CRAN PPA for R 4.0+, git listfiles.
This commit is contained in:
parent
97d779e028
commit
23f78b67a0
GPG Key ID:
147ABE6CEB9E20FF
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@ -11,18 +11,20 @@
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#
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# Set to True if you want install from the CRAN deb repository
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r_install_cran_repo: False
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# “Michael Rutter marutter@gmail.com” with key ID 0x51716619e084dab9
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# E298A3A825C0D65DFD57CBB651716619E084DAB9
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r_cran_repo_apt_key: 'E298A3A825C0D65DFD57CBB651716619E084DAB9'
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# Use 'cran35' for R 3.6
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r_cran_repo_version: 'cran40'
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r_cran_repo_url: 'https://cloud.r-project.org/bin/linux/ubuntu {{ ansible_distribution_release }}-{{ r_cran_repo_version }}/'
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# Use 'marutter/c2d4u3.5' for R 3.6
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r_cran_ubuntu_packages_ppa: 'ppa:marutter/c2d4u'
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r_cran_ubuntu_packages_ppa_trusty: 'ppa:marutter/c2d4u'
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# 4.1, Ubuntu 18.04+
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r_cran_ubuntu_packages_ppa: 'ppa:c2d4u.team/c2d4u4.0+'
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r_apt_additional_repos_trusty:
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- 'ppa:opencpu/jq'
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r_apt_additional_repos:
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- 'ppa:cran/v8'
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- 'ppa:ubuntugis/ppa'
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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: 4.0.3
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r_base_pkg_version: 4.1.0
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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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@ -30,10 +32,13 @@ r_plugins_from_deb: True
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r_packages_cleanup: False
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#
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r_packages_updater: True
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r_package_updater_via_subversion: True
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r_package_updater_via_subversion: False
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r_package_updater_subversion_repo: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/
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r_packages_svn_base_dir: /srv/r_updater
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r_packages_svn_files_prefix: ''
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r_package_updater_via_git: True
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r_package_updater_git_repo: 'https://code-repo.d4science.org/gCubeSystem/r-packages-list'
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r_packages_git_base_dir: /srv/r_updater
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r_packages_files_prefix: ''
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r_packages_updater_also_upgrades_installed_packages: False
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# They need to be flat text files
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# 1 package per line
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@ -49,47 +54,39 @@ r_packages_updater_also_upgrades_installed_packages: False
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r_source_plugins_dest_dir: /var/cache/R
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r_distribution_required_packages: []
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# - gdal-bin
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# - dans-gdal-scripts
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# - libgdal1-dev
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# - libgeos-dev
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# - libspatialite-dev
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# - proj
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# - proj-bin
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# - proj-data
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# - libproj-dev
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r_base_packages_list:
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- r-base
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- r-base-core
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- r-base-dev
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- r-base-html
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- r-mathlib
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r_distribution_required_packages:
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- jags
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- git
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- subversion
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- gdal-bin
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- libgdal-dev
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- libgeos-dev
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- libspatialite-dev
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- proj-bin
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- proj-data
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- libproj-dev
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- libcurl4-openssl-dev
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- texlive
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- texlive-base
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- texlive-binaries
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- texlive-latex-base
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- texlive-latex-extra
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- texlive-formats-extra
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- texlive-xetex
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- libnetcdf-dev
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- netcdf-bin
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# Some packages must be put on hold
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r_base_packages_hold_list: []
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r_plugins_packages_list:
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- jags
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- r-cran-rjags
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- r-cran-abind
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- r-cran-boot
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- r-cran-class
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- r-cran-cluster
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- r-cran-coda
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- r-cran-codetools
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- r-cran-foreign
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- r-cran-lattice
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- r-cran-maptools
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- r-cran-mass
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- r-cran-matrix
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- r-cran-mgcv
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- r-cran-nlme
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- r-cran-nnet
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- r-cran-rpart
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- r-cran-sp
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- r-cran-spatial
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- r-cran-survival
