Merge pull request #39 from furrer-lab/33-remove-abn-from-the-install…

…ed-packages

33 remove abn from the installed packages

.gitignore

@@ -7,3 +7,4 @@
 .Rprofile
 renv.lock
 renv/
+*.code-workspace

containers/debian/Dockerfile

@@ -86,4 +86,7 @@ RUN git clone --depth=1 https://$REPO_PATH target
 WORKDIR target/
 # get a list of all dependencies; install remaining packages
 # escape=\
-RUN R -e "renv::deactivate();pckgs<-unique(renv::dependencies('$PACKAGE_PATH')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs)])"
+# Get the package name based on the repository from the Description file
+RUN PACKAGE_NAME=$(R -s -e "package<-desc::desc(file=file.path('${PACKAGE_PATH}','DESCRIPTION'))\$get_field('Package');writeLines(package)")
+# Install all dependencies of PACKAGE_NAME but not the package it self
+RUN R -e "renv::deactivate();pckgs<-unique(renv::dependencies('$PACKAGE_PATH')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs) & !(pckgs == '$PACKAGE_NAME')])"

containers/fedora/Dockerfile

@@ -104,4 +104,7 @@ RUN git clone --depth=1 https://$REPO_PATH target
 WORKDIR target/
 # get a list of all dependencies; install remaining packages
 # escape=\
-RUN R -e "renv::deactivate();pckgs<-unique(renv::dependencies('$PACKAGE_PATH')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs)])"
+# Get the package name based on the repository from the Description file
+RUN PACKAGE_NAME=$(R -s -e "package<-desc::desc(file=file.path('${PACKAGE_PATH}','DESCRIPTION'))\$get_field('Package');writeLines(package)")
+# Install all dependencies of PACKAGE_NAME but not the package it self
+RUN R -e "renv::deactivate();pckgs<-unique(renv::dependencies('$PACKAGE_PATH')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs) & !(pckgs == '$PACKAGE_NAME')])"