update list of dependencies

.gitlab-ci.yml

@@ -10,8 +10,9 @@ before_script:
   - apt-get install -y --no-install-recommends ${APT_PKGS}
   - apt-get install -y --no-install-recommends qpdf pandoc pandoc-citeproc
   - R -e 'install.packages(c("testthat", "rmarkdown"));'
-  # install all packages in description file not yet installed:
-  # (only works with CRAN packages like this)
+  - R -e "install.packages(c('parallel', 'data.table', 'ggplot2', 'gridExtra', 'glmmTMB', 'magrittr', 'MASS', 'reshape2', 'rlang', 'stats', 'utils', 'BiocManager', 'car'))" 
+  - R -e "BiocManager::install('S4Vectors', update = FALSE)"
+  - R -e "BiocManager::install('DESeq2', update = FALSE)" 
   - R -e 'install.packages(setdiff(desc::desc()$get_deps()$package, c(installed.packages(), "R")));'
   - git submodule init && git submodule update