fix windows node_modules errors

Author: bschilder

.Rbuildignore

@@ -19,6 +19,10 @@ rworkflows-merged
 ^Meta$
 ^codecov\.yml$
 ^_pkgdown\.yml$
+^node_modules$
+^package-lock\.json$
+^package\.json$
+
 ^docs$
 ^pkgdown$
 ^Dockerfile$

.github/workflows/rworkflows_static.yml

@@ -21,11 +21,12 @@ env:
   run_covr: ${{ true }}
   run_pkgdown: ${{ false }}
   has_runit: ${{ false }}
-  has_latex: ${{ true }}
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  has_latex: ${{ false }}
   run_docker: ${{ false }}
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
   cache_version: cache-v1
+  enable_act: ${{ false }}
 jobs:
   rworkflows_static:
     permissions:
@@ -59,7 +60,7 @@ jobs:
       GITHUB_REPO: ${{ github.repository }}
       RGL_USE_NULL: ${{ true }}
     steps:
-    - name: Set GitHub environment variables
+    - name: "Set GitHub environment variables \U0001F3DE️"
       run: |
         echo "GITHUB_TOKEN=${{ env.GITHUB_TOKEN }}" >> $GITHUB_ENV
         echo "RGL_USE_NULL=TRUE" >> $GITHUB_ENV
@@ -68,31 +69,31 @@ jobs:
         echo "TZ=UTC" >> $GITHUB_ENV
         echo "NOT_CRAN=${{ !env.as_cran }}" >> $GITHUB_ENV
       shell: bash {0}
-    - name: Set R library home on Linux
+    - name: "Set R library home on Linux \U0001F4DA"
       if: runner.os == 'Linux'
       run: |
         mkdir -p /__w/_temp/Library
         echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
         git config --global --add safe.directory '*'
       shell: bash {0}
-    - name: Checkout repository
-      uses: actions/checkout@v3
-    - name: Setup R and Bioconductor
+    - name: Checkout repository ⏬
+      uses: actions/checkout@v4
+    - name: "Setup R and Bioconductor \U0001F6E0"
       if: runner.os != 'Linux'
       uses: grimbough/bioc-actions/setup-bioc@v1
       with:
         bioc-version: ${{ matrix.config.bioc }}
-    - name: Setup pandoc from r-lib
+    - name: "Setup pandoc from r-lib \U0001F6E0"
       if: runner.os != 'Linux'
       uses: r-lib/actions/setup-pandoc@v2
-    - name: Query dependencies
+    - name: Query dependencies ❔
       run: |
         options(crayon.enabled = TRUE)
         install.packages('remotes')
         remotes::install_github("r-lib/remotes")
         saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
       shell: Rscript {0}
-    - name: Restore R package cache
+    - name: "Restore R package cache \U0001F3E6"
       if: |
         !contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'
       uses: actions/cache@v3
@@ -102,7 +103,7 @@ jobs:
           }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
         restore-keys: ${{ env.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc
           }}-r-${{  matrix.config.r }}-
-    - name: Cache R packages on Linux
+    - name: "Cache R packages on Linux \U0001F3E6"
       if: |
         !contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux'
       uses: actions/cache@v3
@@ -112,15 +113,15 @@ jobs:
           }}-r-${{  matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
         restore-keys: ${{ env.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc
           }}-r-${{  matrix.config.r }}-
-    - name: Install Linux system dependencies
+    - name: "Install Linux system dependencies \U0001F6E0"
       if: runner.os == 'Linux'
       run: |
         sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
         echo $sysreqs
         sudo -s eval "$sysreqs"
         sudo apt-get install -y qpdf rsync
       shell: bash {0}
-    - name: Install macOS system dependencies
+    - name: "Install macOS system dependencies \U0001F6E0"
       if: runner.os == 'macOS'
       run: |
         #### --- Justifications for each package --- ####
@@ -148,30 +149,32 @@ jobs:
         ### Set up xml2 ###
         echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
       shell: bash {0}
-    - name: Install Windows system dependencies
+    - name: "Install Windows system dependencies \U0001F6E0"
