• using R Under development (unstable) (2025-12-11 r89150)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘rworkflows/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘rworkflows’ version ‘1.0.6’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘rworkflows’ can be installed ... [14s/21s] OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [27s/30s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [7s/19s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [28s/48s] ERROR   Running ‘testthat.R’ [28s/47s] 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/RtmpnVBJoU/working_dir/RtmpGuCDJO/file163a4430e2101cmyenv_conda.yml   Saving yaml ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/file163a4430e2101cmyenv_conda.yml   Saving yaml ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/file163a4430e2101cmyenv_conda.yml   name: myenv   channels:   - conda-forge   - nodefaults   dependencies:   - anndata   - scanpy   Saving yaml ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/file163a4430e2101cmyenv_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/RtmpnVBJoU/working_dir/RtmpGuCDJO/DESCRIPTION163a4440947d32   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.   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/RtmpnVBJoU/working_dir/RtmpGuCDJO/devcontainer.json   Using existing dev container config file ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/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/RtmpnVBJoU/working_dir/RtmpGuCDJO/Dockerfile   Using existing Docker file: /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/Dockerfile   Docker file preview:   Creating new Issue Template ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/bug_report.yml   Creating new Issue Template ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/feature_request.yml   Creating new Issue Template ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/config.yml   Using existing Issue Template: /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/bug_report.yml   Issue Template preview:   Using existing Issue Template: /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/feature_request.yml   Issue Template preview:   Using existing Issue Template: /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/config.yml   Issue Template preview:   Creating new README file ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/README.Rmd   Using existing README file: /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/README.Rmd   README file preview:   Creating new vignette file ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/vignettes/docker.Rmd   Using existing vignette file: /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/vignettes/docker.Rmd   Vignette file preview:   Creating new vignette file ==> /tmp/RtmpnVBJoU/working_dir/RtmpGuCDJO/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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [44s/77s] OK
• checking PDF version of manual ... [8s/15s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR