From 7df0f4c652ce7d8ce1345b585685ca2e83981e63 Mon Sep 17 00:00:00 2001 From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr> Date: Thu, 27 Feb 2025 16:08:55 +0100 Subject: [PATCH 1/4] v0 --- .gitlab-ci.yml | 8 ++++---- gitlab-ci/test_psql.gitlab-ci.yml | 2 +- gitlab-ci/test_r.gitlab-ci.yml | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ae6400d..1055415 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -6,14 +6,14 @@ variables: tag_dev: "dev" imagedb_name: "stacomi_db" db_version: "0.6.0" - postgres_version: "14" - postgis_version: "3.2" + postgres_version: "17" + postgis_version: "3.5" POSTGRES_PASSWORD: postgres imager_name: "environnement_test_r" r_version: "0.1" imageR_name: "r4stacomi" - r_base_version: "4.x" - docker_version: "20.10" + r_base_version: "4.4" + docker_version: "28.0" docker_version_dind: "${docker_version}-dind" PG_USER: stacomi_test PG_USER_PASSWORD: stacomi_test diff --git a/gitlab-ci/test_psql.gitlab-ci.yml b/gitlab-ci/test_psql.gitlab-ci.yml index 997d65a..7ab0720 100644 --- a/gitlab-ci/test_psql.gitlab-ci.yml +++ b/gitlab-ci/test_psql.gitlab-ci.yml @@ -4,7 +4,7 @@ # template for the test .test_psql_template: stage: test - image: postgres:${postgres_version} + image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/postgres:${postgres_version} before_script: - echo "En attente de la disponibilité de PostgreSQL" - | diff --git a/gitlab-ci/test_r.gitlab-ci.yml b/gitlab-ci/test_r.gitlab-ci.yml index 11390aa..90e0642 100644 --- a/gitlab-ci/test_r.gitlab-ci.yml +++ b/gitlab-ci/test_r.gitlab-ci.yml @@ -13,7 +13,7 @@ ####################### # for any branch, but main test_r-dev: - image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/rocker/verse + image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/rocker/verse:${r_base_version} needs: - build_db-dev - test_psql-dev @@ -26,7 +26,7 @@ test_r-dev: ####################### # for main banch only test_r-prod: - image: $CI_REGISTRY_IMAGE/$imageR_name:latest + image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/rocker/verse:${r_base_version} needs: - build_db-prod extends: -- GitLab From 505715c15d1b3984d13d61478a0bc2675ee5b421 Mon Sep 17 00:00:00 2001 From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr> Date: Thu, 27 Feb 2025 16:26:43 +0100 Subject: [PATCH 2/4] up --- R.dockerfile | 52 --------------------- db.dockerfile | 2 +- gitlab-ci/build_images_docker.gitlab-ci.yml | 4 +- 3 files changed, 3 insertions(+), 55 deletions(-) delete mode 100644 R.dockerfile diff --git a/R.dockerfile b/R.dockerfile deleted file mode 100644 index cb5c570..0000000 --- a/R.dockerfile +++ /dev/null @@ -1,52 +0,0 @@ -ARG ubuntu_version=22.04 - -FROM ubuntu:${ubuntu_version} - -ENV DEBIAN_FRONTEND=noninteractive - -RUN (apt-get update && apt-get upgrade -y -q && apt-get -y -q autoclean && apt-get -y -q autoremove) - -# base d'utilitaires commun (pour mutualisation avec d'autres dockers) -RUN apt-get update && apt-get install -y -q vim apt-utils \ - sudo wget unzip \ - # pour envsubst - gettext-base \ - # pour pouvoir lancer les services avec systemctl depuis un docker (https://packages.debian.org/bullseye/systemctl) - systemctl \ - build-essential \ - git \ - # # pour le package R curl - # libcurl4-openssl-dev libxml2-dev libssl-dev libz-dev \ - # # pour le package R Rpotsgres - # libpq-dev libssl-dev \ - # pour le package R stacomiR - gfortran qpdf \ - && rm -rf /var/lib/apt/lists/* - -# installation des dépendances -RUN apt-get update && apt-get install -y -q -y --no-install-recommends \ - software-properties-common dirmngr \ - && rm -rf /var/lib/apt/lists/* - -# https://cran.r-project.org/bin/linux/ubuntu/ -RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \ - sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \ - && add-apt-repository --yes "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" && apt-get update -qq \ - && apt-get install -y -q --no-install-recommends r-base \ - && add-apt-repository --yes ppa:c2d4u.team/c2d4u4.0+ && apt-get update -qq \ - && rm -rf /var/lib/apt/lists/* - -# our required R packages -RUN apt-get update -qq && apt-get install -y -q --no-install-recommends \ - r-cran-sqldf \ - r-cran-rpostgresql r-cran-rpostgres r-cran-docopt littler r-cran-rodbc r-cran-devtools r-cran-golem \ - r-cran-hmisc r-cran-shinydashboardplus r-cran-htmltools r-cran-shinybs r-cran-shinyjs \ - r-cran-pool r-cran-shinywidgets r-cran-glue r-cran-rms r-cran-rcurl r-cran-xml r-cran-intervals \ - r-cran-rcolorbrewer r-cran-covr r-cran-dt r-cran-reshape2 r-cran-dplyr r-cran-remotes \ - r-cran-lattice r-cran-hmisc r-cran-lubridate r-cran-mgcv r-cran-ggthemes r-cran-withr r-cran-rmarkdown \ - && rm -rf /var/lib/apt/lists/* - -RUN ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r - -RUN install2.r --deps TRUE --repos "https://pbil.univ-lyon1.fr/CRAN/" \ - --error --skipinstalled stacomirtools graphics utils stats grDevices \ No newline at end of file diff --git a/db.dockerfile b/db.dockerfile index b6d0ee7..af13cf6 100644 --- a/db.dockerfile +++ b/db.dockerfile @@ -2,7 +2,7 @@ ARG postgresql_version=14 ARG postgis_version=3.2 FROM postgis/postgis:${postgresql_version}-${postgis_version} RUN localedef -i fr_FR -c -f UTF-8 -A /usr/share/locale/locale.alias fr_FR.UTF-8 -ENV LANG fr_FR.utf8 +ENV LANG=fr_FR.utf8 # script de construction de la base # attention doit commencer à 11 car il y a un 10_postgis.sh diff --git a/gitlab-ci/build_images_docker.gitlab-ci.yml b/gitlab-ci/build_images_docker.gitlab-ci.yml index e1b3c3a..c791cfb 100644 --- a/gitlab-ci/build_images_docker.gitlab-ci.yml +++ b/gitlab-ci/build_images_docker.gitlab-ci.yml @@ -9,7 +9,7 @@ build_db-dev: image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version stage: build_images services: - - docker:$docker_version_dind + - ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version_dind extends: - .rules_other script: @@ -24,7 +24,7 @@ build_db-prod: image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version stage: build_images services: - - docker:$docker_version_dind + - ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version_dind extends: - .rules_main when: manual -- GitLab From ada237abdcafe7434e0acfe550c2b7788793258e Mon Sep 17 00:00:00 2001 From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr> Date: Thu, 27 Feb 2025 16:50:02 +0100 Subject: [PATCH 3/4] fix --- gitlab-ci/build_images_docker.gitlab-ci.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gitlab-ci/build_images_docker.gitlab-ci.yml b/gitlab-ci/build_images_docker.gitlab-ci.yml index c791cfb..34aedc3 100644 --- a/gitlab-ci/build_images_docker.gitlab-ci.yml +++ b/gitlab-ci/build_images_docker.gitlab-ci.yml @@ -9,7 +9,8 @@ build_db-dev: image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version stage: build_images services: - - ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version_dind + - name: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version_dind + alias: docker extends: - .rules_other script: @@ -24,7 +25,8 @@ build_db-prod: image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version stage: build_images services: - - ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version_dind + - name: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/docker:$docker_version_dind + alias: docker extends: - .rules_main when: manual -- GitLab From 373b519e6a1232a161625b957b97be565e477616 Mon Sep 17 00:00:00 2001 From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr> Date: Thu, 27 Feb 2025 17:03:52 +0100 Subject: [PATCH 4/4] avec version R --- gitlab-ci/test_r.gitlab-ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gitlab-ci/test_r.gitlab-ci.yml b/gitlab-ci/test_r.gitlab-ci.yml index 90e0642..19a755f 100644 --- a/gitlab-ci/test_r.gitlab-ci.yml +++ b/gitlab-ci/test_r.gitlab-ci.yml @@ -4,6 +4,8 @@ # template for the test .test_r_template: stage: test + before_script: + - Rscript -e 'R.version' script: - Rscript -e '1+1' - Rscript -e 'a<-1; a+1' -- GitLab