R Under development (unstable) (2024-01-17 r85813 ucrt) -- "Unsuffered Consequences"
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> # 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\RtmpYrvqjv\file2efd42c70d2cmyenv_conda.yml
Saving yaml ==> D:\temp\RtmpYrvqjv\file2efd42c70d2cmyenv_conda.yml
Saving yaml ==> D:\temp\RtmpYrvqjv\file2efd42c70d2cmyenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> D:\temp\RtmpYrvqjv\file2efd42c70d2cmyenv_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 (>= 4.4)
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\RtmpYrvqjv\DESCRIPTION2efd4740f4a43
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\RtmpYrvqjv/devcontainer.json
Using existing dev container config file ==> D:\temp\RtmpYrvqjv/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\RtmpYrvqjv/Dockerfile
Using existing Docker file: D:\temp\RtmpYrvqjv/Dockerfile
Docker file preview:
Creating new Issue Template ==> D:\temp\RtmpYrvqjv/bug_report.md
Creating new Issue Template ==> D:\temp\RtmpYrvqjv/feature_request.md
Using existing Issue Template: D:\temp\RtmpYrvqjv/bug_report.md
Issue Template preview:
Using existing Issue Template: D:\temp\RtmpYrvqjv/feature_request.md
Issue Template preview:
Creating new README file ==> D:\temp\RtmpYrvqjv/README.Rmd
Using existing README file: D:\temp\RtmpYrvqjv/README.Rmd
README file preview:
Creating new vignette file ==> D:\temp\RtmpYrvqjv/vignettes/docker.Rmd
Using existing vignette file: D:\temp\RtmpYrvqjv/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> D:\temp\RtmpYrvqjv/vignettes/mypackage.Rmd
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 93 ]

══ 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'

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 93 ]
> 
> proc.time()
   user  system elapsed 
   4.84    0.54    9.01