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/Rtmp7E7eV2/file78f98468557e9myenv_conda.yml
  Saving yaml ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/file78f98468557e9myenv_conda.yml
  Saving yaml ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/file78f98468557e9myenv_conda.yml
  name: myenv
  channels:
  - conda-forge
  - nodefaults
  dependencies:
  - anndata
  - scanpy
  Saving yaml ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/file78f98468557e9myenv_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/Rtmp7E7eV2/DESCRIPTION78f982975c6b2
  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/Rtmp7E7eV2/devcontainer.json
  Using existing dev container config file ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/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/Rtmp7E7eV2/Dockerfile
  Using existing Docker file: /home/hornik/tmp/scratch/Rtmp7E7eV2/Dockerfile
  Docker file preview:
  Creating new Issue Template ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/bug_report.yml
  Creating new Issue Template ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/feature_request.yml
  Creating new Issue Template ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/config.yml
  Using existing Issue Template: /home/hornik/tmp/scratch/Rtmp7E7eV2/bug_report.yml
  Issue Template preview:
  Using existing Issue Template: /home/hornik/tmp/scratch/Rtmp7E7eV2/feature_request.yml
  Issue Template preview:
  Using existing Issue Template: /home/hornik/tmp/scratch/Rtmp7E7eV2/config.yml
  Issue Template preview:
  Creating new README file ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/README.Rmd
  Using existing README file: /home/hornik/tmp/scratch/Rtmp7E7eV2/README.Rmd
  README file preview:
  Creating new vignette file ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/vignettes/docker.Rmd
  Using existing vignette file: /home/hornik/tmp/scratch/Rtmp7E7eV2/vignettes/docker.Rmd
  Vignette file preview:
  Creating new vignette file ==> /home/hornik/tmp/scratch/Rtmp7E7eV2/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