From 54f4566022342638a2766d80c312ccdfeec70fca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 20:37:13 +0200
Subject: [PATCH 01/10] Debug .gitlab-ci.yml
---
.gitlab-ci.yml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 59dad5d..abbb462 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -23,6 +23,8 @@ building:
- mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR
- Rscript -e "remotes::install_deps(dependencies = TRUE, lib = Sys.getenv('R_LIBS_USER'))"
# Install packages required by covr and pkgdown
+ - export # list value of all environmental variables
+ - ls -l $R_LIBS_USER
- Rscript -e "install.packages(c('DT', 'pkgdown'), lib = Sys.getenv('R_LIBS_USER'))"
- Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'))"
cache:
--
GitLab
From 048bcb0e7713f12c67ea7201227afa1037fc0a2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 20:42:53 +0200
Subject: [PATCH 02/10] Print libpaths from within R.
---
.gitlab-ci.yml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index abbb462..5d7ccc5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -26,6 +26,8 @@ building:
- export # list value of all environmental variables
- ls -l $R_LIBS_USER
- Rscript -e "install.packages(c('DT', 'pkgdown'), lib = Sys.getenv('R_LIBS_USER'))"
+ - Rscript -e ".libPaths()"
+ - Rscript -e "rownames(installed.packages())"
- Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'))"
cache:
key: default_3
--
GitLab
From 80202f21dcc758e2055ac7ac5e18c9d6fd16c8b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 20:45:03 +0200
Subject: [PATCH 03/10] Try loading {dm}.
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5d7ccc5..7548aa7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -28,6 +28,7 @@ building:
- Rscript -e "install.packages(c('DT', 'pkgdown'), lib = Sys.getenv('R_LIBS_USER'))"
- Rscript -e ".libPaths()"
- Rscript -e "rownames(installed.packages())"
+ - Rscript -e "library(dm)"
- Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'))"
cache:
key: default_3
--
GitLab
From ce80e3b63b4cc7a0d8d86c4b249f3947c89ea5d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 20:51:33 +0200
Subject: [PATCH 04/10] Try installing sit.
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7548aa7..af9ee0b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,6 +29,7 @@ building:
- Rscript -e ".libPaths()"
- Rscript -e "rownames(installed.packages())"
- Rscript -e "library(dm)"
+ - Rscript -e "devtools::install()"
- Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'))"
cache:
key: default_3
--
GitLab
From 6dfef3994f2fe104b5ae371be423255cd4471259 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 22:20:39 +0200
Subject: [PATCH 05/10] Pass env_var R_LIBS_USER to check.
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index af9ee0b..cb1857d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,7 +30,7 @@ building:
- Rscript -e "rownames(installed.packages())"
- Rscript -e "library(dm)"
- Rscript -e "devtools::install()"
- - Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'))"
+ - Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'), env_vars = c(NOT_CRAN = "true", R_LIBS_USER = Sys.getenv('R_LIBS_USER')))"
cache:
key: default_3
paths:
--
GitLab
From d810b3e2edffb9b7e54a921ea24434a599ce8b5f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 22:35:03 +0200
Subject: [PATCH 06/10] Environment variables used by devtools.
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cb1857d..764588a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,6 +30,7 @@ building:
- Rscript -e "rownames(installed.packages())"
- Rscript -e "library(dm)"
- Rscript -e "devtools::install()"
+ - Rscript -e "devtools::r_env_vars()"
- Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'), env_vars = c(NOT_CRAN = "true", R_LIBS_USER = Sys.getenv('R_LIBS_USER')))"
cache:
key: default_3
--
GitLab
From 216ab7c1a10faff92d7ffaae59241d4ac04b76f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 22:47:13 +0200
Subject: [PATCH 07/10] Checking env_vars argument.
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 764588a..3b1c900 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -31,6 +31,7 @@ building:
- Rscript -e "library(dm)"
- Rscript -e "devtools::install()"
- Rscript -e "devtools::r_env_vars()"
+ - Rscript -e "c(NOT_CRAN = "true", R_LIBS_USER = Sys.getenv('R_LIBS_USER'))"
- Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'), env_vars = c(NOT_CRAN = "true", R_LIBS_USER = Sys.getenv('R_LIBS_USER')))"
cache:
key: default_3
--
GitLab
From a5417e9f23777a2863e4115d627efe1ef9bf498b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 22:51:19 +0200
Subject: [PATCH 08/10] Fix quotes.
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3b1c900..8684eda 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -32,7 +32,7 @@ building:
- Rscript -e "devtools::install()"
- Rscript -e "devtools::r_env_vars()"
- Rscript -e "c(NOT_CRAN = "true", R_LIBS_USER = Sys.getenv('R_LIBS_USER'))"
- - Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'), env_vars = c(NOT_CRAN = "true", R_LIBS_USER = Sys.getenv('R_LIBS_USER')))"
+ - Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'), env_vars = c(NOT_CRAN = 'true', R_LIBS_USER = Sys.getenv('R_LIBS_USER')))"
cache:
key: default_3
paths:
--
GitLab
From c6c2ea725bcb285488655326412ec26865551222 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Fri, 29 Oct 2021 22:53:40 +0200
Subject: [PATCH 09/10] Fix the quotes also in the previous line!
---
.gitlab-ci.yml | 1 -
1 file changed, 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8684eda..cb36926 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -31,7 +31,6 @@ building:
- Rscript -e "library(dm)"
- Rscript -e "devtools::install()"
- Rscript -e "devtools::r_env_vars()"
- - Rscript -e "c(NOT_CRAN = "true", R_LIBS_USER = Sys.getenv('R_LIBS_USER'))"
- Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'), env_vars = c(NOT_CRAN = 'true', R_LIBS_USER = Sys.getenv('R_LIBS_USER')))"
cache:
key: default_3
--
GitLab
From bc1dc49f36d2d388765fc369000c2c5d6209b8e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@cirad.fr>
Date: Sat, 30 Oct 2021 14:24:10 +0200
Subject: [PATCH 10/10] Fix check() error by using --no-environ.
---
.gitlab-ci.yml | 12 ++++--------
1 file changed, 4 insertions(+), 8 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cb36926..694d64a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -23,15 +23,11 @@ building:
- mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR
- Rscript -e "remotes::install_deps(dependencies = TRUE, lib = Sys.getenv('R_LIBS_USER'))"
# Install packages required by covr and pkgdown
- - export # list value of all environmental variables
- - ls -l $R_LIBS_USER
- Rscript -e "install.packages(c('DT', 'pkgdown'), lib = Sys.getenv('R_LIBS_USER'))"
- - Rscript -e ".libPaths()"
- - Rscript -e "rownames(installed.packages())"
- - Rscript -e "library(dm)"
- - Rscript -e "devtools::install()"
- - Rscript -e "devtools::r_env_vars()"
- - Rscript -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'), env_vars = c(NOT_CRAN = 'true', R_LIBS_USER = Sys.getenv('R_LIBS_USER')))"
+ # Use --no-environ to prevent setting the environment variable R_LIBS from Rprofile.site
+ # which caused R_LIBS_USER to appear last in .libPaths(), which in turn prevented check()
+ # to find the packages installed in R_LIBS_USER, leading to a installation error.
+ - Rscript --no-environ -e "devtools::check(check_dir = Sys.getenv('CHECK_DIR'))"
cache:
key: default_3
paths:
--
GitLab