CRAN Package Check Results for Package rworkflows

Last updated on 2025-12-11 05:50:15 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0.6	8.59	146.36	154.95	OK
r-devel-linux-x86_64-debian-gcc	1.0.6	6.19	101.62	107.81	ERROR
r-devel-linux-x86_64-fedora-clang	1.0.6	57.00	180.36	237.36	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0.6	17.00	225.56	242.56	ERROR
r-devel-windows-x86_64	1.0.6	12.00	163.00	175.00	OK
r-patched-linux-x86_64	1.0.6	8.61	134.78	143.39	OK
r-release-linux-x86_64	1.0.6	6.73	136.41	143.14	OK
r-release-macos-arm64	1.0.6				OK
r-release-macos-x86_64	1.0.6	6.00	150.00	156.00	OK
r-release-windows-x86_64	1.0.6	10.00	158.00	168.00	OK
r-oldrel-macos-arm64	1.0.6				OK
r-oldrel-macos-x86_64	1.0.6	8.00	173.00	181.00	OK
r-oldrel-windows-x86_64	1.0.6	16.00	190.00	206.00	OK

Check Details

Version: 1.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [8s/16s] 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/RtmpSXQdFp/file2f75a5e764960myenv_conda.yml Saving yaml ==> /tmp/RtmpSXQdFp/file2f75a5e764960myenv_conda.yml Saving yaml ==> /tmp/RtmpSXQdFp/file2f75a5e764960myenv_conda.yml name: myenv channels: - conda-forge - nodefaults dependencies: - anndata - scanpy Saving yaml ==> /tmp/RtmpSXQdFp/file2f75a5e764960myenv_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' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 bytes Updating: Package --> MyPackageName Updating: Title --> This Package Does Awesome Stuff Updating: Description --> MyPackageName does several awesome things. Describe thing1. Describe thing2. Describe thing3. Updating: Authors --> yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId) Updating: Depends --> R (>= 4.6) Deleting field: Suggests Updating: biocViews --> Genetics, SystemsBiology Updating: URL --> https://github.com/OwnerName/MyPackageName Updating: BugReports --> https://github.com/OwnerName/MyPackageName/issues Saving updated file: /tmp/RtmpSXQdFp/DESCRIPTION2f75a564809276 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. Cannot find DESCRIPTION for: typoooo Cannot find DESCRIPTION file for: typoooo Cannot import DESCRIPTION file: typo Cannot import DESCRIPTION file: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rworkflows.Rcheck/tests/DESCRIPTION When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. trying URL 'https://github.com/neurogenomics/MAGMA_Celltyping/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 2110 bytes ================================================== downloaded 2110 bytes Cannot find DESCRIPTION for: MAGMA_Celltyping Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN Constructing DESCRIPTION files for 1 R package(s). Constructing DESCRIPTION for: ABSSeq Skipping test. Cannot find DESCRIPTION for: orthogene trying URL 'https://github.com/neurogenomics/orthogene/raw/main/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 1680 bytes ================================================== downloaded 1680 bytes Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). Cannot import DESCRIPTION file: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rworkflows.Rcheck/tests/DESCRIPTION Skipping test. Cannot import DESCRIPTION file: NULL Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). 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). Finding hex sticker(s) for 1 package(s). 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). Skipping test. Skipping test. Loading required namespace: biocViews trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 bytes Saving _problems/test-infer_docker_org-14.R Hello world Creating new dev container config file ==> /tmp/RtmpSXQdFp/devcontainer.json Using existing dev container config file ==> /tmp/RtmpSXQdFp/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/RtmpSXQdFp/Dockerfile Using existing Docker file: /tmp/RtmpSXQdFp/Dockerfile Docker file preview: Creating new Issue Template ==> /tmp/RtmpSXQdFp/bug_report.yml Creating new Issue Template ==> /tmp/RtmpSXQdFp/feature_request.yml Creating new Issue Template ==> /tmp/RtmpSXQdFp/config.yml Using existing Issue Template: /tmp/RtmpSXQdFp/bug_report.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpSXQdFp/feature_request.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpSXQdFp/config.yml Issue Template preview: Creating new README file ==> /tmp/RtmpSXQdFp/README.Rmd Using existing README file: /tmp/RtmpSXQdFp/README.Rmd README file preview: Creating new vignette file ==> /tmp/RtmpSXQdFp/vignettes/docker.Rmd Using existing vignette file: /tmp/RtmpSXQdFp/vignettes/docker.Rmd Vignette file preview: Creating new vignette file ==> /tmp/RtmpSXQdFp/vignettes/mypackage.Rmd [ FAIL 1 | WARN 3 | SKIP 10 | PASS 92 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (10): '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_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 ════════════════════════════════════════════════════════════════ ── Failure ('test-infer_docker_org.R:14:3'): infer_docker_org works ──────────── Expected `out` to equal "vubiostat". Differences: `actual`: "r-lib" `expected`: "vubiostat" [ FAIL 1 | WARN 3 | SKIP 10 | PASS 92 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [19s/66s] 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/RtmpjpXmDF/working_dir/Rtmp1LPRkz/fileaf44770b661cmyenv_conda.yml Saving yaml ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/fileaf44770b661cmyenv_conda.yml Saving yaml ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/fileaf44770b661cmyenv_conda.yml name: myenv channels: - conda-forge - nodefaults dependencies: - anndata - scanpy Saving yaml ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/fileaf44770b661cmyenv_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' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 bytes Updating: Package --> MyPackageName Updating: Title --> This Package Does Awesome Stuff Updating: Description --> MyPackageName does several awesome things. Describe thing1. Describe thing2. Describe thing3. Updating: Authors --> yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId) Updating: Depends --> R (>= 4.6) Deleting field: Suggests Updating: biocViews --> Genetics, SystemsBiology Updating: URL --> https://github.com/OwnerName/MyPackageName Updating: BugReports --> https://github.com/OwnerName/MyPackageName/issues Saving updated file: /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/DESCRIPTIONaf44711bdf819 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. Cannot find DESCRIPTION for: typoooo Cannot find DESCRIPTION file for: typoooo Cannot import DESCRIPTION file: typo Cannot import DESCRIPTION file: /data/gannet/ripley/R/packages/tests-clang/rworkflows.Rcheck/tests/DESCRIPTION When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. trying URL 'https://github.com/neurogenomics/MAGMA_Celltyping/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 2110 bytes ================================================== downloaded 2110 bytes Cannot find DESCRIPTION for: MAGMA_Celltyping Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN Constructing DESCRIPTION files for 1 R package(s). Constructing DESCRIPTION for: ABSSeq Skipping test. Cannot find DESCRIPTION for: orthogene Importing cached file: /data/gannet/ripley/.cache/R/rworkflows/neurogenomics.orthogene_DESCRIPTION Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). Cannot import DESCRIPTION file: /data/gannet/ripley/R/packages/tests-clang/rworkflows.Rcheck/tests/DESCRIPTION Skipping test. Cannot import DESCRIPTION file: NULL Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). 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). Finding hex sticker(s) for 1 package(s). 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). Skipping test. Skipping test. Loading required namespace: biocViews trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 bytes Saving _problems/test-infer_docker_org-14.R Hello world Creating new dev container config file ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/devcontainer.json Using existing dev container config file ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/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/RtmpjpXmDF/working_dir/Rtmp1LPRkz/Dockerfile Using existing Docker file: /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/Dockerfile Docker file preview: Creating new Issue Template ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/bug_report.yml Creating new Issue Template ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/feature_request.yml Creating new Issue Template ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/config.yml Using existing Issue Template: /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/bug_report.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/feature_request.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/config.yml Issue Template preview: Creating new README file ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/README.Rmd Using existing README file: /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/README.Rmd README file preview: Creating new vignette file ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/vignettes/docker.Rmd Using existing vignette file: /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/vignettes/docker.Rmd Vignette file preview: Creating new vignette file ==> /tmp/RtmpjpXmDF/working_dir/Rtmp1LPRkz/vignettes/mypackage.Rmd [ FAIL 1 | WARN 3 | SKIP 10 | PASS 92 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (10): '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_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 ════════════════════════════════════════════════════════════════ ── Failure ('test-infer_docker_org.R:14:3'): infer_docker_org works ──────────── Expected `out` to equal "vubiostat". Differences: `actual`: "r-lib" `expected`: "vubiostat" [ FAIL 1 | WARN 3 | SKIP 10 | PASS 92 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [31s/48s] 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/RtmpVOXKz4/working_dir/RtmplhzzcF/file3ec80d263b7ca9myenv_conda.yml Saving yaml ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/file3ec80d263b7ca9myenv_conda.yml Saving yaml ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/file3ec80d263b7ca9myenv_conda.yml name: myenv channels: - conda-forge - nodefaults dependencies: - anndata - scanpy Saving yaml ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/file3ec80d263b7ca9myenv_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' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 bytes Updating: Package --> MyPackageName Updating: Title --> This Package Does Awesome Stuff Updating: Description --> MyPackageName does several awesome things. Describe thing1. Describe thing2. Describe thing3. Updating: Authors --> yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId) Updating: Depends --> R (>= 4.6) Deleting field: Suggests Updating: biocViews --> Genetics, SystemsBiology Updating: URL --> https://github.com/OwnerName/MyPackageName Updating: BugReports --> https://github.com/OwnerName/MyPackageName/issues Saving updated file: /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/DESCRIPTION3ec80d78871144 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. Cannot find DESCRIPTION for: typoooo Cannot find DESCRIPTION file for: typoooo Cannot import DESCRIPTION file: typo Cannot import DESCRIPTION file: /data/gannet/ripley/R/packages/tests-devel/rworkflows.Rcheck/tests/DESCRIPTION When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. trying URL 'https://github.com/neurogenomics/MAGMA_Celltyping/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 2110 bytes ================================================== downloaded 2110 bytes Cannot find DESCRIPTION for: MAGMA_Celltyping Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN Constructing DESCRIPTION files for 1 R package(s). Constructing DESCRIPTION for: ABSSeq Skipping test. Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). 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). Finding hex sticker(s) for 1 package(s). 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). Finding hex sticker(s) for 1 package(s). 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). Skipping test. Skipping test. Loading required namespace: biocViews trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 bytes Saving _problems/test-infer_docker_org-14.R Hello world Creating new dev container config file ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/devcontainer.json Using existing dev container config file ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/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/RtmpVOXKz4/working_dir/RtmplhzzcF/Dockerfile Using existing Docker file: /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/Dockerfile Docker file preview: Creating new Issue Template ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/bug_report.yml Creating new Issue Template ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/feature_request.yml Creating new Issue Template ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/config.yml Using existing Issue Template: /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/bug_report.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/feature_request.yml Issue Template preview: Using existing Issue Template: /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/config.yml Issue Template preview: Creating new README file ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/README.Rmd Using existing README file: /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/README.Rmd README file preview: Creating new vignette file ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/vignettes/docker.Rmd Using existing vignette file: /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/vignettes/docker.Rmd Vignette file preview: Creating new vignette file ==> /tmp/RtmpVOXKz4/working_dir/RtmplhzzcF/vignettes/mypackage.Rmd [ FAIL 1 | WARN 3 | SKIP 10 | PASS 92 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (10): '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_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 ════════════════════════════════════════════════════════════════ ── Failure ('test-infer_docker_org.R:14:3'): infer_docker_org works ──────────── Expected `out` to equal "vubiostat". Differences: `actual`: "r-lib" `expected`: "vubiostat" [ FAIL 1 | WARN 3 | SKIP 10 | PASS 92 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc