remove unwanted deps on renv.lock (#180)

* remove unwanted deps on renv.lock * remove duplicate * update DEPS_IGNORE * fix cat cmd * apply suggestions --------- Co-authored-by: pharmaverse-bot <[email protected]>
pharmaverse · Jan 17, 2024 · e4c13f0 · e4c13f0
1 parent a25b02b
commit e4c13f0
Showing 1 changed file with 20 additions and 7 deletions.
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
@@ -40,23 +40,35 @@ jobs:
       R_KEEP_PKG_SOURCE: true
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       R_REPOS: "https://cran.r-project.org"
+      DEPS_IGNORE: >-
+        pharmaversesdtm,
+        pharmaverseadam,
+        admiral,
+        admiraldev,
+        admiralophtha,
+        admiralonco,
+        admiralvaccine,
+        staged.dependencies
+
+      # DEPS_IGNORE: env variable to ignore package when building renv.lock (step Upload dependencies artifact)
+      # (improvments ideas : get this list of deps to ignore from staged.dependencies yml file)
 
     steps:
       ##################### BEGIN boilerplate steps #####################
       - name: Get branch names
         id: branch-name
-        uses: tj-actions/branch-names@v5.4
+        uses: tj-actions/branch-names@v8
 
       - name: Checkout repo (PR) 🛎
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         if: |
           github.event_name == 'pull_request'
         with:
           ref: ${{ steps.branch-name.outputs.head_ref_branch }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         if: |
           github.event_name != 'pull_request'
         with:
@@ -100,14 +112,15 @@ jobs:
           dir.create("/workspace/tmp")
           library(dplyr)
           installed_packages <- as.data.frame(installed.packages())
+          packages_to_remove <- Sys.getenv("DEPS_IGNORE", "")
+          packages_to_remove <- unlist(strsplit(packages_to_remove, ","))
+          installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>%  # remove pre-built deps
+          filter(!Package %in% packages_to_remove)
           # save deps as csv file
           write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE)
           # create also renv.lock file
           setwd("/workspace/tmp")
 
-          installed_packages <- as.data.frame(installed.packages())
-          installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library")
-
           renv_lock <- list(
             "R" = list(
               "Version" = paste(R.version$major, R.version$minor, sep=".")
@@ -152,7 +165,7 @@ jobs:
           # Write the list to a JSON file (renv.lock)
           writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock")
           print("generated renv.lock content")
-          system("cat renv.lock")
+          system("cat renv-${{ matrix.r_version }}.lock")
         shell: Rscript {0}
 
       - name: Upload deps.csv and renv.lock artifacts