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r_apt_additional_repos:
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- 'ppa:opencpu/jq'
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r_plugins_packages_list: []
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# RHEL/CentOS:
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# http://springdale.princeton.edu/data/springdale/7/x86_64/os/Computational/
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@ -113,30 +110,140 @@ r_base_packages_java_dev_el:
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r_distribution_required_el_packages: []
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r_cran_ubuntu_packages: []
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r_cran_ubuntu_packages:
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- r-cran-abind
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- r-cran-askpass
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- r-cran-backports
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- r-cran-base64enc
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- r-cran-bayesplot
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- r-cran-bh
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- r-cran-boot
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- r-cran-bslib
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- r-cran-cachem
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- r-cran-callr
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- r-cran-checkmate
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- r-cran-class
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- r-cran-cli
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- r-cran-cluster
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- r-cran-coda
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- r-cran-codetools
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- r-cran-colorspace
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- r-cran-colourpicker
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- r-cran-commonmark
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- r-cran-cpp11
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- r-cran-crayon
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- r-cran-crosstalk
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- r-cran-curl
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- r-cran-desc
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- r-cran-digest
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- r-cran-dplyr
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- r-cran-dt
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- r-cran-dygraphs
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- r-cran-ellipsis
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- r-cran-fansi
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- r-cran-farver
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- r-cran-fastmap
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- r-cran-foreign
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- r-cran-fs
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- r-cran-generics
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- r-cran-ggplot2
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- r-cran-ggridges
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- r-cran-glue
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- r-cran-gridextra
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- r-cran-gtable
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- r-cran-gtools
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- r-cran-htmltools
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- r-cran-htmlwidgets
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- r-cran-httpuv
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- r-cran-igraph
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- r-cran-inline
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- r-cran-isoband
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- r-cran-jquerylib
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- r-cran-jsonlite
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- r-cran-kernsmooth
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- r-cran-labeling
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- r-cran-later
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- r-cran-lattice
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- r-cran-lazyeval
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- r-cran-lifecycle
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- r-cran-littler
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- r-cran-lme4
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- r-cran-loo
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- r-cran-magrittr
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- r-cran-maptools
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- r-cran-markdown
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- r-cran-mass
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- r-cran-matrix
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- r-cran-matrixstats
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- r-cran-mgcv
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- r-cran-mime
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- r-cran-miniui
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- r-cran-minqa
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- r-cran-munsell
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- r-cran-nlme
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- r-cran-nloptr
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- r-cran-nnet
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- r-cran-openssl
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- r-cran-packrat
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- r-cran-pillar
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- r-cran-pkgbuild
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- r-cran-pkgconfig
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- r-cran-plyr
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- r-cran-prettyunits
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- r-cran-processx
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- r-cran-promises
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- r-cran-ps
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- r-cran-purrr
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- r-cran-r6
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- r-cran-rappdirs
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- r-cran-rcolorbrewer
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- r-cran-rcpp
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- r-cran-rcppeigen
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- r-cran-rcppparallel
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- r-cran-reshape2
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- r-cran-rjags
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- r-cran-rlang
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- r-cran-rodbc
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- r-cran-rpart
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- r-cran-rprojroot
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- r-cran-rsconnect
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- r-cran-rstan
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- r-cran-rstanarm
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- r-cran-rstantools
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- r-cran-rstudioapi
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- r-cran-sass
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- r-cran-scales
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- r-cran-shiny
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- r-cran-shinyjs
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- r-cran-shinystan
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- r-cran-shinythemes
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- r-cran-sourcetools
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- r-cran-sp
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- r-cran-spatial
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- r-cran-stanheaders
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- r-cran-stringi
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- r-cran-stringr
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||||
- r-cran-survival
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||||
- r-cran-svglite
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||||
- r-cran-sys
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||||
- r-cran-systemfonts
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||||
- r-cran-threejs
|
||||
- r-cran-tibble
|
||||
- r-cran-tidyselect
|
||||
- r-cran-utf8
|
||||
- r-cran-v8
|
||||
- r-cran-vctrs
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||||
- r-cran-viridislite
|
||||
- r-cran-withr
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||||
- r-cran-xfun
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||||
- r-cran-xtable
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||||
- r-cran-xts
|
||||
- r-cran-yaml
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||||
- r-cran-zoo
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r_cran_install_from_sources: True
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||||
r_plugins_list_to_install: []
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# - { name: 'R2WinBUGS', repo: '{{ r_cran_mirror_site }}' }
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||||
# - { name: 'R2jags', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'bayesmix', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'coda', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'rjags', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'runjags', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'base', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'compiler', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'datasets', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'grDevices', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'graphics', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'grid', repo: '{{ r_cran_mirror_site }}' }
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||||
# - { name: 'methods', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'parallel', repo: '{{ r_cran_mirror_site }}' }
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||||
# - { name: 'reshape', repo: '{{ r_cran_mirror_site }}' }
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||||
# - { name: 'splines', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'stats', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'stats4', repo: '{{ r_cran_mirror_site }}' }
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||||
# - { name: 'tcltk', repo: '{{ r_cran_mirror_site }}' }
|
||||
# - { name: 'tools', repo: '{{ r_cran_mirror_site }}' }
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||||
# - { name: 'utils', repo: '{{ r_cran_mirror_site }}' }
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# - { name: 'robis', repo: '{{ r_cran_mirror_site }}' }
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|
||||
r_plugins_from_sources: []
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# - { name: 'plyr', version: '1.7.1', source: 'plyr_1.7.1.tar.gz', url: 'http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.7.1.tar.gz' }
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@ -2,9 +2,9 @@
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- import_tasks: r-packages_cleanup.yml
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when:
|
||||
- r_packages_cleanup
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- ansible_distribution_file_variety == "Debian"
|
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- ansible_distribution == "Ubuntu"
|
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- import_tasks: r-installation-deb.yml
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when: ansible_distribution_file_variety == "Debian"
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when: ansible_distribution == "Ubuntu"
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- import_tasks: r-installation-el.yml
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when: ansible_distribution_file_variety == "RedHat"
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- import_tasks: r-packages-install.yml
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@ -1,18 +1,48 @@
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---
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- block:
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- name: Add the cran repository key
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apt_key: id={{ r_cran_repo_apt_key }} keyserver=keyserver.ubuntu.com state=present
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tags: [ 'r_software', 'r_repo', 'r_repo_key' ]
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- name: Add the CRAN repository (Ubuntu Trusty PPA)
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apt_repository:
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repo: '{{ r_cran_ubuntu_packages_ppa_trusty }}'
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state: present
|
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update_cache: yes
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|
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- name: Add the CRAN repository
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apt_repository: repo='deb {{ r_cran_repo_url }}' state=present update_cache=yes
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||||
- name: Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
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apt_repository:
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repo: '{{ item }}'
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state: present
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update_cache: yes
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loop: '{{ r_apt_additional_repos_trusty }}'
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|
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when: r_install_cran_repo
|
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when:
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- r_install_cran_repo
|
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- ansible_distribution_version is version_compare('14.04', '==')
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tags: [ 'r_software', 'r_repo' ]
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|
||||
- block:
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||||
- name: Add the CRAN repository (Ubuntu Bionic PPA)
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||||
apt_repository:
|
||||
repo: '{{ r_cran_ubuntu_packages_ppa }}'
|
||||
state: present
|
||||
update_cache: yes
|
||||
|
||||
- name: Install some additional repositories. They provide dependencies for some R packages. Ubuntu Bionic
|
||||
apt_repository:
|
||||
repo: '{{ item }}'
|
||||
state: present
|
||||
update_cache: yes
|
||||
loop: '{{ r_apt_additional_repos }}'
|
||||
|
||||
when:
|
||||
- r_install_cran_repo
|
||||
- ansible_distribution_version is version_compare('18.04', '>=')
|
||||
tags: [ 'r_software', 'r_repo' ]
|
||||
|
||||
- block:
|
||||
- name: Remove the CRAN repository
|
||||
apt_repository: repo='deb {{ r_cran_repo_url }}' state=absent update_cache=yes
|
||||
apt_repository:
|
||||
repo: '{{ r_cran_ubuntu_packages_ppa }}'
|
||||
state: absent
|
||||
update_cache: yes
|
||||
|
||||
when: not r_install_cran_repo
|
||||
tags: [ 'r_software', 'r_repo' ]
|
||||
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@ -26,7 +56,10 @@
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tags: [ 'r_software', 'r_pkg', 'r_pkg_hold' ]
|
||||
|
||||
- name: Install the R base packages.
