Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 530/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.25.1  (landing page)
Rosario M. Piro
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: devel
git_last_commit: 3e9ef90
git_last_commit_date: 2025-07-22 22:46:58 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    TIMEOUT  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for decompTumor2Sig on lconway

To the developers/maintainers of the decompTumor2Sig package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decompTumor2Sig.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: decompTumor2Sig
Version: 2.25.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data decompTumor2Sig
StartedAt: 2025-10-10 16:48:17 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 16:51:33 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 195.8 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 decompTumor2Sig
###
##############################################################################
##############################################################################


* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* preparing ‘decompTumor2Sig’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘decompTumor2Sig.Rmd’ using rmarkdown

Quitting from decompTumor2Sig.Rmd:469-491 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mergeNamedAtomicVectors()`:
! sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
---
Backtrace:
     ▆
  1. └─decompTumor2Sig::adjustSignaturesForRegionSet(...)
  2.   └─decompTumor2Sig:::compNucFreq(...)
  3.     ├─Biostrings::getSeq(refGenome, regions)
  4.     └─Biostrings::getSeq(refGenome, regions)
  5.       └─BSgenome (local) .local(x, ...)
  6.         ├─base::merge(seqinfo(x), seqinfo(names))
  7.         └─Seqinfo::merge(seqinfo(x), seqinfo(names))
  8.           └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
  9.             └─Seqinfo:::.merge_two_Seqinfo_objects(x, y)
 10.               └─Seqinfo:::mergeNamedAtomicVectors(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'decompTumor2Sig.Rmd' failed with diagnostics:
sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
--- failed re-building ‘decompTumor2Sig.Rmd’

SUMMARY: processing the following file failed:
  ‘decompTumor2Sig.Rmd’

Error: Vignette re-building failed.
Execution halted