[macOS] Some tests fail [ FAIL 5 | WARN 0 | SKIP 0 | PASS 177 ]

[barracuda156]

R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # 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")
Assuming container is on DockerHub.
Checking public container repository exists: 'bioconductor/bioconductor_docker'
Checking tag exists: 'devel'
Assuming container is on DockerHub.
Checking public container repository exists: 'bioconductor/bioconductor_docker'
Assuming container is on DockerHub.
Checking public container repository exists: 'bioconductor/bioconductor_typooooo'
Assuming container is on DockerHub.
Checking public container repository exists: 'bioconductor/bioconductor_docker'
Checking tag exists: 'typooo'
Loading required namespace: rvest
Checking public container repository exists: 'bioconductor/bioconductor_docker'
Checking tag exists: 'devel'
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/filea33350a7ae61myenv_conda.yml
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/filea33350a7ae61myenv_conda.yml
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/filea33350a7ae61myenv_conda.yml
name: myenv
channels:
- conda-forge
- nodefaults
dependencies:
- anndata
- scanpy
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/filea33350a7ae61myenv_conda.yml
Loading required namespace: reticulate
Only tag name supplied to 'cont'. Assuming default= 'bioconductor/bioconductor_docker'
Applying the same 'bioc' parameter to all 3 'os': 'devel'
Applying the same 'python_version' parameter to all 3 'os': '3.9'
trying URL 'https://raw.githubusercontent.com/actions/python-versions/main/versions-manifest.json'
Content type 'text/plain; charset=utf-8' length 235020 bytes (229 KB)
==================================================
downloaded 229 KB

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 707 bytes
==================================================
downloaded 707 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 (>= 4.3)
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: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/DESCRIPTIONa33330a98ba5
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
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
Cannot find DESCRIPTION for: orthogene
Requested package ('orthogene') != retrieved package ('rworkflows') in DESCRIPTION. Returning 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 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).
Reading yaml.
Validating python_version.
Reading yaml.
Validating python_version.
Reading yaml.
Validating python_version.
Reading yaml.
Validating python_version.
Reading yaml.
Validating python_version.
Loading required namespace: biocViews
Inferring biocViews.
2 biocViews inferred: 
 - Software
 - WorkflowManagement
Inferring biocViews.
4 biocViews inferred: 
 - Software
 - Genetics
 - Transcriptomics
 - WorkflowManagement
trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION'
Content type 'text/plain; charset=utf-8' length 707 bytes
==================================================
downloaded 707 bytes

Hello world
Finding hex sticker(s) for 1 package(s).
Adding CRAN release version.
Adding CRAN checks.
Adding CRAN downloads: last-month
Adding CRAN downloads: grand-total
Adding license.
Adding DOI.
Adding lifecycle.
Adding version.
Adding code size
Adding commit.
Adding actions.
Adding codecov.
Adding authors.
When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL.
<img src='https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png' title='Hex sticker for rworkflows' height='300'><br>
[![](https://www.r-pkg.org/badges/version/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows)
[![CRAN checks](https://badges.cranchecks.info/summary/rworkflows.svg)](https://cran.r-project.org/web/checks/check_results_rworkflows.html)
[![](http://cranlogs.r-pkg.org/badges/last-month/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows)
[![](http://cranlogs.r-pkg.org/badges/grand-total/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows)
[![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
[![](https://img.shields.io/badge/doi-doi:000000-blue.svg)](https://doi.org/doi:000000)
[![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
<br>
[![](https://img.shields.io/badge/devel%20version-1.0.0-black.svg)](https://github.com/neurogenomics/rworkflows)
[![](https://img.shields.io/github/languages/code-size/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows)
[![](https://img.shields.io/github/last-commit/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows/commits/master)
<br>
[![R build status](https://github.com/neurogenomics/rworkflows/workflows/rworkflow/badge.svg)](https://github.com/neurogenomics/rworkflows/actions)
[![](https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graph/badge.svg)](https://app.codecov.io/gh/neurogenomics/rworkflows)
<br>
<a href='https://app.codecov.io/gh/neurogenomics/rworkflows/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graphs/sunburst.svg' title='Codecov sunburst graph' width='200' height='50' style='vertical-align: top;'></a>
<a href='https://app.codecov.io/gh/neurogenomics/rworkflows/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graphs/tree.svg' title='Codecov tree graph' width='200' height='50' style='vertical-align: top;'></a>
<a href='https://app.codecov.io/gh/neurogenomics/rworkflows/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>
<h4>Authors: <i>Brian Schilder, Alan Murphy, Nathan Skene</i></h4>Creating new dev container config file ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/devcontainer.json
Using existing dev container config file ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/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 ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/Dockerfile
Using existing Docker file: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/Dockerfile
Docker file preview:
Creating new Issue Template ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/bug_report.md
Creating new Issue Template ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/feature_request.md
Using existing Issue Template: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/bug_report.md
Issue Template preview:
Using existing Issue Template: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/feature_request.md
Issue Template preview:
Creating new README file ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/README.Rmd
Using existing README file: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/README.Rmd
README file preview:
Creating new vignette file ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/vignettes/docker.Rmd
Using existing vignette file: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/vignettes/docker.Rmd
Vignette file preview:
Creating new vignette file ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/vignettes/mypackage.Rmd
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/.github/workflows/rworkflows.yml
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/rworkflows.yml
Using existing workflow file: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/rworkflows.yml
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/rworkflows_static.yml
name: test
channels:
- conda-forge
- nodefaults
dependencies:
- python>=3.9
- anndata
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/conda.yml
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/rworkflows.yml
python-version not set for runner os='ubuntu-latest'. Using default.
python-version not set for runner os='macOS-latest'. Using default.
python-version not set for runner os='windows-latest'. Using default.
Saving yaml ==> /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-rworkflows/R-rworkflows/work/.tmp/RtmpZ03WDv/rworkflows.yml
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 177 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_description.R:62:5'): get_description works ──────────────
d7[[1]] is not NULL

`actual` is an R6 object of class <description>
`expected` is NULL
── Failure ('test-get_description.R:101:5'): get_description works ─────────────
methods::is(d14[[1]], "description") is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-get_hex.R:16:5'): get_hex works ──────────────────────────────
hex3[[1]] is not NULL

`actual` is a character vector ('<img src=\'https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png\' title=\'Hex sticker for rworkflows\' height=\'300\'>')
`expected` is NULL
── Failure ('test-infer_biocviews.R:10:5'): infer_biocviews works ──────────────
`infer_biocviews(include_branch = FALSE)` did not throw the expected error.
── Failure ('test-infer_biocviews.R:19:5'): infer_biocviews works ──────────────
`infer_biocviews(biocviews = biocviews_manual)` did not throw the expected error.

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 177 ]
Error: Test failures
Execution halted

[bschilder]

@barracuda156 sorry, im a bit confused. what is the context for this? where is it being run? on what package?

[bschilder]

Ok, so it seems like you're trying to run testthat:: test_check("rworkflows") somewhere (locally on your machine?).
What is your goal?

[bschilder]

Also, please make sure to use the provided bug template, rather than deleting it.

[barracuda156]

Sorry for not being clear. I am adding R packages to Macports and test them whenever tests are provided. When something fails, I normally notify the upstream, since a) there may be an interest to fix it generally (provided it is indeed a bug), and b) if it is not a bug, but an error on our side, I could fix that, following recommendations from upstream, if there are any.

[bschilder]

Sorry for not being clear. I am adding R packages to Macports and test them whenever tests are provided. When something fails, I normally notify the upstream, since a) there may be an interest to fix it generally (provided it is indeed a bug), and b) if it is not a bug, but an error on our side, I could fix that, following recommendations from upstream, if there are any.

Ok, thanks for that. I'm not familiar with Macports, could you provide some background describe and how it relates to rworkflows?
Also please:

• clarify where these tests are being run (local machine, VM, Docker container, GitHub Actions, etc).
• Fill out the bug template (this will provide us both with essential information to assess the issue)

[bschilder]

@barracuda156 without further information, my best guess is that your issue stems from which directory and environment you're running the test_check function in. If you run checks using the "Check" button in Rstudio, or via the rworkflows action, all checks pass.

[barracuda156]

@bschilder Sorry, I was just too busy with other stuff.

Macports runs tests from a dedicated directory. sudo port -v test will build a package and runs its tests.
You could try it locally, since the package in question is available in Macports normally.

sudo port -v test R-rworkflows

[barracuda156]

@bschilder P. S. I will fill a template today, apologize for missing on that. (I need to get to the machine to do it, now on mobile.)

[barracuda156]

1. Bug description

When running test for rworkflows in Macports environment, a few tests fail.

Console output

--->  Testing R-rworkflows
* using log directory ‘/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rworkflows/R-rworkflows/work/rworkflows/rworkflows.Rcheck’
* using R version 4.3.2 (2023-10-31)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
    gcc-mp-13 (MacPorts gcc13 13.2.0_3) 13.2.0
    GNU Fortran (MacPorts gcc12 12.3.0_0) 12.3.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using option ‘--ignore-vignettes’
* checking for file ‘rworkflows/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rworkflows’ version ‘1.0.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
* checking package 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 R 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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’ ... SKIPPED
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-get_hex.R:16:5'): get_hex works ──────────────────────────────
  hex3[[1]] is not NULL
  
  `actual` is a character vector ('<img src=\'https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png\' title=\'Hex sticker for rworkflows\' height=\'300\'>')
  `expected` is NULL
  ── Failure ('test-infer_biocviews.R:10:5'): infer_biocviews works ──────────────
  `infer_biocviews(include_branch = FALSE)` did not throw the expected error.
  ── Failure ('test-infer_biocviews.R:19:5'): infer_biocviews works ──────────────
  `infer_biocviews(biocviews = biocviews_manual)` did not throw the expected error.
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 177 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs

Expected behaviour

Tests should pass.

2. Reproducible example

Code

sudo port -v test R-rworkflows

Data

(If possible, upload a small sample of your data so that we can reproduce the bug on our end. If that's not possible, please at least include a screenshot of your data and other relevant details.)

3. Session info

(Add output of the R function utils::sessionInfo() below. This helps us assess version/OS conflicts which could be causing bugs.)

36-198% /opt/local/bin/r

R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(rworkflows)
> utils::sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)
Running under: OS X Snow Leopard 10.6

Matrix products: default
BLAS:   /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRblas.dylib 
LAPACK: /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8

time zone: Asia/Taipei
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rworkflows_1.0.0

loaded via a namespace (and not attached):
 [1] gtable_0.3.4        jsonlite_1.8.7      renv_1.0.3         
 [4] dplyr_1.1.3         compiler_4.3.2      BiocManager_1.30.22
 [7] tidyselect_1.2.0    rvcheck_0.2.1       scales_1.2.1       
[10] yaml_2.3.7          fastmap_1.1.1       here_1.0.1.9007    
[13] ggplot2_3.4.4       R6_2.5.1.9000       generics_0.1.3     
[16] yulab.utils_0.1.0   tibble_3.2.1.9009   desc_1.4.2         
[19] dlstats_0.1.7       munsell_0.5.0       rprojroot_2.0.4    
[22] pillar_1.9.0.9003   RColorBrewer_1.1-3  rlang_1.1.2        
[25] utf8_1.2.4          cachem_1.0.8        badger_0.2.3       
[28] fs_1.6.3            memoise_2.0.1       cli_3.6.1.9000     
[31] magrittr_2.0.3      digest_0.6.33       grid_4.3.2         
[34] lifecycle_1.0.3     vctrs_0.6.4         glue_1.6.2         
[37] data.table_1.14.8   fansi_1.0.5         colorspace_2.1-0   
[40] tools_4.3.2         pkgconfig_2.0.3