|
||||
apt: pkg={{ r_base_packages_list }} state={{ r_packages_main_state }} update_cache=yes cache_valid_time=3600
|
||||
apt:
|
||||
pkg: '{{ r_base_packages_list }}'
|
||||
state: '{{ r_packages_main_state }}'
|
||||
cache_valid_time: 3600
|
||||
|
||||
- name: When we install specific R deb packages, put them on hold
|
||||
shell: apt-mark hold {{ item }}
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||||
|
|
@ -36,17 +69,16 @@
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|||
tags: [ 'r_software', 'r_pkg', 'r_pkg_hold' ]
|
||||
|
||||
- name: Install the R additional modules from the deb repo
|
||||
apt: pkg={{ r_plugins_packages_list | default([]) }} state={{ r_packages_state }} force=yes
|
||||
when: r_plugins_from_deb
|
||||
|
||||
- name: Install some additional repositories. They provide dependencies for some R packages
|
||||
apt_repository: repo={{ item }} state=present update_cache=yes
|
||||
with_items: '{{ r_apt_additional_repos }}'
|
||||
when: ansible_distribution_version is version_compare('18.04', '<')
|
||||
tags: [ 'r_software', 'r_apt_repo', 'r_deps' ]
|
||||
apt:
|
||||
pkg: '{{ r_plugins_packages_list }}'
|
||||
state: '{{ r_packages_state }}'
|
||||
cache_valid_time: 3600
|
||||
|
||||
- name: Install some packages needed by R packages when installed from source
|
||||
apt: pkg={{ r_distribution_required_packages | default([]) }} state={{ r_packages_state }} update_cache=yes force=yes cache_valid_time=3600
|
||||
apt:
|
||||
pkg: '{{ r_distribution_required_packages }}'
|
||||
state: '{{ r_packages_state }}'
|
||||
cache_valid_time: 3600
|
||||
tags: [ 'r_software', 'r_pkg', 'r_deps' ]
|
||||
|
||||
tags: [ 'r_software', 'r_pkg' ]
|
||||
|
|
|
|||
|
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@ -1,7 +1,12 @@
|
|||
---
|
||||
- block:
|
||||
- name: Configure the default CRAN mirror
|
||||
template: src=Rprofile.site.j2 dest=/etc/R/Rprofile.site owner=root group=root mode=0444
|
||||
template:
|
||||
src: Rprofile.site.j2
|
||||
dest: /etc/R/Rprofile.site
|
||||
owner: root
|
||||
group: root
|
||||
mode: 0444
|
||||
tags: [ 'r_software', 'r_profile', 'r_pkg' ]
|
||||
|
||||
- name: Configure the JDK environment
|
||||
|
|
@ -14,18 +19,22 @@
|
|||
tags: [ 'r_software', 'r_profile', 'r_pkg', 'r_java' ]
|
||||
|
||||
- name: Ensure that the R packages sources directory exists
|
||||
file: dest={{ r_source_plugins_dest_dir }} state=directory owner=root group=root
|
||||
file:
|
||||
dest: '{{ r_source_plugins_dest_dir }}'
|
||||
state: directory
|
||||
owner: root
|
||||
group: root
|
||||
when: r_plugins_from_sources is defined
|
||||
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_version' ]
|
||||
|
||||
- block:
|
||||
- name: Add the Ubuntu PPA '{{ r_cran_ubuntu_packages_ppa }}'
|
||||
apt_repository: repo='{{ r_cran_ubuntu_packages_ppa }}' state=present update_cache=yes
|
||||
|
||||
- name: Install the R plugins from the Ubuntu PPA
|
||||
apt: pkg={{ r_cran_ubuntu_packages }} state=present cache_valid_time=3600
|
||||
apt:
|
||||
pkg: '{{ r_cran_ubuntu_packages }}'
|
||||
state: present
|
||||
cache_valid_time: 3600
|
||||
|
||||
when: ansible_distribution_file_variety == "Debian"
|
||||
when: ansible_distribution == "Ubuntu"
|
||||
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_deb_plugins' ]
|
||||
|
||||
- block:
|
||||
|
|
|
|||
|
|
@ -1,4 +1,35 @@
|
|||
---
|
||||
- name: Manage the subversion repository
|
||||
block:
|
||||
- name: Create the R packages updater SVN base directory
|
||||
file:
|
||||
dest: '{{ r_packages_svn_base_dir }}'
|
||||
state: directory
|
||||
|
||||
when:
|
||||
- r_cran_install_from_sources
|
||||
- r_packages_updater
|
||||
- r_package_updater_via_subversion
|
||||
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]
|
||||
|
||||
- name: Manage the git repository of the packages lists
|
||||
block:
|
||||
- name: Remove the R packages updater SVN base directory
|
||||
file:
|
||||
dest: '{{ r_packages_svn_base_dir }}/RPackagesManagement'
|
||||
state: absent
|
||||
|
||||
- name: Create the R packages updater git base directory
|
||||
file:
|
||||
dest: '{{ r_packages_git_base_dir }}'
|
||||
state: directory
|
||||
|
||||
when:
|
||||
- r_cran_install_from_sources
|
||||
- r_packages_updater
|
||||
- r_package_updater_via_git
|
||||
tags: [ 'r_software', 'r_pkg', 'r_plugins', 'r_plugins_github', 'r_cran_pkgs', 'r_github_pkgs', 'r_packages_updater' ]
|
||||
|
||||
- block:
|
||||
- name: Install the R packages updater script
|
||||
template:
|
||||
|
|
@ -8,11 +39,6 @@
|
|||
group: root
|
||||
mode: '0755'
|
||||
|
||||
- name: Create the R packages updater SVN base directory
|
||||
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"
|
||||
|
|
|
|||
|
|
@ -18,13 +18,23 @@ TMP_FILES_DIR=/var/tmp/r_pkgs_update
|
|||
# We cannot answer questions
|
||||
DEBIAN_FRONTEND=noninteractive
|
||||
R_CRAN_MIRROR="{{ r_cran_mirror_site }}"
|
||||
{% if r_package_updater_via_git %}
|
||||
R_PKGS_FROM_SVN="False"
|
||||
R_PKGS_FROM_GIT="{{ r_package_updater_via_git }}"
|
||||
R_PKGS_DIR="r-packages-list"
|
||||
R_PKGS_URL="{{ r_package_updater_git_repo }}"
|
||||
R_PKGS_BASE_DIR="{{ r_packages_git_base_dir }}"
|
||||
GIT_UPDATE_STATUS=
|
||||
{% elif r_package_updater_via_subversion %}
|
||||
R_PKGS_FROM_SVN="{{ r_package_updater_via_subversion }}"
|
||||
R_PKGS_SVN_DIR=RPackagesManagement
|
||||
R_PKGS_SVN_URL="{{ r_package_updater_subversion_repo }}"
|
||||
R_PKGS_SVN_BASE_DIR="{{ r_packages_svn_base_dir }}"
|
||||
R_PKGS_FILES_PREFIX="{{ r_packages_svn_files_prefix }}"
|
||||
RSCRIPT_OPTIONS="--slave --no-site-file --no-init-file --no-save --no-restore-history"
|
||||
R_PKGS_FROM_GIT="False"
|
||||
R_PKGS_DIR=RPackagesManagement
|
||||
R_PKGS_URL="{{ r_package_updater_subversion_repo }}"
|
||||
R_PKGS_BASE_DIR="{{ r_packages_svn_base_dir }}"
|
||||
SVN_UPDATE_STATUS=
|
||||
{% endif %}
|
||||
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
|
||||
# - debian packages list format:
|
||||
|
|
@ -146,21 +156,39 @@ function get_data_files() {
|
|||
|
||||
function get_data_files_from_svn() {
|
||||
logger "update_r_packages: files from a SVN repo."
