Last updated on 2026-01-02 03:50:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.6 | 8.70 | 150.52 | 159.22 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.6 | 5.68 | 105.17 | 110.85 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.6 | 14.00 | 211.23 | 225.23 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.6 | 13.00 | 243.42 | 256.42 | ERROR | |
| r-devel-windows-x86_64 | 1.0.6 | 13.00 | 166.00 | 179.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.6 | 8.03 | 137.92 | 145.95 | ERROR | |
| r-release-linux-x86_64 | 1.0.6 | 6.82 | 136.14 | 142.96 | ERROR | |
| r-release-macos-arm64 | 1.0.6 | OK | ||||
| r-release-macos-x86_64 | 1.0.6 | 5.00 | 151.00 | 156.00 | OK | |
| r-release-windows-x86_64 | 1.0.6 | 12.00 | 158.00 | 170.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.6 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0.6 | 5.00 | 176.00 | 181.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.6 | 15.00 | 198.00 | 213.00 | ERROR |
Version: 1.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/24s]
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 ==> /home/hornik/tmp/scratch/RtmpbfBqTn/file3710a5fda80dcmyenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/RtmpbfBqTn/file3710a5fda80dcmyenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/RtmpbfBqTn/file3710a5fda80dcmyenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /home/hornik/tmp/scratch/RtmpbfBqTn/file3710a5fda80dcmyenv_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: /home/hornik/tmp/scratch/RtmpbfBqTn/DESCRIPTION3710a55c3fbdd6
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-clang/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-clang/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 ==> /home/hornik/tmp/scratch/RtmpbfBqTn/devcontainer.json
Using existing dev container config file ==> /home/hornik/tmp/scratch/RtmpbfBqTn/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 ==> /home/hornik/tmp/scratch/RtmpbfBqTn/Dockerfile
Using existing Docker file: /home/hornik/tmp/scratch/RtmpbfBqTn/Dockerfile
Docker file preview:
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpbfBqTn/bug_report.yml
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpbfBqTn/feature_request.yml
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpbfBqTn/config.yml
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpbfBqTn/bug_report.yml
Issue Template preview:
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpbfBqTn/feature_request.yml
Issue Template preview:
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpbfBqTn/config.yml
Issue Template preview:
Creating new README file ==> /home/hornik/tmp/scratch/RtmpbfBqTn/README.Rmd
Using existing README file: /home/hornik/tmp/scratch/RtmpbfBqTn/README.Rmd
README file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/RtmpbfBqTn/vignettes/docker.Rmd
Using existing vignette file: /home/hornik/tmp/scratch/RtmpbfBqTn/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/RtmpbfBqTn/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-clang
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/Rtmp5lnG1l/fileeeac23549f764myenv_conda.yml
Saving yaml ==> /tmp/Rtmp5lnG1l/fileeeac23549f764myenv_conda.yml
Saving yaml ==> /tmp/Rtmp5lnG1l/fileeeac23549f764myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /tmp/Rtmp5lnG1l/fileeeac23549f764myenv_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/Rtmp5lnG1l/DESCRIPTIONeeac225c8d4aa
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/Rtmp5lnG1l/devcontainer.json
Using existing dev container config file ==> /tmp/Rtmp5lnG1l/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/Rtmp5lnG1l/Dockerfile
Using existing Docker file: /tmp/Rtmp5lnG1l/Dockerfile
Docker file preview:
Creating new Issue Template ==> /tmp/Rtmp5lnG1l/bug_report.yml
Creating new Issue Template ==> /tmp/Rtmp5lnG1l/feature_request.yml
Creating new Issue Template ==> /tmp/Rtmp5lnG1l/config.yml
Using existing Issue Template: /tmp/Rtmp5lnG1l/bug_report.yml
Issue Template preview:
Using existing Issue Template: /tmp/Rtmp5lnG1l/feature_request.yml
Issue Template preview:
Using existing Issue Template: /tmp/Rtmp5lnG1l/config.yml
Issue Template preview:
Creating new README file ==> /tmp/Rtmp5lnG1l/README.Rmd
Using existing README file: /tmp/Rtmp5lnG1l/README.Rmd
README file preview:
Creating new vignette file ==> /tmp/Rtmp5lnG1l/vignettes/docker.Rmd
Using existing vignette file: /tmp/Rtmp5lnG1l/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /tmp/Rtmp5lnG1l/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’ [18s/99s]
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/Rtmp92hYw7/working_dir/Rtmp4dNTX6/file2045e466dd331amyenv_conda.yml
Saving yaml ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/file2045e466dd331amyenv_conda.yml
Saving yaml ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/file2045e466dd331amyenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/file2045e466dd331amyenv_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/Rtmp92hYw7/working_dir/Rtmp4dNTX6/DESCRIPTION2045e456056c72
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/Rtmp92hYw7/working_dir/Rtmp4dNTX6/devcontainer.json
Using existing dev container config file ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/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/Rtmp92hYw7/working_dir/Rtmp4dNTX6/Dockerfile
Using existing Docker file: /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/Dockerfile
Docker file preview:
Creating new Issue Template ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/bug_report.yml
Creating new Issue Template ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/feature_request.yml
Creating new Issue Template ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/config.yml
Using existing Issue Template: /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/bug_report.yml
Issue Template preview:
Using existing Issue Template: /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/feature_request.yml
Issue Template preview:
Using existing Issue Template: /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/config.yml
Issue Template preview:
Creating new README file ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/README.Rmd
Using existing README file: /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/README.Rmd
README file preview:
Creating new vignette file ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/vignettes/docker.Rmd
Using existing vignette file: /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /tmp/Rtmp92hYw7/working_dir/Rtmp4dNTX6/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/44s]
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/RtmpbnzLLB/working_dir/Rtmpk4wI3I/fileaf44f3a7faeb5myenv_conda.yml
Saving yaml ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/fileaf44f3a7faeb5myenv_conda.yml
Saving yaml ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/fileaf44f3a7faeb5myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/fileaf44f3a7faeb5myenv_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/RtmpbnzLLB/working_dir/Rtmpk4wI3I/DESCRIPTIONaf44f6af914f5
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.
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: /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/RtmpbnzLLB/working_dir/Rtmpk4wI3I/devcontainer.json
Using existing dev container config file ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/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/RtmpbnzLLB/working_dir/Rtmpk4wI3I/Dockerfile
Using existing Docker file: /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/Dockerfile
Docker file preview:
Creating new Issue Template ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/bug_report.yml
Creating new Issue Template ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/feature_request.yml
Creating new Issue Template ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/config.yml
Using existing Issue Template: /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/bug_report.yml
Issue Template preview:
Using existing Issue Template: /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/feature_request.yml
Issue Template preview:
Using existing Issue Template: /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/config.yml
Issue Template preview:
Creating new README file ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/README.Rmd
Using existing README file: /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/README.Rmd
README file preview:
Creating new vignette file ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/vignettes/docker.Rmd
Using existing vignette file: /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /tmp/RtmpbnzLLB/working_dir/Rtmpk4wI3I/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
Version: 1.0.6
Check: tests
Result: ERROR
Running 'testthat.R' [14s]
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 ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI\file6480557f966myenv_conda.yml
Saving yaml ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI\file6480557f966myenv_conda.yml
Saving yaml ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI\file6480557f966myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI\file6480557f966myenv_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: D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI\DESCRIPTION64802124671
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: D:/RCompile/CRANpkg/local/4.6/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: C:\Users\CRAN\AppData\Local/R/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: D:/RCompile/CRANpkg/local/4.6/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
[1] 0
Creating new dev container config file ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/devcontainer.json
Using existing dev container config file ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/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 ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/Dockerfile
Using existing Docker file: D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/Dockerfile
Docker file preview:
Creating new Issue Template ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/bug_report.yml
Creating new Issue Template ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/feature_request.yml
Creating new Issue Template ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/config.yml
Using existing Issue Template: D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/bug_report.yml
Issue Template preview:
Using existing Issue Template: D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/feature_request.yml
Issue Template preview:
Using existing Issue Template: D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/config.yml
Issue Template preview:
Creating new README file ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/README.Rmd
Using existing README file: D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/README.Rmd
README file preview:
Creating new vignette file ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/vignettes/docker.Rmd
Using existing vignette file: D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> D:\temp\2025_12_28_01_50_00_8710\Rtmp4uglZI/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-windows-x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/22s]
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 ==> /home/hornik/tmp/scratch/RtmpzpkROD/file2fdda11bfae3a4myenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/RtmpzpkROD/file2fdda11bfae3a4myenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/RtmpzpkROD/file2fdda11bfae3a4myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /home/hornik/tmp/scratch/RtmpzpkROD/file2fdda11bfae3a4myenv_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: /home/hornik/tmp/scratch/RtmpzpkROD/DESCRIPTION2fdda178730d75
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-patched-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-patched-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 ==> /home/hornik/tmp/scratch/RtmpzpkROD/devcontainer.json
Using existing dev container config file ==> /home/hornik/tmp/scratch/RtmpzpkROD/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 ==> /home/hornik/tmp/scratch/RtmpzpkROD/Dockerfile
Using existing Docker file: /home/hornik/tmp/scratch/RtmpzpkROD/Dockerfile
Docker file preview:
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpzpkROD/bug_report.yml
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpzpkROD/feature_request.yml
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpzpkROD/config.yml
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpzpkROD/bug_report.yml
Issue Template preview:
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpzpkROD/feature_request.yml
Issue Template preview:
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpzpkROD/config.yml
Issue Template preview:
Creating new README file ==> /home/hornik/tmp/scratch/RtmpzpkROD/README.Rmd
Using existing README file: /home/hornik/tmp/scratch/RtmpzpkROD/README.Rmd
README file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/RtmpzpkROD/vignettes/docker.Rmd
Using existing vignette file: /home/hornik/tmp/scratch/RtmpzpkROD/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/RtmpzpkROD/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-patched-linux-x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/22s]
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 ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/file38801412a58307myenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/file38801412a58307myenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/file38801412a58307myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/file38801412a58307myenv_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: /home/hornik/tmp/scratch/Rtmp9Qg7Rh/DESCRIPTION3880149ad0c57
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-release-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-release-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 ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/devcontainer.json
Using existing dev container config file ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/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 ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/Dockerfile
Using existing Docker file: /home/hornik/tmp/scratch/Rtmp9Qg7Rh/Dockerfile
Docker file preview:
Creating new Issue Template ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/bug_report.yml
Creating new Issue Template ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/feature_request.yml
Creating new Issue Template ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/config.yml
Using existing Issue Template: /home/hornik/tmp/scratch/Rtmp9Qg7Rh/bug_report.yml
Issue Template preview:
Using existing Issue Template: /home/hornik/tmp/scratch/Rtmp9Qg7Rh/feature_request.yml
Issue Template preview:
Using existing Issue Template: /home/hornik/tmp/scratch/Rtmp9Qg7Rh/config.yml
Issue Template preview:
Creating new README file ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/README.Rmd
Using existing README file: /home/hornik/tmp/scratch/Rtmp9Qg7Rh/README.Rmd
README file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/vignettes/docker.Rmd
Using existing vignette file: /home/hornik/tmp/scratch/Rtmp9Qg7Rh/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/Rtmp9Qg7Rh/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-release-linux-x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running 'testthat.R' [14s]
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 ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO\file5ae841f77809myenv_conda.yml
Saving yaml ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO\file5ae841f77809myenv_conda.yml
Saving yaml ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO\file5ae841f77809myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO\file5ae841f77809myenv_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: D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO\DESCRIPTION5ae8772d206b
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: D:/RCompile/CRANpkg/local/4.5/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: C:\Users\CRAN\AppData\Local/R/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: D:/RCompile/CRANpkg/local/4.5/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
[1] 0
Creating new dev container config file ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/devcontainer.json
Using existing dev container config file ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/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 ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/Dockerfile
Using existing Docker file: D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/Dockerfile
Docker file preview:
Creating new Issue Template ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/bug_report.yml
Creating new Issue Template ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/feature_request.yml
Creating new Issue Template ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/config.yml
Using existing Issue Template: D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/bug_report.yml
Issue Template preview:
Using existing Issue Template: D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/feature_request.yml
Issue Template preview:
Using existing Issue Template: D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/config.yml
Issue Template preview:
Creating new README file ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/README.Rmd
Using existing README file: D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/README.Rmd
README file preview:
Creating new vignette file ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/vignettes/docker.Rmd
Using existing vignette file: D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> D:\temp\2025_12_30_01_50_00_15946\RtmpMvxqPO/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-release-windows-x86_64
Version: 1.0.6
Check: tests
Result: ERROR
Running 'testthat.R' [17s]
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 ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm\file4d2443c457bdmyenv_conda.yml
Saving yaml ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm\file4d2443c457bdmyenv_conda.yml
Saving yaml ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm\file4d2443c457bdmyenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm\file4d2443c457bdmyenv_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] (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: D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm\DESCRIPTION4d24461e6775
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: D:/RCompile/CRANpkg/local/4.4/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: C:\Users\CRAN\AppData\Local/R/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: D:/RCompile/CRANpkg/local/4.4/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
[1] 0
Creating new dev container config file ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/devcontainer.json
Using existing dev container config file ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/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 ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/Dockerfile
Using existing Docker file: D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/Dockerfile
Docker file preview:
Creating new Issue Template ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/bug_report.yml
Creating new Issue Template ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/feature_request.yml
Creating new Issue Template ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/config.yml
Using existing Issue Template: D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/bug_report.yml
Issue Template preview:
Using existing Issue Template: D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/feature_request.yml
Issue Template preview:
Using existing Issue Template: D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/config.yml
Issue Template preview:
Creating new README file ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/README.Rmd
Using existing README file: D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/README.Rmd
README file preview:
Creating new vignette file ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/vignettes/docker.Rmd
Using existing vignette file: D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> D:\temp\2025_12_29_16_12_34_1110\RtmpUl9Rxm/vignettes/mypackage.Rmd
[ FAIL 1 | WARN 1 | 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 1 | SKIP 10 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64