Different way to manage the github upgrades.

defaults/main.yml

@@ -43,7 +43,8 @@ r_package_updater_via_git: True
 r_package_updater_git_repo: 'https://code-repo.d4science.org/gCubeSystem/r-packages-list'
 r_packages_git_base_dir: /srv/r_updater
 r_packages_files_prefix: ''
-r_packages_updater_also_upgrades_installed_packages: False
+r_packages_updater_also_upgrades_installed_packages: True
+r_packages_updater_for_github_only: True
 # They need to be flat text files
 # 1 package per line
 #r_debian_packages_list_url

templates/update_r_packages.sh.j2

@@ -37,6 +37,11 @@ R_PKGS_FILES_PREFIX="{{ r_packages_files_prefix }}"
 RSCRIPT_OPTIONS="--slave --no-site-file --no-init-file --no-save --no-restore-history"
 # In seconds. 60*60*6=21600s (6h)
 UPDATER_PROCESS_MAX_RUNTIME=21600
+{% if r_packages_updater_for_github_only %}
+UPDATER_DEFAULT_BEHAVIOUR="github_only"
+{% else %}
+UPDATER_DEFAULT_BEHAVIOUR="everything"
+{% endif %}
 # - debian packages list format:
 # one package per line
 DEB_PKGS_SKIP=0
@@ -250,7 +255,9 @@ function r_cran_pkgs() {
                 mirror=$R_CRAN_MIRROR
             fi
             if [ "$ACTION" == "upgrade" ] ; then
-                Rscript $RSCRIPT_OPTIONS -e "install.packages(pkgs='$pkg', repos=c('$mirror/'));"
+                if [ "$UPDATER_DEFAULT_BEHAVIOUR" == "everything" ] ; then
+                    Rscript $RSCRIPT_OPTIONS -e "install.packages(pkgs='$pkg', repos=c('$mirror/'));"
+                fi
             else
                 Rscript $RSCRIPT_OPTIONS -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { install.packages(pkgs='$pkg', repos=c('$mirror/')); }"
             fi
@@ -267,7 +274,9 @@ function r_cran_versioned_pkgs() {
             pkg=$( echo $l | cut -d : -f 1 )
             version=$( echo $l | cut -d : -f 2 )
             if [ "$ACTION" == "upgrade" ] ; then
-                Rscript $RSCRIPT_OPTIONS -e "require(devtools); install_version('$pkg', '$version', repos=c('$mirror/'));"
+                if [ "$UPDATER_DEFAULT_BEHAVIOUR" == "everything" ] ; then
+                    Rscript $RSCRIPT_OPTIONS -e "require(devtools); install_version('$pkg', '$version', repos=c('$mirror/'));"
+                fi
             else
                 Rscript $RSCRIPT_OPTIONS -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { require(devtools); install_version('$pkg', '$version', repos=c('$mirror/')); }"
             fi
@@ -289,7 +298,7 @@ function r_github_pkgs() {
             else
                 github_version_to_install="$github_pkg_version"
             fi
-            if [ "$ACTION" == "upgrade" -o "$R_PKGS_ALWAYS_UPGRADE_GITHUB" ] ; then
+            if [ "$ACTION" == "upgrade" ] ; then
                 Rscript $RSCRIPT_OPTIONS -e "require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$github_pkg' ; refs <- jsonlite::read_json(sprintf('https://api.github.com/repos/%s/releases', package_to_install)) ; ref_to_install <- '$github_pkg_version'; if(length(refs)>0) { ref_to_install <- refs[[1]][['tag_name']] } ; devtools::install_github(package_to_install, ref = ref_to_install, upgrade='never')"
 
             else
@@ -311,14 +320,14 @@ init_env
 if [ $R_PKGS_FROM_GIT == 'True' ] ; then
     get_data_files_from_git
     if [ $GIT_UPDATE_STATUS -ne 1 -a "$ACTION" == "install" ] ; then
-        logger "update_r_packages: nothing new to install from git, exiting"
+        logger "update_r_packages: nothing new to install from git"
         cleanup
         exit 0
     fi
 elif [ $R_PKGS_FROM_SVN == 'True' ] ; then
     get_data_files_from_svn
     if [ $SVN_UPDATE_STATUS -ne 0 -a "$ACTION" == "install" ] ; then
-        logger "update_r_packages: nothing new to install from SVN, exiting"
+        logger "update_r_packages: nothing new to install from SVN."
         cleanup
         exit 0
     fi