CRAN Package Check Results for Maintainer ‘Brian Schilder <brian_schilder at alumni.brown.edu>’

Last updated on 2026-01-27 09:50:02 CET.

Package	ERROR	NOTE	OK
rworkflows	1	1	11

Package rworkflows

Current CRAN status: ERROR: 1, NOTE: 1, OK: 11

Version: 1.0.8
Check: examples
Result: ERROR Running examples in ‘rworkflows-Ex.R’ failed The error most likely occurred in: > ### Name: fill_description > ### Title: Fill _DESCRIPTION_ > ### Aliases: fill_description > > ### ** Examples > > #### Get example DESCRIPTION file #### > url <- "https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION" > path <- tempfile(fileext = "DESCRIPTION") > utils::download.file(url,path) trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Warning in utils::download.file(url, path) : URL 'https://raw.githubusercontent.com/neurogenomics/templateR/master/DESCRIPTION': Timeout of 60 seconds was reached Error in utils::download.file(url, path) : cannot open URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.8
Check: tests
Result: ERROR Running ‘testthat.R’ [0m/17m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(rworkflows) > > test_check("rworkflows") Saving yaml ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/file33b157602c0060myenv_conda.yml Saving yaml ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/file33b157602c0060myenv_conda.yml Saving yaml ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/file33b157602c0060myenv_conda.yml name: myenv channels: - conda-forge - nodefaults dependencies: - anndata - scanpy Saving yaml ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/file33b157602c0060myenv_conda.yml Loading required namespace: reticulate Only tag name supplied to 'cont'. Assuming default= 'bioconductor/bioconductor_docker' Constructing DESCRIPTION files for 1 R package(s). Constructing DESCRIPTION for: ABSSeq trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Saving _problems/test-fill_description-5.R Cannot import DESCRIPTION file: NULL When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Cannot import DESCRIPTION file: /data/gannet/ripley/R/packages/tests-devel/rworkflows.Rcheck/tests/DESCRIPTION Skipping test. Cannot import DESCRIPTION file: NULL Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Finding hex sticker(s) for 1 package(s). Cannot find hex URL domain name. Returning NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Saving _problems/test-get_hex-66.R Skipping test. Skipping test. Loading required namespace: biocViews trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Saving _problems/test-infer_deps-7.R Hello world Creating new dev container config file ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/devcontainer.json Using existing dev container config file ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/devcontainer.json Config file preview: {"image":["ghcr.io/neurogenomics/rworkflows:dev"],"features":{"ghcr.io/devcontainers/features/conda:1":[]},"customizations":{"vscode":{"settings":[],"extensions":[["reditorsupport.r"],["visualstudioexptteam.vscodeintellicode"],["ionutvmi.path-autocomplete"]]}}}Creating new Docker file ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/Dockerfile Using existing Docker file: /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/Dockerfile Docker file preview: Creating new Issue Template ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/bug_report.yml Creating new Issue Template ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/feature_request.yml Creating new Issue Template ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/config.yml Using existing Issue Template: /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/bug_report.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/feature_request.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/config.yml Issue Template preview: Creating new README file ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/README.Rmd Using existing README file: /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/README.Rmd README file preview: Creating new vignette file ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/vignettes/docker.Rmd Using existing vignette file: /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/vignettes/docker.Rmd Vignette file preview: Creating new vignette file ==> /tmp/RtmpE6wNy2/working_dir/RtmpnXU4Gq/vignettes/mypackage.Rmd [ FAIL 3 | WARN 4 | SKIP 11 | PASS 60 ] ══ Skipped tests (11) ══════════════════════════════════════════════════════════ • On CRAN (11): 'test-bioc_r_versions.R:3:3', 'test-check_cont.R:4:5', 'test-check_r_version.R:3:3', 'test-construct_cont.R:22:3', 'test-construct_runners.R:3:3', 'test-get_description.R:1:1', 'test-get_yaml.R:2:3', 'test-gha_python_versions.R:3:3', 'test-url_exists.R:3:3', 'test-use_badges.R:2:3', 'test-use_workflow.R:2:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-fill_description.R:5:3'): fill_description works ─────────────── Error in `utils::download.file(url, path)`: cannot open URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Backtrace: ▆ 1. └─utils::download.file(url, path) at test-fill_description.R:5:3 ── Failure ('test-get_hex.R:64:3'): get_hex works ────────────────────────────── Expected `hex11[[1]]` to equal "https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png". Differences: `actual` is NULL `expected` is a character vector ('https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png') ── Error ('test-infer_deps.R:7:3'): infer_deps works ─────────────────────────── Error in `utils::download.file(url, path)`: cannot open URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Backtrace: ▆ 1. └─utils::download.file(url, path) at test-infer_deps.R:7:3 [ FAIL 3 | WARN 4 | SKIP 11 | PASS 60 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.8
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘bioconductor.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘bioconductor.Rmd’ --- re-building ‘depgraph.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘depgraph.Rmd’ --- re-building ‘docker.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘docker.Rmd’ --- re-building ‘repos.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘repos.Rmd’ --- re-building ‘rworkflows.Rmd’ using rmarkdown Quitting from rworkflows.Rmd:80-82 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `file()`: ! cannot open the connection to 'https://raw.githubusercontent.com/neurogenomics/rworkflows/master/DESCRIPTION' --- Backtrace: ▆ 1. └─rworkflows::use_badges() 2. └─badger::badge_github_version(pkg = ref, color = colors$github) 3. └─badger::ver_devel(pkg) 4. └─rvcheck::check_github(pkg) 5. └─rvcheck:::check_github_gitlab(pkg, "github") 6. └─base::readLines(url) 7. └─base::file(con, "r") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rworkflows.Rmd' failed with diagnostics: cannot open the connection to 'https://raw.githubusercontent.com/neurogenomics/rworkflows/master/DESCRIPTION' --- failed re-building ‘rworkflows.Rmd’ SUMMARY: processing the following file failed: ‘rworkflows.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.8
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘BiocPkgTools’ Flavor: r-oldrel-macos-arm64

Version: 1.0.8
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘BiocPkgTools’ Flavor: r-oldrel-macos-arm64