From 867e65d95d30894e7e5595c4405dda390191dfa3 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 17:37:31 +0200
Subject: [PATCH 01/30] fix(CI): pb install dependencies
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f5298c7..40a251d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,5 +1,5 @@
# test config
-image: rocker/tidyverse
+image: registry.forgemia.inra.fr/stacomi/stacomi_db/r4stacomi:4.x-dev
stages: # List of stages for jobs, and their order of execution
- build
@@ -31,7 +31,7 @@ buildbinary:
- R -e 'install.packages(pkgs=c("testthat"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")'
- R -e 'install.packages(pkgs=c("devtools"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")'
# below TRUE is shorthand for "Depends", "Imports", "LinkingTo" and "Suggests".
- - R -e 'devtools::install_deps(dependencies = TRUE, lib = Sys.getenv("R_LIBS_USER"))'
+ - R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
cache:
key: "$CI_COMMIT_REF_SLUG"
--
GitLab
From cad8b32f92b6bd00342f7a54a537596033efe03b Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 20:08:07 +0200
Subject: [PATCH 02/30] fix(CI): packages
---
.gitlab-ci.yml | 5 -----
DESCRIPTION | 4 ++--
2 files changed, 2 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 40a251d..692a95c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,7 +17,6 @@ variables:
# there are three lines added there so the uploaded packages will end up there
before_script:
- apt-get update
- - apt-get install -y qpdf
- mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR $BUILD_DIR
- echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
@@ -27,10 +26,6 @@ before_script:
buildbinary:
stage: build
script:
- # dependencies =TRUE only supports one
- - R -e 'install.packages(pkgs=c("testthat"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")'
- - R -e 'install.packages(pkgs=c("devtools"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")'
- # below TRUE is shorthand for "Depends", "Imports", "LinkingTo" and "Suggests".
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
cache:
diff --git a/DESCRIPTION b/DESCRIPTION
index bc69275..e27d21b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,8 +39,8 @@ Language: en-US
URL: https://forgemia.inra.fr/stacomi/stacoshiny
BugReports: https://forgemia.inra.fr/stacomi/stacoshiny/issues
Remotes:
- git::git@forgemia.inra.fr:stacomi/stacomirtools.git,
- git::git@forgemia.inra.fr:stacomi/stacomir.git
+ git::https://forgemia.inra.fr/stacomi/stacomirtools.git,
+ git::https://forgemia.inra.fr/stacomi/stacomir.git
VignetteBuilder: knitr
Depends:
R (>= 2.10)
--
GitLab
From 5c9d4562a1dd1845c7c44dbcce2d68dbe410a47d Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 20:50:45 +0200
Subject: [PATCH 03/30] fix(CI): lib R
---
.gitlab-ci.yml | 3 ---
1 file changed, 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 692a95c..d9c7d98 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,9 +18,6 @@ variables:
before_script:
- apt-get update
- mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR $BUILD_DIR
- - echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
- - echo 'R_LIBS_SITE=$R_LIBS_USER' >> .Renviron
# below CI_COMMIT_REF_SLUG is CI_COMMIT_REF_NAME The branch or tag name for which project is built, in lowercase, shortened to 63 bytes
buildbinary:
--
GitLab
From 46c42bf9dcbeafa8d46732d0b76bbdf65fb4b3ef Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 21:04:57 +0200
Subject: [PATCH 04/30] fix(CI): restore Rlibs for user only
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d9c7d98..26dc6b4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,6 +18,7 @@ variables:
before_script:
- apt-get update
- mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR $BUILD_DIR
+ - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
# below CI_COMMIT_REF_SLUG is CI_COMMIT_REF_NAME The branch or tag name for which project is built, in lowercase, shortened to 63 bytes
buildbinary:
--
GitLab
From d74cb8ffb6876b82ed1e55eaa88a667f94524dd3 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 21:25:16 +0200
Subject: [PATCH 05/30] fix(CI): cache R lib
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 26dc6b4..d354d61 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,7 +29,7 @@ buildbinary:
cache:
key: "$CI_COMMIT_REF_SLUG"
paths:
- - "$R_LIBS_USER"
+ - /usr/local/lib/R/site-library
artifacts:
paths:
- "$BUILD_DIR"
@@ -46,7 +46,7 @@ checkerrors:
- R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
cache:
paths:
- - $R_LIBS_USER
+ - /usr/local/lib/R/site-library
coverage:
stage: covr
--
GitLab
From 5ae99d82ff8cff13cdc12a84f0c9cb671ea8371c Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 22:14:06 +0200
Subject: [PATCH 06/30] refactor(CI)
---
.gitlab-ci.yml | 28 ++++++++++++------
gitlab-ci/build_images_docker.gitlab-ci.yml | 32 +++++++++++++++++++++
gitlab-ci/image.gitlab-ci.yml | 11 +++++++
gitlab-ci/rules.gitlab-ci.yml | 13 +++++++++
4 files changed, 76 insertions(+), 8 deletions(-)
create mode 100644 gitlab-ci/build_images_docker.gitlab-ci.yml
create mode 100644 gitlab-ci/image.gitlab-ci.yml
create mode 100644 gitlab-ci/rules.gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d354d61..21a60f4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,24 +1,34 @@
-# test config
-image: registry.forgemia.inra.fr/stacomi/stacomi_db/r4stacomi:4.x-dev
+include:
+ - local: '/gitlab-ci/rules.gitlab-ci.yml' # generic rules to be used for main branch or others
+ - local: '/gitlab-ci/image.gitlab-ci.yml' # image to be used for main branch or others
+ - local: '/gitlab-ci/build_images_docker.gitlab-ci.yml' # building docker images
stages: # List of stages for jobs, and their order of execution
- build
- document
- check
- covr
+ - build_images
variables:
R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib"
CHECK_DIR: "$CI_PROJECT_DIR/ci/logs"
BUILD_DIR: "$CI_PROJECT_DIR/ci/build"
BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs/$CI_PROJECT_NAME.Rcheck"
+ r_image_path: "registry.forgemia.inra.fr/stacomi/stacomi_db/"
+ r_image_name: "r4stacomi"
+ r_image_tagdev: "4.x-dev"
+ docker_version: "20.10"
+ docker_version_dind: "${docker_version}-dind"
+ stacoshiny_image_name: "stacoshiny"
+ stacoshiny_version: "0.0.0.9000"
# the .Renviron in the document folder contains the path to the libraries in the form R_LIBS=$CI_PROJECT_DIR/ci/lib
# there are three lines added there so the uploaded packages will end up there
before_script:
- apt-get update
- - mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR $BUILD_DIR
- - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
+ - mkdir -p ${R_LIBS_USER} ${BUILD_LOGS_DIR} ${BUILD_DIR}
+ - echo 'R_LIBS_USER=${R_LIBS_USER}' >> .Renviron
# below CI_COMMIT_REF_SLUG is CI_COMMIT_REF_NAME The branch or tag name for which project is built, in lowercase, shortened to 63 bytes
buildbinary:
@@ -26,13 +36,14 @@ buildbinary:
script:
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
+ - cp /usr/local/lib/R/site-library ${R_LIBS_USER}
cache:
- key: "$CI_COMMIT_REF_SLUG"
+ key: $CI_COMMIT_REF_SLUG
paths:
- - /usr/local/lib/R/site-library
+ - ${R_LIBS_USER}
artifacts:
paths:
- - "$BUILD_DIR"
+ - ${BUILD_DIR}
documentation:
stage: document
@@ -45,8 +56,9 @@ checkerrors:
- R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
cache:
+ key: $CI_COMMIT_REF_SLUG
paths:
- - /usr/local/lib/R/site-library
+ - ${R_LIBS_USER}
coverage:
stage: covr
diff --git a/gitlab-ci/build_images_docker.gitlab-ci.yml b/gitlab-ci/build_images_docker.gitlab-ci.yml
new file mode 100644
index 0000000..7e94cec
--- /dev/null
+++ b/gitlab-ci/build_images_docker.gitlab-ci.yml
@@ -0,0 +1,32 @@
+# build docker images
+
+#######################
+# for any branch, but main
+build_stacoshiny-dev:
+ image: docker:$docker_version
+ stage: build_images
+ services:
+ - docker:$docker_version_dind
+ extends:
+ - .rules_other
+ script:
+ - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
+ - docker build -t $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:${stacoshiny_version}-$tag_dev -f stacoshiny.dockerfile .
+ - docker push --all-tags $CI_REGISTRY_IMAGE/${stacoshiny_image_name}
+
+#######################
+# for main banch only
+build_stacoshiny-prod:
+ image: docker:$docker_version
+ stage: build_images
+ services:
+ - docker:$docker_version_dind
+ extends:
+ - .rules_main
+ when: manual
+ script:
+ - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
+ - docker build -t $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:${stacoshiny_version} -f stacoshiny.dockerfile .
+ - docker tag $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:${stacoshiny_version} $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:latest
+ - docker push --all-tags $CI_REGISTRY_IMAGE/${stacoshiny_image_name}
+
\ No newline at end of file
diff --git a/gitlab-ci/image.gitlab-ci.yml b/gitlab-ci/image.gitlab-ci.yml
new file mode 100644
index 0000000..0ebdffc
--- /dev/null
+++ b/gitlab-ci/image.gitlab-ci.yml
@@ -0,0 +1,11 @@
+# to use the right docker db image
+
+#######################
+# for any branch, but main
+.image-dev:
+ image: ${r_image_path}/${r_image_name}:${r_image_tagdev}
+
+#######################
+# for main banch only
+.image-prod:
+ image: ${r_image_path}/${r_image_name}:latest
\ No newline at end of file
diff --git a/gitlab-ci/rules.gitlab-ci.yml b/gitlab-ci/rules.gitlab-ci.yml
new file mode 100644
index 0000000..f876262
--- /dev/null
+++ b/gitlab-ci/rules.gitlab-ci.yml
@@ -0,0 +1,13 @@
+# generic rules to be used for main branch or others
+
+#######################
+# for any branch, but main
+.rules_other:
+ rules:
+ - if: '$CI_COMMIT_BRANCH != "main"' # only if there is changes in branch other than main
+
+#######################
+# for main banch only
+.rules_main:
+ rules:
+ - if: '$CI_COMMIT_BRANCH == "main"' # only if there is changes in the main branch
\ No newline at end of file
--
GitLab
From ffa2b37bc52eff4829f5db3cd3e45e1402bc1be0 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 22:30:28 +0200
Subject: [PATCH 07/30] refactor(CI)
---
.gitlab-ci.yml | 24 ++----------------------
gitlab-ci/before_script.gitlab-ci.yml | 6 ++++++
gitlab-ci/build_binary.gitlab-ci.yml | 13 +++++++++++++
3 files changed, 21 insertions(+), 22 deletions(-)
create mode 100644 gitlab-ci/before_script.gitlab-ci.yml
create mode 100644 gitlab-ci/build_binary.gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 21a60f4..2932538 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,6 +1,8 @@
include:
- local: '/gitlab-ci/rules.gitlab-ci.yml' # generic rules to be used for main branch or others
- local: '/gitlab-ci/image.gitlab-ci.yml' # image to be used for main branch or others
+ - local: '/gitlab-ci/before_script.gitlab-ci.yml'
+ - local: '/gitlab-ci/build_binary.gitlab-ci.yml'
- local: '/gitlab-ci/build_images_docker.gitlab-ci.yml' # building docker images
stages: # List of stages for jobs, and their order of execution
@@ -23,28 +25,6 @@ variables:
stacoshiny_image_name: "stacoshiny"
stacoshiny_version: "0.0.0.9000"
-# the .Renviron in the document folder contains the path to the libraries in the form R_LIBS=$CI_PROJECT_DIR/ci/lib
-# there are three lines added there so the uploaded packages will end up there
-before_script:
- - apt-get update
- - mkdir -p ${R_LIBS_USER} ${BUILD_LOGS_DIR} ${BUILD_DIR}
- - echo 'R_LIBS_USER=${R_LIBS_USER}' >> .Renviron
-
-# below CI_COMMIT_REF_SLUG is CI_COMMIT_REF_NAME The branch or tag name for which project is built, in lowercase, shortened to 63 bytes
-buildbinary:
- stage: build
- script:
- - R -e 'remotes::install_deps(upgrade = "never")'
- - R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
- - cp /usr/local/lib/R/site-library ${R_LIBS_USER}
- cache:
- key: $CI_COMMIT_REF_SLUG
- paths:
- - ${R_LIBS_USER}
- artifacts:
- paths:
- - ${BUILD_DIR}
-
documentation:
stage: document
script:
diff --git a/gitlab-ci/before_script.gitlab-ci.yml b/gitlab-ci/before_script.gitlab-ci.yml
new file mode 100644
index 0000000..171bab9
--- /dev/null
+++ b/gitlab-ci/before_script.gitlab-ci.yml
@@ -0,0 +1,6 @@
+# the .Renviron in the document folder contains the path to the libraries in the form R_LIBS=$CI_PROJECT_DIR/ci/lib
+# there are three lines added there so the uploaded packages will end up there
+before_script:
+ - apt-get update
+ - mkdir -p ${R_LIBS_USER} ${BUILD_LOGS_DIR} ${BUILD_DIR}
+ - echo 'R_LIBS_USER=${R_LIBS_USER}' >> .Renviron
\ No newline at end of file
diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml
new file mode 100644
index 0000000..a8ecfcf
--- /dev/null
+++ b/gitlab-ci/build_binary.gitlab-ci.yml
@@ -0,0 +1,13 @@
+buildbinary:
+ stage: build
+ script:
+ - R -e 'remotes::install_deps(upgrade = "never")'
+ - R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
+ - cp /usr/local/lib/R/site-library ${R_LIBS_USER}
+ cache:
+ key: $CI_COMMIT_REF_SLUG
+ paths:
+ - ${R_LIBS_USER}
+ artifacts:
+ paths:
+ - ${BUILD_DIR}
\ No newline at end of file
--
GitLab
From 60cbc57e59c0cacd9f3f809cb1590bb669022d63 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 22:35:25 +0200
Subject: [PATCH 08/30] refactor(CI): test image
---
gitlab-ci/build_binary.gitlab-ci.yml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml
index a8ecfcf..d5623fa 100644
--- a/gitlab-ci/build_binary.gitlab-ci.yml
+++ b/gitlab-ci/build_binary.gitlab-ci.yml
@@ -1,5 +1,7 @@
buildbinary:
stage: build
+ extends:
+ - .image-dev
script:
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
--
GitLab
From 25afb7398f661f2a5ac8505c8c8b868a6ebd8491 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 22:49:32 +0200
Subject: [PATCH 09/30] fix(CI): pb with image path
---
.gitlab-ci.yml | 2 +-
gitlab-ci/build_binary.gitlab-ci.yml | 2 ++
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2932538..daf1de7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,7 +17,7 @@ variables:
CHECK_DIR: "$CI_PROJECT_DIR/ci/logs"
BUILD_DIR: "$CI_PROJECT_DIR/ci/build"
BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs/$CI_PROJECT_NAME.Rcheck"
- r_image_path: "registry.forgemia.inra.fr/stacomi/stacomi_db/"
+ r_image_path: "registry.forgemia.inra.fr/stacomi/stacomi_db"
r_image_name: "r4stacomi"
r_image_tagdev: "4.x-dev"
docker_version: "20.10"
diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml
index d5623fa..62209a3 100644
--- a/gitlab-ci/build_binary.gitlab-ci.yml
+++ b/gitlab-ci/build_binary.gitlab-ci.yml
@@ -2,6 +2,8 @@ buildbinary:
stage: build
extends:
- .image-dev
+ - .rules_other
+ - .rules_main
script:
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
--
GitLab
From 72394a3a8eabb1c862d6e508496fdbe7601697fd Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 22:51:26 +0200
Subject: [PATCH 10/30] refactor(CI)
---
gitlab-ci/build_binary.gitlab-ci.yml | 1 -
1 file changed, 1 deletion(-)
diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml
index 62209a3..534ee96 100644
--- a/gitlab-ci/build_binary.gitlab-ci.yml
+++ b/gitlab-ci/build_binary.gitlab-ci.yml
@@ -3,7 +3,6 @@ buildbinary:
extends:
- .image-dev
- .rules_other
- - .rules_main
script:
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
--
GitLab
From c959448394c1fa9208da3df9b1e69d258e16215f Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 22:55:23 +0200
Subject: [PATCH 11/30] fix(CI): missing --recursive in cp
---
gitlab-ci/build_binary.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml
index 534ee96..b417575 100644
--- a/gitlab-ci/build_binary.gitlab-ci.yml
+++ b/gitlab-ci/build_binary.gitlab-ci.yml
@@ -6,7 +6,7 @@ buildbinary:
script:
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
- - cp /usr/local/lib/R/site-library ${R_LIBS_USER}
+ - cp --recursive /usr/local/lib/R/site-library ${R_LIBS_USER}
cache:
key: $CI_COMMIT_REF_SLUG
