Merge pull request #152 from neurogenomics/static-fix

Fix static workflow: Dependency installation failure

Author: HDash

.github/workflows/rworkflows_static.yml

@@ -30,6 +30,10 @@ env:
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
   ncpus: 2.0
+  timeout: 2000.0
+  force_install: ${{ false }}
+  run_telemetry: ${{ true }}
+  free_diskspace: ${{ false }}
   cache_version: cache-v1
   miniforge_variant: ${{ false }}
   activate_environment: test
@@ -44,18 +48,20 @@ jobs:
       matrix:
         config:
         - os: ubuntu-latest
+          bioc: devel
           r: auto
-          bioc: release
-          cont: ghcr.io/bioconductor/bioconductor_docker:latest
-          python-version: 3.11
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
         - os: macOS-latest
-          r: latest
           bioc: release
-          python-version: 3.11
+          r: auto
+          cont: ~
+          rspm: ~
         - os: windows-latest
-          r: latest
           bioc: release
-          python-version: 3.11
+          r: auto
+          cont: ~
+          rspm: ~
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: ${{ true }}
       RSPM: ${{ matrix.config.rspm }}
@@ -81,13 +87,6 @@ jobs:
         echo "TZ=UTC" >> $GITHUB_ENV
         echo "NOT_CRAN=${{ !env.as_cran }}" >> $GITHUB_ENV
       shell: bash {0}
-    - name: "\U0001F4DA Set R library home on Linux"
-      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@v4
     - name: "\U0001F40D Setup Miniconda"
@@ -101,6 +100,13 @@ jobs:
         activate-environment: ${{ env.activate_environment }}
         environment-file: ${{ env.environment_file }}
         channels: ${{ env.channels }}
+    - name: "\U0001F4DA Set R library home on Linux"
+      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: "\U0001F6E0 Setup R and Bioconductor"
       if: runner.os != 'Linux'
       uses: grimbough/bioc-actions/setup-bioc@v1
@@ -211,7 +217,7 @@ jobs:
         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"), Ncpus=as.integer(Sys.getenv("ncpus")))
         ## For running the checks
         message(paste('****', Sys.time(), 'installing rcmdcheck ****'))
-        install.packages(c("rcmdcheck","rmarkdown","BiocManager"), dependencies = TRUE)
+        install.packages(c("rmarkdown","BiocManager"), dependencies = TRUE)
         message(paste('****', Sys.time(), 'pass number 1 at installing dependencies****'))
         message(paste('**** Using', Sys.getenv("ncpus"), 'cores for installation.'))
         repos <- BiocManager::repositories()

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rworkflows
 Type: Package
 Title: Test, Document, Containerise, and Deploy R Packages
-Version: 1.0.10
+Version: 1.0.11
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",

NEWS.md

@@ -1,3 +1,13 @@
+# rworkflows 1.0.11
+
+## Bug Fixes
+
+* Fix `use_workflow(template="rworkflows_static")` not generating the `timeout`,
+`force_install`, `run_telemetry`, and `free_diskspace` environment variables. (#146)
+* Add `as.integer()` coercion to all R `options(timeout=...)` calls for robustness.
+These were causing `download.file()` to fail with `cannot download any files`
+when the timeout was not properly converted to a numeric value.
+
 # rworkflows 1.0.10
 
 ## Miscellaneous

R/fill_yaml.R

@@ -36,9 +36,13 @@ fill_yaml <- function(## function-level args
                       codecov_token,
                       docker_user,
                       docker_org,
-                      docker_token,
-                      ncpus,
-                      cache_version, 
+                       docker_token,
+                       ncpus,
+                       timeout,
+                       force_install,
+                       run_telemetry,
+                       free_diskspace,
+                       cache_version,
                       miniforge_variant,
                       miniforge_version,
                       activate_environment,

R/use_workflow.R

@@ -103,6 +103,14 @@
 #' @param ncpus Number of CPUs to use for R package installation. Higher values
 #' can speed up the dependency installation process but may result in spurious
 #' errors. (default = \code{2})
+#' @param timeout The maximum time to wait for long R processes like
+#' dependency installations, downloads, and code checks. (default = \code{2000})
+#' @param force_install Whether to force install packages. If \code{true}, all 
+#' packages will be reinstalled, bypassing the cache.
+#' @param run_telemetry Whether to run the workflow telemetry action:
+#' https://github.com/catchpoint/workflow-telemetry-action
+#' @param free_diskspace Whether to free up additional disk space by deleting 
+#' non-essential software.
 #' @param miniforge_variant If provided, this variant of Miniforge will be
 #'  downloaded and installed. If \code{miniforge_variant=false}, 
 #'  Miniforge will not be installed at all.
@@ -163,9 +171,13 @@ use_workflow <- function(## action-level args
                          ### General
                          github_token="${{ secrets.GITHUB_TOKEN }}",
                          cache_version="cache-v1",
-                         enable_act=FALSE,
-                         ncpus=2,
-                         ### Checks
+                          enable_act=FALSE,
+                          ncpus=2,
+                          timeout=2000,
+                          force_install=FALSE,
+                          run_telemetry=TRUE,
+                          free_diskspace=FALSE,
+                          ### Checks
                          run_bioccheck=FALSE,
                          run_rcmdcheck=TRUE, 
                          as_cran=TRUE,
@@ -271,9 +283,13 @@ use_workflow <- function(## action-level args
                    environment_file=environment_file,
                    channels=channels,
                    cache_version=cache_version,
-                   enable_act=enable_act,
-                   ncpus=ncpus)
-  #### Preview ####
+                    enable_act=enable_act,
+                    ncpus=ncpus,
+                    timeout=timeout,
+                    force_install=force_install,
+                    run_telemetry=run_telemetry,
+                    free_diskspace=free_diskspace)
+   #### Preview ####
   if(isTRUE(preview)){
     preview_yaml(yml=yml) 
   }

README.md

@@ -6,7 +6,7 @@
 GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
 [![](https://img.shields.io/badge/doi-https://doi.org/10.5281/zenodo.10048573-blue.svg)](https://doi.org/https://doi.org/10.5281/zenodo.10048573)
 <br>
-[![](https://img.shields.io/badge/devel%20version-1.0.8-black.svg)](https://github.com/neurogenomics/rworkflows)
+[![](https://img.shields.io/badge/devel%20version-1.0.11-black.svg)](https://github.com/neurogenomics/rworkflows)
 [![](https://img.shields.io/github/languages/code-size/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows)
 [![](https://img.shields.io/github/last-commit/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows/commits/master)
 <br> [![R build
@@ -320,7 +320,7 @@ utils::sessionInfo()
     ## [22] pillar_1.11.1       RColorBrewer_1.1-3  rlang_1.1.7        
     ## [25] badger_0.2.5        xfun_0.56           fs_1.6.6           
     ## [28] S7_0.2.1            otel_0.2.0          cli_3.6.5          
-    ## [31] magrittr_2.0.4      rworkflows_1.0.10   digest_0.6.39      
+    ## [31] magrittr_2.0.4      rworkflows_1.0.11   digest_0.6.39      
     ## [34] grid_4.6.0          rstudioapi_0.18.0   rappdirs_0.3.4     
     ## [37] lifecycle_1.0.5     vctrs_0.7.1         data.table_1.18.2.1
     ## [40] evaluate_1.0.5      glue_1.8.0          farver_2.1.2       

action.yml

@@ -349,7 +349,7 @@ runs:
         force_install: ${{ inputs.force_install }}
         ncpus: ${{ inputs.ncpus }}
       run: |
-         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"), Ncpus=as.integer(Sys.getenv("ncpus")))
+         options(crayon.enabled = TRUE, timeout=as.integer(Sys.getenv("timeout")), Ncpus=as.integer(Sys.getenv("ncpus")))
          ## For running the checks
          message(paste('****', Sys.time(), 'installing rcmdcheck ****'))
          install.packages(c("rmarkdown","BiocManager"), dependencies = TRUE)
@@ -366,7 +366,7 @@ runs:
         GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}
         ncpus: ${{ inputs.ncpus }}
       run: |
-        options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"), Ncpus=as.integer(Sys.getenv("ncpus")))
+        options(crayon.enabled = TRUE, timeout=as.integer(Sys.getenv("timeout")), Ncpus=as.integer(Sys.getenv("ncpus")))
         message(paste('****', Sys.time(), 'pass number 2 at installing dependencies****'))
         repos <- BiocManager::repositories()
         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=FALSE)
@@ -426,7 +426,7 @@ runs:
         timeout: ${{ inputs.timeout }}
         GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}
       run: |
-        options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
+        options(crayon.enabled = TRUE, timeout=as.integer(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"
@@ -450,7 +450,7 @@ runs:
         timeout: ${{ inputs.timeout }}
         GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}
       run: |
-        options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
+        options(crayon.enabled = TRUE, timeout=as.integer(Sys.getenv("timeout")))
         BiocGenerics:::testPackage()
       shell: Rscript {0}
 
@@ -464,7 +464,7 @@ runs:
         timeout: ${{ inputs.timeout }}
         GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}
       run: |
-        options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
+        options(crayon.enabled = TRUE, timeout=as.integer(Sys.getenv("timeout")))
         #### Install deps ####
         if(!require("BiocManager", quietly=TRUE)) install.packages("BiocManager")
         if(!require("BiocCheck", quietly=TRUE)) BiocManager::install("BiocCheck")

man/use_workflow.Rd

@@ -39,9 +39,14 @@ test_that("use_workflow works", {
                        force_new = TRUE,
                        tinytex_installer = "TinyTeX",
                        save_dir = tempdir())
-  testthat::expect_equal(yml$on,yml3$on)
-  testthat::expect_equal(length(yml$jobs[[1]]$steps),1)
-  testthat::expect_gte(length(yml3$jobs[[1]]$steps),20)
+testthat::expect_equal(yml$on,yml3$on)
+   testthat::expect_equal(length(yml$jobs[[1]]$steps),1)
+   testthat::expect_gte(length(yml3$jobs[[1]]$steps),20)
+   #### Test that new env vars are properly set for rworkflows_static ####
+   testthat::expect_equal(yml3$env$timeout, 2000)
+   testthat::expect_equal(yml3$env$force_install, "${{ false }}")
+   testthat::expect_equal(yml3$env$run_telemetry, "${{ true }}")
+   testthat::expect_equal(yml3$env$free_diskspace, "${{ false }}")
 
   #### Modify conda args ####
   environment_file <- construct_conda_yml(dependencies = c("python>=3.9","anndata"),