Multiple platform build/check report for BioC 3.22 - BUILD results for factR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4814
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4603
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4547
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4553
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 factR on lconway

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

Version: 1.11.0

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

StartedAt: 2025-09-19 16:51:52 -0400 (Fri, 19 Sep 2025)

EndedAt: 2025-09-19 16:54:33 -0400 (Fri, 19 Sep 2025)

EllapsedTime: 161.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data factR
###
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* checking for file ‘factR/DESCRIPTION’ ... OK
* preparing ‘factR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘factR.Rmd’ using rmarkdown
2025-09-19 16:52:21.683 R[46519:328479756] XType: com.apple.fonts is not accessible.
2025-09-19 16:52:21.684 R[46519:328479756] XType: XTFontStaticRegistry is enabled.
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz'
Content type 'unknown' length 28542432 bytes (27.2 MB)
==================================================

Quitting from factR.Rmd:312-314 [buildcds]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.get_data_frame_col_as_numeric()`:
! the "start" column is not an atomic vector or an Rle object
---
Backtrace:
    ▆
 1. ├─factR::buildCDS(custom_new.gtf, ref.gtf, Mmusculus)
 2. │ └─factR:::.runbuildCDS(query, ref, fasta, argnames)
 3. │   └─factR:::.getCDS(order_query, order_ref, fasta)
 4. │     ├─base::suppressMessages(...)
 5. │     │ └─base::withCallingHandlers(...)
 6. │     └─... %>% ...
 7. └─GenomicRanges::makeGRangesFromDataFrame(., keep.extra.columns = TRUE)
 8.   └─GenomicRanges:::.drop_rows_with_na_start_end(...)
 9.     └─GenomicRanges:::.get_data_frame_col_as_numeric(df, corecol_map[["start"]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'factR.Rmd' failed with diagnostics:
the "start" column is not an atomic vector or an Rle object
--- failed re-building ‘factR.Rmd’

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

Error: Vignette re-building failed.
Execution halted