paths:
--
GitLab
From c1f70874ee9fd2a9190798958b1f788222939e0e Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:11:53 +0200
Subject: [PATCH 12/30] CI: introduce a rule to shut down a job
---
.gitlab-ci.yml | 10 +++++++---
gitlab-ci/rules.gitlab-ci.yml | 8 +++++++-
2 files changed, 14 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index daf1de7..7e83088 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -27,11 +27,15 @@ variables:
documentation:
stage: document
+ extends:
+ - .rules_shut_down
script:
- R -e 'devtools::document()'
checkerrors:
stage: check
+ extends:
+ - .rules_shut_down
script:
- R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
@@ -42,8 +46,8 @@ checkerrors:
coverage:
stage: covr
+ extends:
+ - .rules_shut_down
script:
- R -e 'install.packages(pkgs=c("covr"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")'
- - R -e 'covr::package_coverage(Sys.getenv("CI_PROJECT_DIR"))'
-
-
\ No newline at end of file
+ - R -e 'covr::package_coverage(Sys.getenv("CI_PROJECT_DIR"))'
\ No newline at end of file
diff --git a/gitlab-ci/rules.gitlab-ci.yml b/gitlab-ci/rules.gitlab-ci.yml
index f876262..2f3d5c7 100644
--- a/gitlab-ci/rules.gitlab-ci.yml
+++ b/gitlab-ci/rules.gitlab-ci.yml
@@ -10,4 +10,10 @@
# for main banch only
.rules_main:
rules:
- - if: '$CI_COMMIT_BRANCH == "main"' # only if there is changes in the main branch
\ No newline at end of file
+ - if: '$CI_COMMIT_BRANCH == "main"' # only if there is changes in the main branch
+
+#######################
+# for shutting down the job
+.rules_shut_down:
+ rules:
+ - FALSE # only if there is changes in the main branch
\ No newline at end of file
--
GitLab
From f342d3ac297fc748c0ab81487b4e73224e13b91c Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:37:51 +0200
Subject: [PATCH 13/30] fix(CI): cache
---
.gitlab-ci.yml | 9 +++++----
gitlab-ci/build_binary.gitlab-ci.yml | 4 ----
2 files changed, 5 insertions(+), 8 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7e83088..afb3edf 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -25,6 +25,11 @@ variables:
stacoshiny_image_name: "stacoshiny"
stacoshiny_version: "0.0.0.9000"
+cache:
+ key: $CI_COMMIT_REF_SLUG
+ paths:
+ - ${R_LIBS_USER}/
+
documentation:
stage: document
extends:
@@ -39,10 +44,6 @@ checkerrors:
script:
- R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
- cache:
- key: $CI_COMMIT_REF_SLUG
- paths:
- - ${R_LIBS_USER}
coverage:
stage: covr
diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml
index b417575..d7c47bb 100644
--- a/gitlab-ci/build_binary.gitlab-ci.yml
+++ b/gitlab-ci/build_binary.gitlab-ci.yml
@@ -7,10 +7,6 @@ buildbinary:
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
- cp --recursive /usr/local/lib/R/site-library ${R_LIBS_USER}
- cache:
- key: $CI_COMMIT_REF_SLUG
- paths:
- - ${R_LIBS_USER}
artifacts:
paths:
- ${BUILD_DIR}
\ No newline at end of file
--
GitLab
From d6942eb888494d11cf3dc279649f6cc54a3fdc9b Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:42:41 +0200
Subject: [PATCH 14/30] fix(CI): rules
---
gitlab-ci/rules.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gitlab-ci/rules.gitlab-ci.yml b/gitlab-ci/rules.gitlab-ci.yml
index 2f3d5c7..c8b6d71 100644
--- a/gitlab-ci/rules.gitlab-ci.yml
+++ b/gitlab-ci/rules.gitlab-ci.yml
@@ -16,4 +16,4 @@
# for shutting down the job
.rules_shut_down:
rules:
- - FALSE # only if there is changes in the main branch
\ No newline at end of file
+ - if: FALSE # only if there is changes in the main branch
\ No newline at end of file
--
GitLab
From 22527cc8090e20d22a9d9b815353538d8e9ba04a Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:44:21 +0200
Subject: [PATCH 15/30] fix(CI): rule
---
gitlab-ci/rules.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gitlab-ci/rules.gitlab-ci.yml b/gitlab-ci/rules.gitlab-ci.yml
index c8b6d71..f58f838 100644
--- a/gitlab-ci/rules.gitlab-ci.yml
+++ b/gitlab-ci/rules.gitlab-ci.yml
@@ -16,4 +16,4 @@
# for shutting down the job
.rules_shut_down:
rules:
- - if: FALSE # only if there is changes in the main branch
\ No newline at end of file
+ - when: never # only if there is changes in the main branch
\ No newline at end of file
--
GitLab
From b5eeec42acbcfd2f74c729ee7109c9590cf614d2 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:48:38 +0200
Subject: [PATCH 16/30] fix(CI): cache
---
.gitlab-ci.yml | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index afb3edf..00e5438 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,10 +21,6 @@ variables:
r_image_name: "r4stacomi"
r_image_tagdev: "4.x-dev"
docker_version: "20.10"
- docker_version_dind: "${docker_version}-dind"
- stacoshiny_image_name: "stacoshiny"
- stacoshiny_version: "0.0.0.9000"
-
cache:
key: $CI_COMMIT_REF_SLUG
paths:
@@ -33,10 +29,10 @@ cache:
documentation:
stage: document
extends:
- - .rules_shut_down
+ - .rules_other
script:
- R -e 'devtools::document()'
-
+
checkerrors:
stage: check
extends:
--
GitLab
From 46a9422329117f1dab4a8432f8fe0e1e029fca9a Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:53:29 +0200
Subject: [PATCH 17/30] CI: separate documentation and shut down build image
---
.gitlab-ci.yml | 8 +-------
gitlab-ci/documentation.gitlab-ci.yml | 7 +++++++
2 files changed, 8 insertions(+), 7 deletions(-)
create mode 100644 gitlab-ci/documentation.gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 00e5438..67d1e88 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,6 +3,7 @@ include:
- local: '/gitlab-ci/image.gitlab-ci.yml' # image to be used for main branch or others
- local: '/gitlab-ci/before_script.gitlab-ci.yml'
- local: '/gitlab-ci/build_binary.gitlab-ci.yml'
+ - local: '/gitlab-ci/documentation.gitlab-ci.yml'
- local: '/gitlab-ci/build_images_docker.gitlab-ci.yml' # building docker images
stages: # List of stages for jobs, and their order of execution
@@ -26,13 +27,6 @@ cache:
paths:
- ${R_LIBS_USER}/
-documentation:
- stage: document
- extends:
- - .rules_other
- script:
- - R -e 'devtools::document()'
-
checkerrors:
stage: check
extends:
diff --git a/gitlab-ci/documentation.gitlab-ci.yml b/gitlab-ci/documentation.gitlab-ci.yml
new file mode 100644
index 0000000..d703639
--- /dev/null
+++ b/gitlab-ci/documentation.gitlab-ci.yml
@@ -0,0 +1,7 @@
+documentation:
+ stage: document
+ extends:
+ - .image-dev
+ - .rules_other
+ script:
+ - R -e 'devtools::document()'
\ No newline at end of file
--
GitLab
From 95718b062823280ae0adeca42b84ea5d2881565e Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:54:14 +0200
Subject: [PATCH 18/30] CI: shut down build image
---
gitlab-ci/build_images_docker.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gitlab-ci/build_images_docker.gitlab-ci.yml b/gitlab-ci/build_images_docker.gitlab-ci.yml
index 7e94cec..f34dc68 100644
--- a/gitlab-ci/build_images_docker.gitlab-ci.yml
+++ b/gitlab-ci/build_images_docker.gitlab-ci.yml
@@ -8,7 +8,7 @@ build_stacoshiny-dev:
services:
- docker:$docker_version_dind
extends:
- - .rules_other
+ - .rules_shut_down
script:
- echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
- docker build -t $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:${stacoshiny_version}-$tag_dev -f stacoshiny.dockerfile .
@@ -22,7 +22,7 @@ build_stacoshiny-prod:
services:
- docker:$docker_version_dind
extends:
- - .rules_main
+ - .rules_shut_down
when: manual
script:
- echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
--
GitLab
From 554f3deaade282c5cfa83bf87663c197343b4663 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 20 Oct 2022 23:58:24 +0200
Subject: [PATCH 19/30] fix(CI): cache
---
gitlab-ci/documentation.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/gitlab-ci/documentation.gitlab-ci.yml b/gitlab-ci/documentation.gitlab-ci.yml
index d703639..206678c 100644
--- a/gitlab-ci/documentation.gitlab-ci.yml
+++ b/gitlab-ci/documentation.gitlab-ci.yml
@@ -4,4 +4,5 @@ documentation:
- .image-dev
- .rules_other
script:
+ - echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- R -e 'devtools::document()'
\ No newline at end of file
--
GitLab
From f0f34b2b80b002d6b517fe24a190da922fbb81fd Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:02:36 +0200
Subject: [PATCH 20/30] CI: activate check
---
.gitlab-ci.yml | 8 --------
gitlab-ci/check.gitlab-ci.yml | 9 +++++++++
2 files changed, 9 insertions(+), 8 deletions(-)
create mode 100644 gitlab-ci/check.gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 67d1e88..3d46421 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -27,14 +27,6 @@ cache:
paths:
- ${R_LIBS_USER}/
-checkerrors:
- stage: check
- extends:
- - .rules_shut_down
- script:
- - R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- - R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
-
coverage:
stage: covr
extends:
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
new file mode 100644
index 0000000..b79a383
--- /dev/null
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -0,0 +1,9 @@
+checkerrors:
+ stage: check
+ extends:
+ - .image-dev
+ - .rules_shut_down
+ script:
+ - echo 'R_LIBS=$R_LIBS_USER' > .Renviron
+ - R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
+ - R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
\ No newline at end of file
--
GitLab
From 7a25dedb752acb4b95d56c8eef12cc367555c4b6 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:03:31 +0200
Subject: [PATCH 21/30] CI: activate check
---
gitlab-ci/check.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index b79a383..31d7a25 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -2,7 +2,7 @@ checkerrors:
stage: check
extends:
- .image-dev
- - .rules_shut_down
+ - .rules_other
script:
- echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
--
GitLab
From 13aa5c6cf16e0b814f1aa295153bcb16783c230a Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:04:38 +0200
Subject: [PATCH 22/30] CI: activate check
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3d46421..3a836bb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,6 +4,7 @@ include:
- local: '/gitlab-ci/before_script.gitlab-ci.yml'
- local: '/gitlab-ci/build_binary.gitlab-ci.yml'
- local: '/gitlab-ci/documentation.gitlab-ci.yml'
+ - local: '/gitlab-ci/check.gitlab-ci.yml'
- local: '/gitlab-ci/build_images_docker.gitlab-ci.yml' # building docker images
stages: # List of stages for jobs, and their order of execution
--
GitLab
From 607fff2d90a5289326aa1acb11de581da9503f40 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:19:06 +0200
Subject: [PATCH 23/30] fix(CI): ggthemes
---
gitlab-ci/check.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index 31d7a25..e1a4c5b 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -5,5 +5,5 @@ checkerrors:
- .rules_other
script:
- echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
+ - R -e 'install.packages("ggthemes") ; devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
\ No newline at end of file
--
GitLab
From 29faaf81f34d5ef4a569a04f556bf46d08cfa933 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:23:19 +0200
Subject: [PATCH 24/30] fix(CI): ggthemes
---
gitlab-ci/check.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index e1a4c5b..a5bf90f 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -5,5 +5,6 @@ checkerrors:
- .rules_other
script:
- echo 'R_LIBS=$R_LIBS_USER' > .Renviron
+ - R -e 'packageVersion("ggthemes")'
- R -e 'install.packages("ggthemes") ; devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
\ No newline at end of file
--
GitLab
From fad6b2afc5a19fa3238f5450c5dec1bbb12cf76f Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:25:46 +0200
Subject: [PATCH 25/30] fix(CI): ggthemes
---
gitlab-ci/check.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index a5bf90f..5526c92 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -5,6 +5,6 @@ checkerrors:
- .rules_other
script:
- echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - R -e 'packageVersion("ggthemes")'
- - R -e 'install.packages("ggthemes") ; devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- - R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
\ No newline at end of file
+ - Rscript -e 'packageVersion("ggthemes")'
+ - Rscript -e 'install.packages("ggthemes") ; devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
+ - Rscript -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
\ No newline at end of file
--
GitLab
From 04c0bcf9b29c1cb740024191ecaf8694460758de Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:39:33 +0200
Subject: [PATCH 26/30] fix(CI): System has not been booted with systemd as
init system (PID 1). Can't operate.
---
gitlab-ci/check.gitlab-ci.yml | 1 +
gitlab-ci/image.gitlab-ci.yml | 4 +++-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index 5526c92..664cd0a 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -5,6 +5,7 @@ checkerrors:
- .rules_other
script:
- echo 'R_LIBS=$R_LIBS_USER' > .Renviron
+ - Rscript -e 'library(ggthemes)'
- Rscript -e 'packageVersion("ggthemes")'
- Rscript -e 'install.packages("ggthemes") ; devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- Rscript -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
\ No newline at end of file
diff --git a/gitlab-ci/image.gitlab-ci.yml b/gitlab-ci/image.gitlab-ci.yml
index 0ebdffc..c9ffd55 100644
--- a/gitlab-ci/image.gitlab-ci.yml
+++ b/gitlab-ci/image.gitlab-ci.yml
@@ -3,7 +3,9 @@
#######################
# for any branch, but main
.image-dev:
- image: ${r_image_path}/${r_image_name}:${r_image_tagdev}
+ image:
+ - name: ${r_image_path}/${r_image_name}:${r_image_tagdev}
+ - entrypoint: ["/usr/sbin/init", "systemctl"]
#######################
# for main banch only
--
GitLab
From 72971f907945a8dc34de0c14d7c3f0bc9a2f543d Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:45:39 +0200
Subject: [PATCH 27/30] fix(CI): System has not been booted with systemd as
init system (PID 1). Can't operate.
---
gitlab-ci/image.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gitlab-ci/image.gitlab-ci.yml b/gitlab-ci/image.gitlab-ci.yml
index c9ffd55..bbffc85 100644
--- a/gitlab-ci/image.gitlab-ci.yml
+++ b/gitlab-ci/image.gitlab-ci.yml
@@ -4,8 +4,8 @@
# for any branch, but main
.image-dev:
image:
- - name: ${r_image_path}/${r_image_name}:${r_image_tagdev}
- - entrypoint: ["/usr/sbin/init", "systemctl"]
+ name: ${r_image_path}/${r_image_name}:${r_image_tagdev}
+ entrypoint: ["/usr/sbin/init", "systemctl"]
#######################
# for main banch only
--
GitLab
From 44c7b4b1cc9ea478d994e1064f219949f6eb07a9 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 00:59:07 +0200
Subject: [PATCH 28/30] fix(CI): System has not been booted with systemd as
init system (PID 1). Can't operate.
---
gitlab-ci/image.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gitlab-ci/image.gitlab-ci.yml b/gitlab-ci/image.gitlab-ci.yml
index bbffc85..d4b43ea 100644
--- a/gitlab-ci/image.gitlab-ci.yml
+++ b/gitlab-ci/image.gitlab-ci.yml
@@ -5,7 +5,7 @@
.image-dev:
image:
name: ${r_image_path}/${r_image_name}:${r_image_tagdev}
- entrypoint: ["/usr/sbin/init", "systemctl"]
+ entrypoint: ["/usr/sbin/init"]
#######################
# for main banch only
--
GitLab
From cffd312af98e4ca98fd9fc87385db0c234d04f7c Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 16:09:51 +0200
Subject: [PATCH 29/30] fix(CI): ggthemes
---
DESCRIPTION | 3 ++-
gitlab-ci/check.gitlab-ci.yml | 4 +---
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index e27d21b..5650813 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,7 +26,8 @@ Imports:
dplyr,
rlang,
shinybusy,
- magrittr
+ magrittr,
+ ggthemes
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.1
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index 664cd0a..e83d0fd 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -5,7 +5,5 @@ checkerrors:
- .rules_other
script:
- echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - Rscript -e 'library(ggthemes)'
- - Rscript -e 'packageVersion("ggthemes")'
- - Rscript -e 'install.packages("ggthemes") ; devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
+ - Rscript -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")'
- Rscript -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
\ No newline at end of file
--
GitLab
From 7fdb6e4cdfa7724272c5f54804516f57c3f8fa93 Mon Sep 17 00:00:00 2001
From: BEAULATON Laurent <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 21 Oct 2022 17:06:18 +0200
Subject: [PATCH 30/30] fix(ci): just check why CI is stuck
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gitlab-ci/build_binary.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml
index d7c47bb..7e85fa8 100644
--- a/gitlab-ci/build_binary.gitlab-ci.yml
+++ b/gitlab-ci/build_binary.gitlab-ci.yml
@@ -4,6 +4,7 @@ buildbinary:
- .image-dev
- .rules_other
script:
+ - echo "install packages"
- R -e 'remotes::install_deps(upgrade = "never")'
- R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)'
- cp --recursive /usr/local/lib/R/site-library ${R_LIBS_USER}
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