update_r_packages.sh: remove the lock files that install.packages() fails to delete.

This commit is contained in:
Andrea Dell'Amico 2018-01-11 17:50:35 +01:00
parent 732fa3f959
commit 67ede2004e
3 changed files with 9 additions and 2 deletions

View File

@ -16,9 +16,10 @@ r_install_cran_repo: absent
r_cran_set_default_mirror: True
r_cran_mirror_site: https://cran.mirror.garr.it/mirrors/CRAN/
r_base_specific_version: False
r_base_pkg_version: 2.14.1
r_base_pkg_version: 3.4.3
r_packages_main_state: present
r_packages_state: '{{ r_packages_main_state }}'
r_sitelib_path: '/usr/local/lib/R/site-library'
r_plugins_from_deb: True
r_packages_cleanup: False
#

View File

@ -7,7 +7,7 @@
file: dest={{ r_packages_svn_base_dir }} state=directory
- name: Cron job that installs new R packages, if any
cron: name="install new R packages" user=root cron_file=install-r-packages minute="*/10" hour="5-0,1-2" job="/usr/local/bin/update_r_packages install >/var/log/install_r_packages 2>&1" state=present
cron: name="install new R packages" user=root cron_file=install-r-packages minute="*/10" hour="5-23,1-2" job="/usr/local/bin/update_r_packages install >/var/log/install_r_packages 2>&1" state=present
- name: Cron job that upgrades existing R packages and installs new ones, if any
cron: name="install new R packages" user=root cron_file=upgrade-r-packages minute="7" hour="3" job="/usr/local/bin/update_r_packages upgrade >/var/log/update_r_packages 2>&1" state=present

View File

@ -163,6 +163,11 @@ function debian_pkgs() {
fi
}
function remove_r_install_packages_lock_files() {
# install.packages leaves lock files around if the process crashes
rm -fr {{ r_sitelib_path }}/00LOCK-*
}
function r_cran_pkgs() {
if [ $CRAN_PKGS_SKIP -eq 0 ] ; then
logger "update_r_packages: Installing R packages from CRAN"
@ -221,6 +226,7 @@ else
get_data_files
fi
debian_pkgs
remove_r_install_packages_lock_files
r_cran_pkgs
r_github_pkgs
cleanup