* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/rworkflows.Rcheck’
* using R Under development (unstable) (2026-04-27 r89966)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-04-28 05:54:47 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘rworkflows/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rworkflows’ version ‘1.0.11’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘BiocPkgTools’
* 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 ... [13s/16s] OK
* 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 ... [31s/41s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... INFO
Package unavailable to check Rd xrefs: ‘BiocPkgTools’
* 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 ... [6s/10s] ERROR
Running examples in ‘rworkflows-Ex.R’ failed
The error most likely occurred in:

> ### Name: fill_description
> ### Title: Fill _DESCRIPTION_
> ### Aliases: fill_description
> 
> ### ** Examples
> 
> #### Get example DESCRIPTION file ####
> url <- "https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION" 
> path <- tempfile(fileext = "DESCRIPTION")
> utils::download.file(url,path)
trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION'
Warning in utils::download.file(url, path) :
  cannot open URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION': HTTP status was '502 Bad Gateway'
Error in utils::download.file(url, path) : 
  cannot open URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [28s/44s]
 [29s/45s] ERROR
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/RtmpjdH3VT/working_dir/Rtmpk7YfFj/filed96df4ef38830myenv_conda.yml
  Saving yaml ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/filed96df4ef38830myenv_conda.yml
  Saving yaml ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/filed96df4ef38830myenv_conda.yml
  name: myenv
  channels:
  - conda-forge
  - nodefaults
  dependencies:
  - anndata
  - scanpy
  Saving yaml ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/filed96df4ef38830myenv_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'
  Saving _problems/test-fill_description-5.R
  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.
  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-MKL/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'
  Saving _problems/test-infer_deps-7.R
  Hello world
  Creating new dev container config file ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/devcontainer.json
  Using existing dev container config file ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/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/RtmpjdH3VT/working_dir/Rtmpk7YfFj/Dockerfile
  Using existing Docker file: /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/Dockerfile
  Docker file preview:
  Creating new Issue Template ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/bug_report.yml
  Creating new Issue Template ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/feature_request.yml
  Creating new Issue Template ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/config.yml
  Using existing Issue Template: /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/bug_report.yml
  Issue Template preview:
  Using existing Issue Template: /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/feature_request.yml
  Issue Template preview:
  Using existing Issue Template: /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/config.yml
  Issue Template preview:
  Creating new README file ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/README.Rmd
  Using existing README file: /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/README.Rmd
  README file preview:
  Creating new vignette file ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/vignettes/docker.Rmd
  Using existing vignette file: /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/vignettes/docker.Rmd
  Vignette file preview:
  Creating new vignette file ==> /tmp/RtmpjdH3VT/working_dir/Rtmpk7YfFj/vignettes/mypackage.Rmd
  [ FAIL 2 | WARN 2 | SKIP 11 | PASS 61 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): '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_description.R:1:1',
    '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 ════════════════════════════════════════════════════════════════
  ── Error ('test-fill_description.R:5:3'): fill_description works ───────────────
  Error in `utils::download.file(url, path)`: cannot open URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION'
  Backtrace:
      ▆
   1. └─utils::download.file(url, path) at test-fill_description.R:5:3
  ── Error ('test-infer_deps.R:7:3'): infer_deps works ───────────────────────────
  Error in `utils::download.file(url, path)`: cannot open URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION'
  Backtrace:
      ▆
   1. └─utils::download.file(url, path) at test-infer_deps.R:7:3
  
  [ FAIL 2 | WARN 2 | SKIP 11 | PASS 61 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [47s/70s] OK
* checking PDF version of manual ... [9s/12s] 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: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-MKL/rworkflows.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:55.95, 233.71 + 24.14