       if: env.has_latex == 'true' && runner.os == 'Windows'
       run: |
         #### npm ####
         npm install curl
       shell: pwsh {0}
-    - name: Install latex
+    - name: "Install latex \U0001F6E0"
       if: env.has_latex == 'true'
       uses: r-lib/actions/setup-tinytex@v2
       env:
-        TINYTEX_INSTALLER: TinyTeX
-    - name: Install additional LaTeX packages (non-Windows)
-      if: env.has_latex == 'true' && runner.os != 'Windows'
-      run: |
-        tlmgr install bera nowidow parnotes marginfix etoolbox titlesec sectsty framed enumitem parskip soul placeins footmisc changepage xstring caption mathtools
-        tlmgr list --only-installed
-      shell: bash {0}
-    - name: Install additional LaTeX packages (Windows)
-      if: env.has_latex == 'true' && runner.os == 'Windows'
+        TINYTEX_INSTALLER: ${{ env.tinytex_installer }}
+        TINYTEX_VERSION: ${{ env.tinytex_version }}
+    - name: "Install latex \U0001F6E0"
+      if: env.has_latex == 'true'
+      env:
+        tinytex_installer: ${{ env.tinytex_installer }}
+        tinytex_version: ${{ env.tinytex_version }}
       run: |
-        tlmgr install bera nowidow parnotes marginfix etoolbox titlesec sectsty framed enumitem parskip soul placeins footmisc changepage xstring caption mathtools
-        tlmgr list --only-installed
-      shell: pwsh
-    - name: Install dependencies pass 1
+        install.packages("tinytex")
+        extra_packages <- c("bera","nowidow","parnotes","marginfix","etoolbox",
+        "titlesec","sectsty","framed","enumitem","parskip","soul","placeins",
+        "footmisc","changepage","xstring","caption","mathtools","fancyhdr",
+        "preprint","ragged2e","pdfcrop","titling","silence","everysel")
+        tinytex::tlmgr_install(pkgs = extra_packages)
+      shell: Rscript {0}
+    - name: "Install dependencies pass 1 \U0001F6E0"
       env:
         timeout: ${{ env.timeout }}
       run: |
@@ -184,7 +187,7 @@ jobs:
         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE)
       continue-on-error: ${{ true }}
       shell: Rscript {0}
-    - name: Install dependencies pass 2
+    - name: "Install dependencies pass 2 \U0001F6E0"
       env:
         timeout: ${{ env.timeout }}
       run: |
@@ -193,25 +196,25 @@ jobs:
         repos <- BiocManager::repositories()
         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE)
       shell: Rscript {0}
-    - name: Install RUnit (via BiocGenerics)
+    - name: "Install RUnit (via BiocGenerics) \U0001F6E0"
       if: env.has_runit == 'true'
       run: |
         options(crayon.enabled = TRUE)
         BiocManager::install("BiocGenerics")
       shell: Rscript {0}
-    - name: Install covr
+    - name: "Install covr \U0001F6E0"
       if: env.run_covr == 'true' && runner.os == 'Linux'
       run: |
         options(crayon.enabled = TRUE)
         install.packages("covr")
       shell: Rscript {0}
-    - name: Install pkgdown
+    - name: "Install pkgdown \U0001F6E0"
       if: env.run_pkgdown == 'true' && runner.os == 'Linux'
       run: |
         options(crayon.enabled = TRUE)
         install.packages("pkgdown")
       shell: Rscript {0}
-    - name: Session info
+    - name: Session info ℹ️
       run: |
         options(width = 100, crayon.enabled = TRUE)
         pkgs <- installed.packages()[,"Package"]
@@ -220,7 +223,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         }, error = function(x){utils::sessionInfo()})
       shell: Rscript {0}
-    - name: Run CMD check
+    - name: Run CMD check ✅
       if: env.run_rcmdcheck == 'true'
       env:
         _R_CHECK_CRAN_INCOMING_: ${{ false }}
@@ -233,27 +236,28 @@ jobs:
         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
         if(!require("rcmdcheck", quietly=TRUE)) install.packages("rcmdcheck")
         as_cran <- if(Sys.getenv("AS_CRAN")=='true') "--as-cran" else NULL
+        run_build_vignettes <- if(Sys.getenv("run_vignettes")=='true') NULL else "--no-build-vignettes"