|
||||
if [ -d $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR ] ; then
|
||||
if [ -d $R_PKGS_BASE_DIR/$R_PKGS_DIR ] ; then
|
||||
logger "update_r_packages: SVN update"
|
||||
cd $R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR
|
||||
cd $R_PKGS_BASE_DIR/$R_PKGS_DIR
|
||||
SVN_CLEANUP_OP=$( svn cleanup )
|
||||
SVN_UPDATE_OP=$( svn update | tail -1 | grep Updated >/dev/null 2>&1 )
|
||||
SVN_UPDATE_STATUS=$?
|
||||
else
|
||||
cd $R_PKGS_SVN_BASE_DIR
|
||||
cd $R_PKGS_BASE_DIR
|
||||
logger "update_r_packages: first SVN checkout."
|
||||
svn co $R_PKGS_SVN_URL >/dev/null 2>&1
|
||||
svn co $R_PKGS_URL >/dev/null 2>&1
|
||||
fi
|
||||
PKGS_LIST=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_deb_pkgs.txt
|
||||
R_PKGS_LIST=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_cran_pkgs.txt
|
||||
R_VERSIONED_PKGS_LIST=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_cran_versioned_pkgs.txt
|
||||
R_PKGS_GITHUB=$R_PKGS_SVN_BASE_DIR/$R_PKGS_SVN_DIR/${R_PKGS_FILES_PREFIX}r_github_pkgs.txt
|
||||
PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_deb_pkgs.txt
|
||||
R_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_pkgs.txt
|
||||
R_VERSIONED_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_versioned_pkgs.txt
|
||||
R_PKGS_GITHUB=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_github_pkgs.txt
|
||||
}
|
||||
|
||||
function get_data_files_from_git() {
|
||||
logger "update_r_packages: files from a git repo."
|
||||
if [ -d $R_PKGS_BASE_DIR/$R_PKGS_DIR ] ; then
|
||||
logger "update_r_packages: git pull"
|
||||
cd $R_PKGS_BASE_DIR/$R_PKGS_DIR
|
||||
GIT_UPDATE_OP=$( git pull | tail -1 | grep Already >/dev/null 2>&1 )
|
||||
GIT_UPDATE_STATUS=$?
|
||||
else
|
||||
cd $R_PKGS_BASE_DIR
|
||||
logger "update_r_packages: first git clone."
