CRAN Package Check Results for Package rworkflows

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

Additional issues

noSuggests

Check Details

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