Back to Workflows build report for BioC 3.21

This page was generated on 2025-09-26 16:30 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
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

Package 24/30HostnameOS / ArchINSTALLBUILD
seqpac 1.8.0  (landing page)
Daniel Natt
Snapshot Date: 2025-09-26 12:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/seqpac
git_branch: RELEASE_3_21
git_last_commit: 062cfbc
git_last_commit_date: 2025-04-15 10:30:00 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  

BUILD results for seqpac on merida1

To the developers/maintainers of the seqpac package:
- 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: seqpac
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data seqpac
StartedAt: 2025-09-26 13:59:33 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 14:02:34 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 181.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘seqpac/DESCRIPTION’ ... OK
* preparing ‘seqpac’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd’ using rmarkdown
# reads processed: 7902
# reads with at least one alignment: 7 (0.09%)
# reads that failed to align: 7895 (99.91%)
Reported 67 alignments

Quitting from seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd:160-189 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `options()`:
! invalid 'scipen'
---
Backtrace:
    ▆
 1. └─seqpac::PAC_mapper(pac, ref = ref_tRNA, override = TRUE)
 2.   └─seqpac::map_reanno(...)
 3.     └─seqpac::import_reanno(...)
 4.       └─base::options(scipen = opt_sci)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd' failed with diagnostics:
invalid 'scipen'
--- failed re-building ‘seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd’

SUMMARY: processing the following file failed:
  ‘seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd’

Error: Vignette re-building failed.
Execution halted