|
||||
git clone $R_PKGS_URL >/dev/null 2>&1
|
||||
fi
|
||||
PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_deb_pkgs.txt
|
||||
R_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_pkgs.txt
|
||||
R_VERSIONED_PKGS_LIST=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_cran_versioned_pkgs.txt
|
||||
R_PKGS_GITHUB=$R_PKGS_BASE_DIR/$R_PKGS_DIR/${R_PKGS_FILES_PREFIX}r_github_pkgs.txt
|
||||
}
|
||||
|
||||
{% if ansible_distribution_file_variety == "Debian" %}
|
||||
|
|
@ -174,9 +202,7 @@ function distribution_pkgs() {
|
|||
logger "update_r_packages: APT cache not updated"
|
||||
fi
|
||||
>/var/log/update_r_debs.log
|
||||
while read deb_pkg ; do
|
||||
apt-get install ${deb_pkg} -q -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >>/var/log/update_r_debs.log 2>&1
|
||||
done < $PKGS_LIST
|
||||
xargs -a $PKGS_LIST apt-get install ${deb_pkg} -q -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >>/var/log/update_r_debs.log 2>&1
|
||||
apt-get autoremove -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >> /var/log/update_r_debs.log 2>&1
|
||||
else
|
||||
logger "update_r_packages: skipping the debian packages installation"
|
||||
|
|
@ -194,12 +220,6 @@ function distribution_pkgs() {
|
|||
if [ $EL_PKGS_SKIP -eq 0 ] ; then
|
||||
# Update the apt cache and install the packages in non interactive mode
|
||||
logger "update_r_packages: Installing the EL dependencies"
|
||||
if [ -z "$(find /var/cache/apt/pkgcache.bin -mmin -360)" ]; then
|
||||
apt-get update -q >/dev/null 2>&1
|
||||
else
|
||||
logger "update_r_packages: APT cache not updated"
|
||||
fi
|
||||
>/var/log/update_r_debs.log
|
||||
while read el_pkg ; do
|
||||
yum -y install ${el_pkg} >>/var/log/update_r_el.log 2>&1
|
||||
done < $PKGS_LIST
|
||||
|
|
@ -261,10 +281,10 @@ function r_github_pkgs() {
|
|||
for l in $( cat $R_PKGS_GITHUB ) ; do
|
||||
pkg=$( echo $l | cut -d "/" -f 2 )
|
||||
if [ "$ACTION" == "upgrade" ] ; then
|
||||
Rscript $RSCRIPT_OPTIONS -e "require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$l' ; refs <- jsonlite::read_json(sprintf('https://api.github.com/repos/%s/releases', package_to_install)) ; ref_to_install <- 'master'; if(length(refs)>0) { ref_to_install <- refs[[1]][['tag_name']] } ; devtools::install_github(package_to_install, ref = ref_to_install, upgrade='always')"
|
||||
Rscript $RSCRIPT_OPTIONS -e "require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$l' ; refs <- jsonlite::read_json(sprintf('https://api.github.com/repos/%s/releases', package_to_install)) ; ref_to_install <- 'master'; if(length(refs)>0) { ref_to_install <- refs[[1]][['tag_name']] } ; devtools::install_github(package_to_install, ref = ref_to_install, upgrade='false')"
|
||||
|
||||
else
|
||||
Rscript $RSCRIPT_OPTIONS -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$l' ; refs <- jsonlite::read_json(sprintf('https://api.github.com/repos/%s/releases', package_to_install)) ; ref_to_install <- 'master'; if(length(refs)>0) { ref_to_install <- refs[[1]][['tag_name']] } ; devtools::install_github(package_to_install, ref = ref_to_install, upgrade='always') }"
|
||||
Rscript $RSCRIPT_OPTIONS -e "if (! ('$pkg' %in% installed.packages()[,'Package'])) { require(devtools); require(methods); require(jsonlite) ; package_to_install <- '$l' ; refs <- jsonlite::read_json(sprintf('https://api.github.com/repos/%s/releases', package_to_install)) ; ref_to_install <- 'master'; if(length(refs)>0) { ref_to_install <- refs[[1]][['tag_name']] } ; devtools::install_github(package_to_install, ref = ref_to_install, upgrade='false') }"
|
||||
fi
|
||||
done
|
||||
else
|
||||
|
|
@ -279,7 +299,14 @@ function r_github_pkgs() {
|
|||
usage
|
||||
get_args
|
||||
init_env
|
||||
if [ $R_PKGS_FROM_SVN == 'True' ] ; then
|
||||
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"
|
||||
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"
|
||||
|
|
|
|||
Loading…
Reference in New Issue