Multiple platform build/check report for BioC 3.21 - BUILD results for cogeqc on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4742
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4459
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for cogeqc on kjohnson3

To the developers/maintainers of the cogeqc package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cogeqc.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: cogeqc

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cogeqc

StartedAt: 2025-03-18 16:00:01 -0400 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 16:00:53 -0400 (Tue, 18 Mar 2025)

EllapsedTime: 52.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cogeqc
###
##############################################################################
##############################################################################


* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* preparing ‘cogeqc’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette_01_assessing_genome_assembly.Rmd’ using rmarkdown

Quitting from vignette_01_assessing_genome_assembly.Rmd:74-85 [get_maize_genomes]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/Zea%20mays/dataset_report?page_size=1000'
---
Backtrace:
    ▆
 1. └─cogeqc::get_genome_stats(taxon = "Zea mays")
 2.   └─jsonlite::read_json(base_url, simplifyVector = TRUE)
 3.     └─jsonlite::parse_json(...)
 4.       └─jsonlite:::parse_and_simplify(...)
 5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
 6.           └─jsonlite:::parse_con(txt, bigint_as_char)
 7.             ├─base::open(con, "rb")
 8.             └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette_01_assessing_genome_assembly.Rmd' failed with diagnostics:
cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/Zea%20mays/dataset_report?page_size=1000'
--- failed re-building ‘vignette_01_assessing_genome_assembly.Rmd’

--- re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’ using rmarkdown
2025-03-18 16:00:48.320 R[93655:749131327] XType: Using static font registry.
--- finished re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’

--- re-building ‘vignette_03_assessing_synteny.Rmd’ using rmarkdown
--- finished re-building ‘vignette_03_assessing_synteny.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_01_assessing_genome_assembly.Rmd’

Error: Vignette re-building failed.
Execution halted