Fix CI check libs issue

Package check()ing was failing with an error about not finding dependencies that were actually correctly installed in the previous steps in the library at the environment variable R_LIBS_USER.

The problem was that the library at R_LIBS_USER appeared last in .libPaths() just after .Library and .Library.site. The order in .libPaths() is determined at startup from the environment variables R_LIBS and R_LIBS_USER, in that order. By default, R_LIBS is unset, causing R_LIBS_USER to appear first in .libPaths(). However, the docker images rocker/verse set R_LIBS within $R_HOME/etc/Renviron.site.

The current solution prevents reading this file at start up using --no-environ, only for check().

.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: