Last updated on 2024-09-19 04:49:44 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 7.92 | 124.97 | 132.89 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 5.90 | 87.17 | 93.07 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 204.59 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 210.06 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.1 | 11.00 | 150.00 | 161.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.1 | 8.09 | 119.59 | 127.68 | OK | |
| r-release-linux-x86_64 | 1.0.1 | 7.79 | 119.79 | 127.58 | OK | |
| r-release-macos-arm64 | 1.0.1 | 98.00 | OK | |||
| r-release-macos-x86_64 | 1.0.1 | 177.00 | OK | |||
| r-release-windows-x86_64 | 1.0.1 | 10.00 | 144.00 | 154.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.1 | 107.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.0.1 | 171.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.0.1 | 12.00 | 173.00 | 185.00 | OK |
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/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/RtmpiSP47w/filedb1426730734fmyenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/RtmpiSP47w/filedb1426730734fmyenv_conda.yml
Saving yaml ==> /home/hornik/tmp/scratch/RtmpiSP47w/filedb1426730734fmyenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /home/hornik/tmp/scratch/RtmpiSP47w/filedb1426730734fmyenv_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 (>= 4.4)
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/RtmpiSP47w/DESCRIPTIONdb1423a553763
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 1677 bytes
==================================================
downloaded 1677 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
Hello world
Creating new dev container config file ==> /home/hornik/tmp/scratch/RtmpiSP47w/devcontainer.json
Using existing dev container config file ==> /home/hornik/tmp/scratch/RtmpiSP47w/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/RtmpiSP47w/Dockerfile
Using existing Docker file: /home/hornik/tmp/scratch/RtmpiSP47w/Dockerfile
Docker file preview:
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpiSP47w/bug_report.md
Creating new Issue Template ==> /home/hornik/tmp/scratch/RtmpiSP47w/feature_request.md
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpiSP47w/bug_report.md
Issue Template preview:
Using existing Issue Template: /home/hornik/tmp/scratch/RtmpiSP47w/feature_request.md
Issue Template preview:
Creating new README file ==> /home/hornik/tmp/scratch/RtmpiSP47w/README.Rmd
Using existing README file: /home/hornik/tmp/scratch/RtmpiSP47w/README.Rmd
README file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/RtmpiSP47w/vignettes/docker.Rmd
Using existing vignette file: /home/hornik/tmp/scratch/RtmpiSP47w/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /home/hornik/tmp/scratch/RtmpiSP47w/vignettes/mypackage.Rmd
[ FAIL 1 | WARN 2 | 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-construct_authors.R:4:3'): construct_authors works ───────────
as.character(a1) (`actual`) not equal to "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)" (`expected`).
actual vs expected
- "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId)"
+ "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)"
[ FAIL 1 | WARN 2 | SKIP 10 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/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 ==> /tmp/RtmpXYUKT0/file148bd727690b44myenv_conda.yml
Saving yaml ==> /tmp/RtmpXYUKT0/file148bd727690b44myenv_conda.yml
Saving yaml ==> /tmp/RtmpXYUKT0/file148bd727690b44myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /tmp/RtmpXYUKT0/file148bd727690b44myenv_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 (>= 4.4)
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/RtmpXYUKT0/DESCRIPTION148bd714ca7d5d
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 1677 bytes
==================================================
downloaded 1677 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
Hello world
Creating new dev container config file ==> /tmp/RtmpXYUKT0/devcontainer.json
Using existing dev container config file ==> /tmp/RtmpXYUKT0/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/RtmpXYUKT0/Dockerfile
Using existing Docker file: /tmp/RtmpXYUKT0/Dockerfile
Docker file preview:
Creating new Issue Template ==> /tmp/RtmpXYUKT0/bug_report.md
Creating new Issue Template ==> /tmp/RtmpXYUKT0/feature_request.md
Using existing Issue Template: /tmp/RtmpXYUKT0/bug_report.md
Issue Template preview:
Using existing Issue Template: /tmp/RtmpXYUKT0/feature_request.md
Issue Template preview:
Creating new README file ==> /tmp/RtmpXYUKT0/README.Rmd
Using existing README file: /tmp/RtmpXYUKT0/README.Rmd
README file preview:
Creating new vignette file ==> /tmp/RtmpXYUKT0/vignettes/docker.Rmd
Using existing vignette file: /tmp/RtmpXYUKT0/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /tmp/RtmpXYUKT0/vignettes/mypackage.Rmd
[ FAIL 1 | WARN 2 | 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-construct_authors.R:4:3'): construct_authors works ───────────
as.character(a1) (`actual`) not equal to "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)" (`expected`).
actual vs expected
- "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId)"
+ "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)"
[ FAIL 1 | WARN 2 | SKIP 10 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: data for non-ASCII characters
Result: NOTE
Note: found 12 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [18s/30s]
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/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/file30f1a36c75846myenv_conda.yml
Saving yaml ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/file30f1a36c75846myenv_conda.yml
Saving yaml ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/file30f1a36c75846myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/file30f1a36c75846myenv_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 (>= 4.4)
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/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/DESCRIPTION30f1a3c353d0a
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
Hello world
Creating new dev container config file ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/devcontainer.json
Using existing dev container config file ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/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/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/Dockerfile
Using existing Docker file: /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/Dockerfile
Docker file preview:
Creating new Issue Template ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/bug_report.md
Creating new Issue Template ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/feature_request.md
Using existing Issue Template: /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/bug_report.md
Issue Template preview:
Using existing Issue Template: /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/feature_request.md
Issue Template preview:
Creating new README file ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/README.Rmd
Using existing README file: /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/README.Rmd
README file preview:
Creating new vignette file ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/vignettes/docker.Rmd
Using existing vignette file: /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /tmp/Rtmpqs2LwM/working_dir/Rtmpv9tw9c/vignettes/mypackage.Rmd
[ FAIL 1 | WARN 0 | 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-construct_authors.R:4:3'): construct_authors works ───────────
as.character(a1) (`actual`) not equal to "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)" (`expected`).
actual vs expected
- "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId)"
+ "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)"
[ FAIL 1 | WARN 0 | SKIP 10 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/28s]
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/RtmpN0fNLi/working_dir/RtmpbUYPDI/file3b8d235fa2a3b8myenv_conda.yml
Saving yaml ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/file3b8d235fa2a3b8myenv_conda.yml
Saving yaml ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/file3b8d235fa2a3b8myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/file3b8d235fa2a3b8myenv_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 (>= 4.4)
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/RtmpN0fNLi/working_dir/RtmpbUYPDI/DESCRIPTION3b8d234f760d64
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
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-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
Hello world
Creating new dev container config file ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/devcontainer.json
Using existing dev container config file ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/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/RtmpN0fNLi/working_dir/RtmpbUYPDI/Dockerfile
Using existing Docker file: /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/Dockerfile
Docker file preview:
Creating new Issue Template ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/bug_report.md
Creating new Issue Template ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/feature_request.md
Using existing Issue Template: /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/bug_report.md
Issue Template preview:
Using existing Issue Template: /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/feature_request.md
Issue Template preview:
Creating new README file ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/README.Rmd
Using existing README file: /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/README.Rmd
README file preview:
Creating new vignette file ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/vignettes/docker.Rmd
Using existing vignette file: /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /tmp/RtmpN0fNLi/working_dir/RtmpbUYPDI/vignettes/mypackage.Rmd
[ FAIL 1 | WARN 0 | 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-construct_authors.R:4:3'): construct_authors works ───────────
as.character(a1) (`actual`) not equal to "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)" (`expected`).
actual vs expected
- "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId)"
+ "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)"
[ FAIL 1 | WARN 0 | SKIP 10 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [13s]
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\RtmpoljNIM\file16f0461076ab3myenv_conda.yml
Saving yaml ==> D:\temp\RtmpoljNIM\file16f0461076ab3myenv_conda.yml
Saving yaml ==> D:\temp\RtmpoljNIM\file16f0461076ab3myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> D:\temp\RtmpoljNIM\file16f0461076ab3myenv_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 (>= 4.4)
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\RtmpoljNIM\DESCRIPTION16f0441db348b
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/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/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
Hello world
[1] 0
Creating new dev container config file ==> D:\temp\RtmpoljNIM/devcontainer.json
Using existing dev container config file ==> D:\temp\RtmpoljNIM/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\RtmpoljNIM/Dockerfile
Using existing Docker file: D:\temp\RtmpoljNIM/Dockerfile
Docker file preview:
Creating new Issue Template ==> D:\temp\RtmpoljNIM/bug_report.md
Creating new Issue Template ==> D:\temp\RtmpoljNIM/feature_request.md
Using existing Issue Template: D:\temp\RtmpoljNIM/bug_report.md
Issue Template preview:
Using existing Issue Template: D:\temp\RtmpoljNIM/feature_request.md
Issue Template preview:
Creating new README file ==> D:\temp\RtmpoljNIM/README.Rmd
Using existing README file: D:\temp\RtmpoljNIM/README.Rmd
README file preview:
Creating new vignette file ==> D:\temp\RtmpoljNIM/vignettes/docker.Rmd
Using existing vignette file: D:\temp\RtmpoljNIM/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> D:\temp\RtmpoljNIM/vignettes/mypackage.Rmd
[ FAIL 1 | WARN 2 | 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-construct_authors.R:4:3'): construct_authors works ───────────
as.character(a1) (`actual`) not equal to "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)" (`expected`).
actual vs expected
- "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (ORCID: yourOrcidId)"
+ "yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)"
[ FAIL 1 | WARN 2 | SKIP 10 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.0.1
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'BiocPkgTools', 'biocViews'
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.0.1
Check: Rd cross-references
Result: NOTE
Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64