Last updated on 2025-12-10 18:50:02 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 | 5.21 | 102.76 | 107.97 | OK | |
| 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 | 10.00 | 158.00 | 168.00 | OK | |
| r-patched-linux-x86_64 | 1.0.6 | 9.02 | 137.11 | 146.13 | 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 |
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