         run_vignettes <- if(Sys.getenv("run_vignettes")=='true') NULL else "--ignore-vignettes"
         rcmdcheck::rcmdcheck(
             args = c("--no-manual", "--timings", as_cran, run_vignettes),
-            build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
+            build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data", run_build_vignettes),
             error_on = "warning",
             check_dir = "check")
       shell: Rscript {0}
-    - name: Reveal testthat details
+    - name: "Reveal testthat details \U0001F4CB"
       if: env.has_testthat == 'true'
       run: |
         find . -name testthat.Rout -exec cat '{}' ';'
       shell: bash {0}
-    - name: Run RUnit tests (via BiocGenerics)
+    - name: "Run RUnit tests (via BiocGenerics) \U0001F4CB"
       if: env.has_runit == 'true'
       env:
         timeout: ${{ env.timeout }}
       run: |
         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
         BiocGenerics:::testPackage()
       shell: Rscript {0}
-    - name: Run BiocCheck
+    - name: Run BiocCheck ✅
       if: env.run_bioccheck == 'true'
       env:
         DISPLAY: 99.0
@@ -278,16 +282,16 @@ jobs:
             `no-check-CRAN` = as_cran,
             `no-check-bioc-help` = as_cran)
       shell: Rscript {0}
-    - name: Test coverage
+    - name: "Test coverage \U0001F4CB"
       if: env.run_covr == 'true' && runner.os == 'Linux'
       run: |
         covr::codecov()
       shell: Rscript {0}
-    - name: Install package
+    - name: "Install package \U0001F6E0️"
       if: env.run_pkgdown == 'true' && runner.os == 'Linux'
       run: R CMD INSTALL .
       shell: bash {0}
-    - name: Get R package info
+    - name: Get R package info ℹ️
       if: runner.os == 'Linux'
       run: |
         #### DockerHub repos must be lowercase (,,) ####
@@ -299,7 +303,7 @@ jobs:
         echo "packageVersion=${version}" >> $GITHUB_ENV
         echo $version
       shell: bash {0}
-    - name: Render README
+    - name: "Render README \U0001F4E6"
       if: env.run_pkgdown == 'true' && runner.os == 'Linux'
       env:
         DISPLAY: 99.0
@@ -310,35 +314,36 @@ jobs:
           rmarkdown::render("README.Rmd", output_format = rmarkdown::github_document(html_preview = FALSE));
         }
       shell: Rscript {0}
-    - name: Build pkgdown site
+    - name: "Build pkgdown site \U0001F4E6"
       if: env.run_pkgdown == 'true' && runner.os == 'Linux'
       run: |
+        options(crayon.enabled = TRUE)
         pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
       shell: Rscript {0}
-    - name: "Deploy pkgdown site to GitHub pages \U0001F680"
+    - name: "Deploy pkgdown site to GitHub pages \U0001F4E6 \U0001F680"
       if: env.run_pkgdown == 'true' && runner.os == 'Linux'
       uses: JamesIves/github-pages-deploy-action@releases/v4
       with:
         clean: ${{ false }}
         branch: gh-pages
         folder: docs
         token: ${{ env.GITHUB_TOKEN }}
-    - name: Upload check results
+    - name: Upload check results ⏫
       if: failure()
       uses: actions/upload-artifact@v3
       with:
         name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r
           }}-results
         path: check
-    - name: Create Docker file
+    - name: "Create Docker file \U0001F433"
       if: |
         (!contains(github.event.head_commit.message, '/nodocker')) && env.run_docker == 'true' && runner.os == 'Linux'
       run: |
         options(crayon.enabled = TRUE)
         if(!require("rworkflows", quietly=TRUE)) remotes::install_github("neurogenomics/rworkflows")
         path <- rworkflows::use_dockerfile()
       shell: Rscript {0}
-    - name: Build and push to DockerHub
+    - name: "Build and push to DockerHub \U0001F433 \U0001F680"
       if: |
         (!contains(github.event.head_commit.message, '/nodocker')) && env.run_docker == 'true' && runner.os == 'Linux'
       uses: docker/build-push-action@v1

NEWS.md

@@ -31,6 +31,7 @@
 * `fill_yaml`
   - Simplify code.
   - Add subfunction `omit_if_default` to omit tinytex args from yaml.
+* `is_rstudio`: new interal helper function.
 
 ## Bug fixes
 
@@ -40,6 +41,10 @@
 * CRAN checks:
   - Downgrade `BiocPkgTools`/`biocViews` to Suggests to 
     compensate for issues with the CRAN server: #65
+* `fill_yaml`:
+  - When `template="rworkflows_static"`, prevent `with2` from simplifying to vector.
+* `construct_runners`
+  - `rspm` wasn't getting added.
 
 # rworkflows 0.99.12
 

R/construct_runners.R

@@ -38,12 +38,12 @@ construct_runners <- function(os=c("ubuntu-latest",
                               cont = construct_cont(
                                 default_tag = bioc[[1]],
                                 run_check_cont = run_check_cont), 
-                              rspm = list(paste0(
+                              rspm = list(
+                                paste0(
                                 "https://packagemanager.rstudio.com/",
-                                "cran/__linux__/latest/release"
-                              ),
-                              NULL,
-                              NULL), 
+                                "cran/__linux__/latest/release"),
+                                NULL,
+                                NULL), 
                               verbose = TRUE
                               ){ 
   # devoptera::args2vars(construct_runners, reassign = TRUE)
@@ -52,7 +52,8 @@ construct_runners <- function(os=c("ubuntu-latest",
   args <- construct_runners_check_args(os = os, 
                                        bioc = bioc, 
                                        r = r, 
-                                       cont = cont)   
+                                       cont = cont,
+                                       rspm = rspm)   
   #### Set runners ####
   runners <- lapply(os, function(o){
     if(isTRUE(versions_explicit)){

R/construct_runners_check_args.R

@@ -2,12 +2,13 @@ construct_runners_check_args <- function(os,
                                          bioc,
                                          r,
                                          cont,
+                                         rspm,
                                          versions_explicit=FALSE,
                                          verbose=TRUE){
 
 
   #### Fill names ####
-  args <- list(os=os, bioc=bioc, r=r, cont=cont)
+  args <- list(os=os, bioc=bioc, r=r, cont=cont, rspm=rspm)
   args2 <- lapply(stats::setNames(names(args),
                                   names(args)), 
          function(nm){
@@ -34,21 +35,12 @@ construct_runners_check_args <- function(os,
          } 
   )
   #### Check names #### 
-  if(!all(os %in% names(args2$bioc))){
-    stp <- paste(
-      "All `os` must be names of elements in `bioc_version` argument.")
-    stop(stp)
-  }
-  if(!all(os %in% names(args2$r))){
-    stp <- paste(
-      "All `os` must be names of elements in `r` argument.")
-    stop(stp)
-  }
-  if(!all(os %in% names(args2$cont))){
-    stp <- paste(
-      "All `os` must be names of elements in `cont` argument.")
-    stop(stp)
-  }
+  for(nm in names(args2)[-1]){
+    if(!all(os %in% names(args2[[nm]]))){
+      stopper("All `os` must be names of elements in",
+              paste0("`",nm,"`"),"argument.")
+    }
+  } 
   #### Return ####
   return(args2)
 }

R/fill_yaml.R

@@ -39,7 +39,7 @@ fill_yaml <- function(yml,
   }
   #### static workflow vs. action ####
   if(template=="rworkflows_static"){
-    with2 <- yml$env
+    with2 <- as.list(yml$env)
   } else if(template=="rworkflows"){
     #### Set tag ####
     yml$jobs[[1]]$steps[[2]]$uses <- paste0("neurogenomics/",template,tag)