update R dependency search; Allow Bioconductor packages (#600)

Author: zkamvar

.github/workflows/template.yml

@@ -137,9 +137,10 @@ jobs:
 
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
         run: |
-          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
-          install.packages(packages, repo="https://cran.rstudio.com/")
+          source('bin/dependencies.R')
+          install_required_packages(.libPaths()[1])
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -149,13 +150,14 @@ jobs:
           source('bin/dependencies.R')
           deps <- identify_dependencies()
           create_description(deps)
+          use_bioc_repos()
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore Package Cache
         if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -172,7 +174,7 @@ jobs:
         run: |
           while read -r cmd
           do
-            eval sudo $cmd
+            eval sudo $cmd || echo "Nothing to update"
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - run: make site

.github/workflows/website.yml

@@ -52,9 +52,9 @@ jobs:
         with:
           r-version: 'release'
 
-      - name: Cache R packages
+      - name: Restore R Cache
         if: steps.check-rmd.outputs.count != 0
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -63,8 +63,8 @@ jobs:
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
         run: |
-          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
-          install.packages(packages, repo="https://cran.rstudio.com/")
+          source('bin/dependencies.R')
+          install_required_packages()
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -73,6 +73,7 @@ jobs:
           source('bin/dependencies.R')
           deps <- identify_dependencies()
           create_description(deps)
+          use_bioc_repos()
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
@@ -83,7 +84,7 @@ jobs:
         run: |
           while read -r cmd
           do
-            eval sudo $cmd
+            eval sudo $cmd || echo "Nothing to update"
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - name: Render the markdown and confirm that the site can be built

bin/dependencies.R

@@ -1,17 +1,19 @@
 install_required_packages <- function(lib = NULL, repos = getOption("repos", default = c(CRAN = "https://cran.rstudio.com/"))) {
 
   if (is.null(lib)) {
-    lib <- .libPaths()
+    lib <- .libPaths()[[1]]
   }
 
   message("lib paths: ", paste(lib, collapse = ", "))
-  required_pkgs <- c("rprojroot", "desc", "remotes", "renv")
+  # Note: RMarkdown is needed for renv to detect packages in Rmd documents.
+  required_pkgs <- c("rprojroot", "desc", "remotes", "renv", "BiocManager", "rmarkdown")
   installed_pkgs <- rownames(installed.packages(lib.loc = lib))
   missing_pkgs <- setdiff(required_pkgs, installed_pkgs)
 
-  # The default installation of R will have "@CRAN@" as the default repository, which directs contrib.url() to either
-  # force the user to choose a mirror if interactive or fail if not. Since we are not interactve, we need to force the
-  # mirror here.
+  # The default installation of R will have "@CRAN@" as the default repository,
+  # which directs contrib.url() to either force the user to choose a mirror if
+  # interactive or fail if not. Since we are not interactve, we need to force
+  # the mirror here.
   if ("@CRAN@" %in% repos) {
     repos <- c(CRAN = "https://cran.rstudio.com/")
   }
@@ -29,30 +31,73 @@ find_root <- function() {
   root
 }
 
+# set the BiocManager repositories and return a function that resets the default
+# repositories.
+#
+# @example
+# bioc_repos_example <- function() {
+#   message("User repos")
+#   as.data.frame(getOption("repos"))
+#   reset_repos <- use_bioc_repos()
+#   on.exit(reset_repos())
+#   message("Bioc repos")
+#   as.data.frame(getOption("repos"))
+# }
+# bioc_repos_example()
+# as.data.frame(getOption("repos")
+use_bioc_repos <- function() {
+  repos <- getOption("repos")
+  suppressMessages(options(repos = BiocManager::repositories()))
+  function() {
+    options(repos = repos)
+  }
+}
+
 identify_dependencies <- function() {
 
   root <- find_root()
 
+  reset_repos <- use_bioc_repos()
+  on.exit(reset_repos(), add = TRUE)
+  eps <- file.path(root, "_episodes_rmd")
+  bin <- file.path(root, "bin")
+
   required_pkgs <- unique(c(
     ## Packages for episodes
-    renv::dependencies(file.path(root, "_episodes_rmd"), progress = FALSE, error = "ignore")$Package,
+    renv::dependencies(eps, progress = FALSE, error = "ignored")$Package,
     ## Packages for tools
-    renv::dependencies(file.path(root, "bin"), progress = FALSE, error = "ignore")$Package
+    renv::dependencies(bin, progress = FALSE, error = "ignored")$Package
   ))
 
   required_pkgs
 }
 
 create_description <- function(required_pkgs) {
   d <- desc::description$new("!new")
-  lapply(required_pkgs, function(x) d$set_dep(x))
+  d$set_deps(data.frame(type = "Imports", package = required_pkgs, version = "*"))
   d$write("DESCRIPTION")
+  # We have to write the description twice to get the hidden dependencies
+  # because renv only considers explicit dependencies.
+  #
+  # This is needed because some of the hidden dependencis will require system
+  # libraries to be configured.
+  suppressMessages(repo <- BiocManager::repositories())
+  deps <- remotes::dev_package_deps(dependencies = TRUE, repos = repo)
+  deps <- deps$package[deps$diff < 0]
+  if (length(deps)) {
+    # only create new DESCRIPTION file if there are dependencies to install
+    d$set_deps(data.frame(type = "Imports", package = deps, version = "*"))
+    d$write("DESCRIPTION")
+  }
 }
 
 install_dependencies <- function(required_pkgs, ...) {
 
+  reset_repos <- use_bioc_repos()
+  on.exit(reset_repos(), add = TRUE)
+
   create_description(required_pkgs)
-  on.exit(file.remove("DESCRIPTION"))
+  on.exit(file.remove("DESCRIPTION"), add = TRUE)
   remotes::install_deps(dependencies = TRUE, ...)
 
   if (require("knitr") && packageVersion("knitr") < '1.9.19') {