Port can be found at: https://ports.macports.org/port/R-rworkflows

[barracuda156]

Session info:

> utils::sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)
Running under: OS X Snow Leopard 10.6

Matrix products: default
BLAS:   /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRblas.dylib 
LAPACK: /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8

time zone: Asia/Taipei
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rworkflows_1.0.0

loaded via a namespace (and not attached):
 [1] gtable_0.3.4        jsonlite_1.8.7      renv_1.0.3         
 [4] dplyr_1.1.3         compiler_4.3.2      BiocManager_1.30.22
 [7] tidyselect_1.2.0    rvcheck_0.2.1       scales_1.2.1       
[10] yaml_2.3.7          fastmap_1.1.1       here_1.0.1.9007    
[13] ggplot2_3.4.4       R6_2.5.1.9000       generics_0.1.3     
[16] yulab.utils_0.1.0   tibble_3.2.1.9009   desc_1.4.2         
[19] dlstats_0.1.7       munsell_0.5.0       rprojroot_2.0.4    
[22] pillar_1.9.0.9003   RColorBrewer_1.1-3  rlang_1.1.2        
[25] utf8_1.2.4          cachem_1.0.8        badger_0.2.3       
[28] fs_1.6.3            memoise_2.0.1       cli_3.6.1.9000     
[31] magrittr_2.0.3      digest_0.6.33       grid_4.3.2         
[34] lifecycle_1.0.3     vctrs_0.6.4         glue_1.6.2         
[37] data.table_1.14.8   fansi_1.0.5         colorspace_2.1-0   
[40] tools_4.3.2         pkgconfig_2.0.3

[barracuda156]

Just in case, I also get these errors on Sonoma, so it is unrelated to either old macOS SDK or powerpc arch:

--->  Testing R-rworkflows
* using log directory ‘/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rworkflows/R-rworkflows/work/rworkflows/rworkflows.Rcheck’
* using R version 4.3.2 (2023-10-31)
* using platform: aarch64-apple-darwin23.1.0 (64-bit)
* R was compiled by
    clang version 15.0.7
    GNU Fortran (MacPorts gcc12 12.3.0_3+stdlib_flag) 12.3.0
* running under: macOS Sonoma 14.1.1
* using session charset: UTF-8
* using option ‘--ignore-vignettes’
* checking for file ‘rworkflows/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rworkflows’ version ‘1.0.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
* checking package 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 R 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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’ ... SKIPPED
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-get_hex.R:16:5'): get_hex works ──────────────────────────────
  hex3[[1]] is not NULL
  
  `actual` is a character vector ('<img src=\'https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png\' title=\'Hex sticker for rworkflows\' height=\'300\'>')
  `expected` is NULL
  ── Failure ('test-infer_biocviews.R:10:5'): infer_biocviews works ──────────────
  `infer_biocviews(include_branch = FALSE)` did not throw the expected error.
  ── Failure ('test-infer_biocviews.R:19:5'): infer_biocviews works ──────────────
  `infer_biocviews(biocviews = biocviews_manual)` did not throw the expected error.
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 177 ]
  Error: Test failures
  Execution halted

[bschilder]

Thanks for the detailed report and apologies for just getting to this now.

I'm not sure how exactly sudo port -v test R-rworkflows is running tests, but I believe the error is due to tests being initiated from directory that is different than how R CMD check initiates them within Rstudio via the Check button.

The directory structure is important for some test expectations that deal with finding DESCRIPTION files, which yield a different result if you're in the main directory of the cloned package vs. in a separate testthat environment.

I've identified all points in tests where this can occur and added conditional test skips. I validated this solution by running devtools::test_coverage() from within the main directory of the rworkflows clone, which now passes:

> devtools::test_coverage()
ℹ Computing test coverage for rworkflows