Multiple platform build/check report for BioC 3.23 - BUILD results for ORFik on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4805
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4539
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 ORFik on nebbiolo1

To the developers/maintainers of the ORFik package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.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: ORFik

Version: 1.31.3

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ORFik

StartedAt: 2026-01-20 19:10:06 -0500 (Tue, 20 Jan 2026)

EndedAt: 2026-01-20 19:15:00 -0500 (Tue, 20 Jan 2026)

EllapsedTime: 293.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ORFik
###
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* checking for file ‘ORFik/DESCRIPTION’ ... OK
* preparing ‘ORFik’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Annotation_Alignment.Rmd’ using rmarkdown
--- finished re-building ‘Annotation_Alignment.Rmd’

--- re-building ‘Importing_Data.Rmd’ using rmarkdown

Quitting from Importing_Data.Rmd:164-177 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://rest.ensembl.org/info/assembly/Saccharomyces_cerevisiae?content-type=application/json'
---
Backtrace:
     ▆
  1. └─ORFik::getGenomeAndAnnotation(...)
  2.   └─ORFik:::get_genome_gtf(...)
  3.     └─biomartr:::getENSEMBL.gtf(...)
  4.       └─biomartr:::getENSEMBL.Annotation(...)
  5.         └─biomartr:::getENSEMBL(...)
  6.           └─biomartr:::test_url_status(url = rest_url, organism = organism)
  7.             └─jsonlite::fromJSON(url)
  8.               └─jsonlite:::parse_and_simplify(...)
  9.                 └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                   └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                     ├─base::open(con, "rb")
 12.                     └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Importing_Data.Rmd' failed with diagnostics:
cannot open the connection to 'https://rest.ensembl.org/info/assembly/Saccharomyces_cerevisiae?content-type=application/json'
--- failed re-building ‘Importing_Data.Rmd’

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

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

--- re-building ‘Ribo-seq_pipeline-human.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-human.Rmd’

--- re-building ‘Ribo-seq_pipeline-yeast.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-yeast.Rmd’

--- re-building ‘Working_with_transcripts.Rmd’ using rmarkdown

Quitting from Working_with_transcripts.Rmd:28-42 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get_genome_fasta()`:
! 'list' object cannot be coerced to type 'logical'
---
Backtrace:
    ▆
 1. └─ORFik::getGenomeAndAnnotation(...)
 2.   └─ORFik:::get_genome_fasta(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Working_with_transcripts.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'logical'
--- failed re-building ‘Working_with_transcripts.Rmd’

SUMMARY: processing the following files failed:
  ‘Importing_Data.Rmd’ ‘Working_with_transcripts.Rmd’

Error: Vignette re-building failed.
Execution halted