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