* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/rworkflows.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (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 ‘1.0.1’
* 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/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 ... [28s/32s] 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 ... NOTE
  Note: found 12 marked UTF-8 strings
* 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 ... [8s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [12s/22s]
 [13s/23s] 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/RtmpsyKZN4/working_dir/RtmpmpykKW/file3ac8430f76dbemyenv_conda.yml
  Saving yaml ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/file3ac8430f76dbemyenv_conda.yml
  Saving yaml ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/file3ac8430f76dbemyenv_conda.yml
  name: myenv
  channels:
  - conda-forge
  - nodefaults
  dependencies:
  - anndata
  - scanpy
  Saving yaml ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/file3ac8430f76dbemyenv_conda.yml
  Loading required namespace: reticulate
  Failed with error:  'there is no package called '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: /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/DESCRIPTION3ac846ab1c6f
  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-Suggests/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-Suggests/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
  Failed with error:  'there is no package called 'biocViews''
  Loading required namespace: biocViews
  Failed with error:  'there is no package called '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/RtmpsyKZN4/working_dir/RtmpmpykKW/devcontainer.json
  Using existing dev container config file ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/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/RtmpsyKZN4/working_dir/RtmpmpykKW/Dockerfile
  Using existing Docker file: /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/Dockerfile
  Docker file preview:
  Creating new Issue Template ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/bug_report.md
  Creating new Issue Template ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/feature_request.md
  Using existing Issue Template: /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/bug_report.md
  Issue Template preview:
  Using existing Issue Template: /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/feature_request.md
  Issue Template preview:
  Creating new README file ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/README.Rmd
  Using existing README file: /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/README.Rmd
  README file preview:
  Creating new vignette file ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/vignettes/docker.Rmd
  Using existing vignette file: /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/vignettes/docker.Rmd
  Vignette file preview:
  Creating new vignette file ==> /tmp/RtmpsyKZN4/working_dir/RtmpmpykKW/vignettes/mypackage.Rmd
  [ FAIL 1 | 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'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-construct_conda_yml.R:33:3'): construct_conda_yml works ────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(name)`: there is no package called 'reticulate'
  Backtrace:
      ▆
   1. └─rworkflows:::conda_installed() at test-construct_conda_yml.R:33:3
   2.   └─utils::getFromNamespace("conda_installed", "reticulate")
   3.     └─base::asNamespace(ns)
   4.       └─base::getNamespace(ns)
   5.         ├─.Internal(getRegisteredNamespace(name)) %||% ...
   6.         └─base::loadNamespace(name)
   7.           └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.             └─base (local) withOneRestart(expr, restarts[[1L]])
   9.               └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 93 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [10s/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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/rworkflows.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:55.94, 165.28 + 17.81