if [ -f $dir/update_problem ]; then
local status="problem"
local color="red"
else
local status="running"
local color="yellow"
fi
fi
local nlines=`cat $dir/update.Rout | wc -l`
echo "| UPDATE PROCESS | " >> $dest_html
echo "$status ($nlines lines) |
" >> $dest_html
echo " |
" >> $dest_html
fi
# INSTALL, for all the install R scripts output files
if [[ "`ls $dir | grep "_install.Rout" | wc -l`" != "0" ]]; then
for elem in `ls $dir/*_install.Rout`; do
local package=`basename $elem`
local package_name=${package/_install.Rout/}
# if the installation went well
if [ -f $dir"/"$package_name"_install_ok" ]; then
local status="ok"
local color="#4EE877"
# if the installation failed
else
if [ -f $dir"/"$package_name"_install_problem" ]; then
local status="problem"
local color="red"
else
local status="running"
local color="yellow"
fi
fi
local log=`cat $dir"/"$package_name"_install.Rout"`
local nlines=`cat $dir"/"$package_name"_install.Rout" | wc -l`
echo "| INSTALL $package_name | " >> $dest_html
echo "$status ($nlines lines) |
" >> $dest_html
echo " |
" >> $dest_html
done
fi
# 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
local package=(`echo "$baselem" | tr "_" "\n"`)
#IFS='_' read -ra package <<< "$baselem"
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"
fi
fi
local log=`cat $dir"/"$package_name".Rcheck/00check.log"`
local nlines=`cat $dir"/"$package_name".Rcheck/00check.log" | wc -l`
echo "| CHECK $package_name V $package_version | " >> $dest_html
echo "$status ($nlines lines) |
" >> $dest_html
echo " |
" >> $dest_html
done
fi
echo "
" >> $dest_html
echo '
' >> $dest_html
}
############### PRINTING FUNCTIONS ###################
txtred=$(tput setaf 1) # Red
txtgrn=$(tput setaf 2) # Green
txtpur=$(tput setaf 5) # Purple
txtrst=$(tput sgr0) # Text reset.
# all of those functions avoid printing colors and right aligned text if the
# output ou rtest was redirected to a file or a pipe
# print left in purple and does NOT put the end-of-line char
function printLeftPurple(){
if [[ -t 1 ]]; then
columns=$(tput cols)
col1="100"
printf "${txtpur}%-*s" "$col1" "$1"
else
printf "%-*s" "$col1" "$1"
fi
export LAST_LENGTH=${#1}
}
# print right in green and DOES put the end-of-line char
function printRightGreen(){
if [[ -t 1 ]]; then
columns=$(tput cols)
col1="100"
let "col2 = $columns - $col1"
printf "${txtgrn}%*s${txtrst}\n" "$col2" "$1"
else
let "place = 120 - $LAST_LENGTH"
printf "%*s\n" "$place" "$1"
fi
}
# print right in red and DOES put the end-of-line char
function printRightRed(){
if [[ -t 1 ]]; then
columns=$(tput cols)
col1="100"
let "col2 = $columns - $col1"
printf "${txtred}%*s${txtrst}\n" "$col2" "$1"
else
let "place = 120 - $LAST_LENGTH"
printf "%*s\n" "$place" "$1"
fi
}
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 :
$0 PACKAGE_TO_TEST [-l|--libuser R_USER_LIB_VALUE] [-d|--dest DESTINATION_DIRECTORY] [-m|--mail MAIL_TO] [-u|--urlresult URL] [-r|--repo PACKAGE_TO_TEST_REPO] [-x | --xvfb XVFB-RUN PATH] [-n | --nbcores NBCORES] [-s | --skipinstall] [-h | --html]
PACKAGE_TO_TEST : package to test
-r | --repo PACKAGE_TO_TEST_REPO : repository of package you want to test (DEFAULT : R-CRAN)
-l | --libuser R_LIBS_USER : directory where packages depending on PACKAGE_TO_TEST are going to be installed (DEFAULT : R will choose it)
This directory can be used several times for several tests. Using same directory several times will save time.
This directory can exist or not. If not, it will be created
-d | --dest DESTINATION_DIRECTORY : result directory where HTML result and test files are produced (DEFAULT : ./check_PKGNAME_DATE)
-m | --mail MAIL_TO : email address for real time user information (DEFAULT : NO MAIL WILL BE SENT)
-u | --urlresult URL : if -m option was set, this http link to test results will be sent instead of a file path (DEFAULT : destination directory absolute path)
-x | --xvfb PATH : Specific path to xvfb-run script (DEFAULT : 'xvfb-run')
-n | --nbcores NBCORES : Number of cores for parallel executions of installations (Ncpu parameter) and number of simultaneous checks (DEFAULT : 1)
-s | --skipinstall : flag to skip the packages update/installation
-h | --html : generate html report in DESTINATION_DIRECTORY/index.html . Will download jquery in destination directory
Don't forget to set JAVA_HOME if some dependencies need java, which is quite probable.
"
}
ARGS=$(getopt -o r:d:m:l:x:n:shu: -l "repo:mail:libuser:dest:xvfb:nbcores:skipinstall,html,urlresult:" -n "$0" -- "$@");
#Bad arguments
if [ $? -ne 0 ] || [ $# -eq 0 ];
then
printUsage
exit
fi
REPOSITORYFLAG=0
MAILTOFLAG=0
DESTINATIONFLAG=0
PACKAGE_TO_TEST=""
NBCORES=1
SKIPINSTALLFLAG=0
HTMLFLAG=0
RESULTURLFLAG=0
eval set -- "$ARGS";
while true; do
case "$1" in
-d|--dest)
shift;
if [ -n "$1" ]; then
if [ -d "$1" ] || [ -f "$1" ]; then
echo "File or directory $1 already exists
"
printUsage
exit
else
DESTINATIONFLAG=1
DESTINATION=$(readlink -f "$1")
fi
else
echo "You have to set a destination directory
"
printUsage
exit
fi
shift;
;;
-l|--libuser)
shift;
if [ -n "$1" ]; then
if ! [ -d "$1" ]; then
mkdir "$1"
echo "CREATING '$1' personnal R library"
fi
export R_LIBS_USER=$(readlink -f "$1")
else
echo "You have to set a non-empty R LIB USER directory
"
printUsage
exit
fi
shift;
;;
-r|--repo)
shift;
if [ -n "$1" ]; then
REPOSITORYFLAG=1
REPOSITORY=$1
else
echo "You have to set a non-empty repository
"
printUsage
exit
fi
shift;
;;
-m|--mail)
shift;
if [ -n "$1" ]; then
MAILTOFLAG=1
MAILTO=$1
else
echo "You have to set a non-empty destination EMAIL ADDRESS
"
printUsage
exit
fi
shift;
;;
-u|--urlresult)
shift;
if [ -n "$1" ]; then
RESULTURLFLAG=1
RESULT_URL=$1
else
echo "You have to set a non-empty result url
"
printUsage
exit
fi
shift;
;;
-x|--xvfb)
shift;
if [ -n "$1" ]; then
XVFBRUN_PATH="$1"
if ! [ -f $XVFBRUN_PATH ]; then
echo "xvfb-run not found...
"
exit
fi
else
echo "You have to set a non-empty XVFB-RUN path
"
printUsage
exit
fi
shift;
;;
-n|--nbcores)
shift;
if [ -n "$1" ]; then
NBCORES="$1"
re='^[0-9]+$'
if ! [[ $NBCORES =~ $re ]] ; then
echo "-n --nbcores parameter must be a number" >&2; exit 1
fi
else
echo "You have to set a non-empty nbcores parameter
"
printUsage
exit
fi
shift;
;;
-s|--skipinstall)
SKIPINSTALLFLAG=1
shift;
;;
-h|--html)
HTMLFLAG=1
shift;
;;
--)
break;
;;
esac
done
# getting non-option arguments : THE MAIN ONE : PACKAGE_TO_TEST !
# only last non-option argument will be taken
shift;
while [ -n "$1" ]; do
PACKAGE_TO_TEST=$1
shift
done
if ! [ -n "$PACKAGE_TO_TEST" ]; then
echo "There must be a package to test
"
printUsage
exit
fi
#### DEFAULT VALUES management
# Default destination directory is ./check_PKGNAME_DATE
if [ $DESTINATIONFLAG == 0 ]; then
DESTINATION=$(readlink -f "./check_${PACKAGE_TO_TEST}_`date '+%Y%m%d.%H%M%S'`")
fi
if [ $RESULTURLFLAG == 0 ]; then
RESULT_URL=$DESTINATION
fi
# RECAP OF ALL PARAMS
echo "PACKAGE TO TEST : $PACKAGE_TO_TEST"
if [ -n "$R_LIBS_USER" ]; then
echo "R_LIBS_USER : $R_LIBS_USER"
else
echo "R_LIBS_USER : EMPTY => DEFAULT"
fi
echo "DESTINATION DIRECTORY : $DESTINATION"
if [[ $MAILTOFLAG == 1 ]]; then
echo "MAIL will be sent to $MAILTO"
else
echo "NO MAILS"
fi
if [[ $RESULTURLFLAG == 1 ]]; then
echo "Result URL is $RESULT_URL"
fi
if [[ $REPOSITORYFLAG == 1 ]]; then
echo "Package REPOSITORY : $REPOSITORY"
else
echo "NO SPECIFIC PACKAGE REPOSITORY"
fi
if [[ $SKIPINSTALLFLAG == 1 ]]; then
echo "Installation of packages will be skipped"
fi
if [[ $HTMLFLAG == 1 ]]; then
echo "HTML report will be generated in $DESTINATION/index.html"
else
echo "NO HTML report will be generated"
fi
echo "rtest will be using $NBCORES simultaneous processes"
# send start mail
if [[ $MAILTOFLAG == 1 ]]; then
echo "Check progress and results are here :
$RESULT_URL
Your test directory is named `basename $DESTINATION`
" | mail -s "Package \"$PACKAGE_TO_TEST\" R check started (`basename $DESTINATION`)" $MAILTO
fi
######## FILE management
# Destination directory creation
mkdir $DESTINATION
cd $DESTINATION
if [[ $HTMLFLAG == 1 ]]; then
echo "Downloading jquery inside result folder..."
wget http://code.jquery.com/jquery-1.7.2.min.js -o $DESTINATION/jquery-1.7.2.min.js
echo
fi
echo
printLeftPurple "Generation of depends.R ... started at `date '+%H:%M:%S'` ... "
# generate depends.R
echo 'if (!"tools" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
install.packages("tools",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=7)
}
old <- getOption("defaultPackages"); r <- getOption("repos")
r["CRAN"] <- "'$DEFAULT_REPOSITORY'"
options(defaultPackages = c(old, "MASS"), repos = r)
require("tools")
reverse_dependencies_with_maintainers <-
function(packages, which = c("Depends", "Imports", "LinkingTo"),
recursive = FALSE)
{
contrib.url(getOption("repos")["CRAN"], "source") # trigger chooseCRANmirror() if required
description <- sprintf("%s/web/packages/packages.rds",
getOption("repos")["CRAN"])
con <- if(substring(description, 1L, 7L) == "file://")
file(description, "rb")
else
url(description, "rb")
on.exit(close(con))
db <- readRDS(gzcon(con))
rownames(db) <- NULL
rdepends <- package_dependencies(packages, db, which,
recursive = recursive,
reverse = TRUE)
rdepends <- sort(unique(unlist(rdepends)))
pos <- match(rdepends, db[, "Package"], nomatch = 0L)
db[pos, c("Package", "Version", "Maintainer")]
}
Sys.setenv(http_proxy = "")
a <- reverse_dependencies_with_maintainers("'$PACKAGE_TO_TEST'", which = c("Depends", "Imports", "Suggests", "LinkingTo"))
a <- a[order(a[,1]),]
ff <- file("depends.txt", open = "w")
cat( paste(sep=",",a[,1],sub("\n","",a[,2]),sub("\n"," ",a[,3]), collapse = "\n"), "\n", file=ff)
close(ff)
' > $DESTINATION/depends.R
printRightGreen "`date '+%H:%M:%S'` : OK"
################ INSTALL of package to test ####################
