forked from ISTI-ansible-roles/ansible-roles
update_r_packages.sh: remove the lock files that install.packages() fails to delete.
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@ -16,9 +16,10 @@ r_install_cran_repo: absent
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r_cran_set_default_mirror: True
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r_cran_mirror_site: https://cran.mirror.garr.it/mirrors/CRAN/
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r_base_specific_version: False
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r_base_pkg_version: 2.14.1
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r_base_pkg_version: 3.4.3
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r_packages_main_state: present
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r_packages_state: '{{ r_packages_main_state }}'
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r_sitelib_path: '/usr/local/lib/R/site-library'
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r_plugins_from_deb: True
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r_packages_cleanup: False
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#
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@ -7,7 +7,7 @@
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file: dest={{ r_packages_svn_base_dir }} state=directory
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- name: Cron job that installs new R packages, if any
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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
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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
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- name: Cron job that upgrades existing R packages and installs new ones, if any
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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
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@ -163,6 +163,11 @@ function debian_pkgs() {
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fi
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}
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function remove_r_install_packages_lock_files() {
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# install.packages leaves lock files around if the process crashes
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rm -fr {{ r_sitelib_path }}/00LOCK-*
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}
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function r_cran_pkgs() {
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if [ $CRAN_PKGS_SKIP -eq 0 ] ; then
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logger "update_r_packages: Installing R packages from CRAN"
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@ -221,6 +226,7 @@ else
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get_data_files
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fi
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debian_pkgs
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remove_r_install_packages_lock_files
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r_cran_pkgs
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r_github_pkgs
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cleanup
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