printLeftPurple "Installing $PACKAGE_TO_TEST ... started at `date '+%H:%M:%S'` ... "
REPO_R_PARAM=""
if [[ $REPOSITORYFLAG == 1 ]]; then
REPO_R_PARAM=", repos=c(\"$REPOSITORY\")"
else
REPO_R_PARAM=", repos=c(\"$DEFAULT_REPOSITORY\")"
fi
R_LIBS_USER_PARAM=""
if [ -n "$R_LIBS_USER" ]; then
R_LIBS_USER_PARAM=", lib=Sys.getenv(\"R_LIBS_USER\")"
fi
echo '
install.packages("'$PACKAGE_TO_TEST'"'$REPO_R_PARAM''$R_LIBS_USER_PARAM', dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=7)
ff <- file("pkg.version", open = "w")
cat( paste(sep=",",packageVersion("'$PACKAGE_TO_TEST'")), file=ff)
close(ff)
' > $DESTINATION/install_pkg.R
R CMD BATCH install_pkg.R
if [[ $HTMLFLAG == 1 ]]; then
generate_html_report $DESTINATION
fi
if [[ $? == 0 ]]; then
touch install_pkg_ok
printRightGreen "`date '+%H:%M:%S'` : OK"
else
touch install_pkg_problem
printRightRed "`date '+%H:%M:%S'` : FAILED"
fi
############### GENERATION OF DEPENDENCY LIST ###################
printLeftPurple "Generating dependency list (should take less than a minute)... started at `date '+%H:%M:%S'` ... "
R CMD BATCH --no-timing depends.R
#cat depends.txt | grep -v structSSI | grep -v SigTree | grep -v SeqFeatR | grep -v gWidgetsRGtk2 | grep -v GrammR | grep -v RADami > list_dependencies.txt
cat depends.txt > list_dependencies.txt
printRightGreen "`date '+%H:%M:%S'` : OK"
#################### UPDATE of R packages in R_LIBS_USER #####################
if [[ "$SKIPINSTALLFLAG" == "0" ]]; then
printLeftPurple "Updating R packages in R_LIBS_USER (takes a very variable time)... started at `date '+%H:%M:%S'` ... "
echo '
chooseBioCmirror(ind=3)
setRepositories(ind=c(1,2,3,4,5,6,7,8,9))
update.packages(lib.loc=Sys.getenv("R_LIBS_USER"), repos=c("'$DEFAULT_REPOSITORY'"),ask=FALSE)
if (!"XML" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
install.packages("XML",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=7)
}
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
biocLite("Heatplus", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
biocLite("qvalue", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
biocLite("graph", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
biocLite("multtest", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
biocLite("widgetTools", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
biocLite("phyloseq", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
biocLite("Rgraphviz", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
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
$XVFBRUN_PATH -n 222 R CMD BATCH --slave --vanilla --quiet update.R
ret_upd=$?
non_zero=`grep -i "non-zero exit status" update.Rout | wc -l`
if [[ $ret_upd == 0 ]] && [[ $non_zero == 0 ]]; then
touch update_ok
printRightGreen "`date '+%H:%M:%S'` : OK"
else
touch update_problem
printRightRed "`date '+%H:%M:%S'` : FAILED"
fi
if [[ $HTMLFLAG == 1 ]]; then
generate_html_report $DESTINATION
fi
fi
################ INSTALL packages if they are not installed in R_LIBS_USER ###################
if [[ "$SKIPINSTALLFLAG" == "0" ]]; then
echo "
Installing `wc -l list_dependencies.txt` 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=7)
}
' > ${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 < list_dependencies.txt
fi
###################### R CMD check #############################
echo "
Checking packages with 'R CMD check'
"
# we don't verify that suggested packages are installed
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 [[ $HTMLFLAG == 1 ]]; then
generate_html_report $DESTINATION
fi
done < list_dependencies.txt
else
# MULTICORE PROCESSING
# FUNCTION DEFINITION
# how many packages are still not processed
function nbToCheck(){
result=0
for i in ${status[@]}; do
if [[ "$i" == "tocheck" ]]; then
let "result = $result + 1"
fi
done
echo $result
}
# how many packages are already processed (finished)
function nbDone(){
result=0
for i in ${status[@]}; do
if [[ "$i" == "done" ]]; then
let "result = $result + 1"
fi
done
echo $result
}
# which packages were not processed
function whatsLeft(){
let "end = $NB_PKG - 1"
echo -ne "TO DO : "
for zz in `seq 0 $end`; do
if [[ "${status[$zz]}" != "done" ]]; then
echo -ne "${names[$zz]} (${status[$zz]}) ; "
fi
done
echo
}
# get index of first not-processed package in status list
function getFirstToCheck(){
result=0
for i in ${status[@]}; do
if [[ "$i" == "tocheck" ]]; then
echo $result
return
fi
let "result = $result + 1"
done
}
# is the package $1 running (processus in activity)
function isRunning(){
slot=$1
pid=${p_pid[$slot]}
pname=${p_pkgname[$slot]}
if [[ "`ps u -p $pid | grep $pname | grep 'R CMD check' | wc -l`" == 0 ]]; then
echo "false"
else
echo "true"
fi
}
# 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 = $i + 1"
done < list_dependencies.txt
NB_PKG=$i
echo "Number of packages : $NB_PKG"
echo
for i in `seq 1 $NBCORES`; do
p_num[$i]=0
p_pid[$i]=0
p_pkgname[$i]=0
p_pkgversion[$i]=0
done
## CHECK LOOP
# while there is still a package to check or running
while [[ "`nbDone`" != "$NB_PKG" ]]; do
# for all slots
for j in `seq 1 $NBCORES`; do
# if the slot is empty OR not running anymore (no ps AND status==running)
if [[ "${p_pkgname[$j]}" == "0" ]] ||
[[ "`isRunning $j`" == "false" &&
${status[${p_num[$j]}]} == "running" ]]; then
# if the slot is not empty AND the process is not running anymore
if [[ "${p_pkgname[$j]}" != "0" ]] && [[ "`isRunning $j`" == "false" ]]; then
status[${p_num[$j]}]="done"
# display counter
nbdone=`nbDone`
let "pc = $nbdone * 100 / $NB_PKG"
#echo -ne "[$nbdone/$NB_PKG] [$pc %] "
printLeftPurple "R CMD check ${p_pkgname[$j]}_${p_pkgversion[$j]}.tar.gz on slot $j ..."
# if there was no error
if [[ "`cat ${p_pkgname[$j]}.Rcheck/00check.log | egrep -i 'error|failed' | grep -v "OK" | grep -v "WARNING" | wc -l`" == "0" ]]; then
touch ${p_pkgname[$j]}.CHECKOK
#echo "R CMD check ${p_pkgname[$j]}_${p_pkgversion[$j]}.tar.gz ... FINISHED SUCCESSFULLY on slot $j at `date '+%H:%M:%S'` ... "
printRightGreen "FINISHED SUCCESSFULLY at `date '+%H:%M:%S'` [$nbdone/$NB_PKG] [$pc%]"
else
touch ${p_pkgname[$j]}.CHECKPROBLEM
#echo "R CMD check ${p_pkgname[$j]}_${p_pkgversion[$j]}.tar.gz ... FINISHED WITH ERROR on slot $j at `date '+%H:%M:%S'` ... "
printRightRed "FINISHED WITH ERROR at `date '+%H:%M:%S'` [$nbdone/$NB_PKG] [$pc%]"
fi
fi
# we start the next package check if there is still one to do
if [[ "`nbToCheck`" != "0" ]]; then
ftc=`getFirstToCheck`
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[$j]=$!
p_num[$j]=$ftc
p_pkgname[$j]=$pname
p_pkgversion[$j]=$pversion
else
echo "SLOT $j has nothing left to do"
fi
fi
done
sleep 5
if [[ $HTMLFLAG == 1 ]]; then
generate_html_report $DESTINATION
fi
done
fi
# Result mail
if [[ $MAILTOFLAG == 1 ]]; then
echo "Check results are here :
$RESULT_URL
Your test directory is named `basename $DESTINATION`
" | mail -s "Package \"$PACKAGE_TO_TEST\" R check DONE (`basename $DESTINATION`)" $MAILTO
fi