Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:07 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 1420/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.19.1 (landing page) Mark van Roosmalen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the MutationalPatterns package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MutationalPatterns.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MutationalPatterns |
Version: 3.19.1 |
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data MutationalPatterns |
StartedAt: 2025-10-10 02:33:54 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 02:38:58 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 303.4 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data MutationalPatterns ### ############################################################################## ############################################################################## * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * preparing ‘MutationalPatterns’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Introduction_to_MutationalPatterns.Rmd’ using rmarkdown Quitting from Introduction_to_MutationalPatterns.Rmd:943-947 [context_potential_damage_analysis] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `mergeNamedAtomicVectors()`: ! sequence chrMT has incompatible circularity flags: - in 'x': TRUE - in 'y': FALSE --- Backtrace: ▆ 1. └─MutationalPatterns::context_potential_damage_analysis(...) 2. └─MutationalPatterns:::.get_cds_sequences(cds_tx, ref_genome) 3. ├─Biostrings::getSeq(ref_genome, cds_tx) 4. └─Biostrings::getSeq(ref_genome, cds_tx) 5. └─BSgenome (local) .local(x, ...) 6. ├─Biostrings::getSeq(x, unlisted_names, as.character = as.character) 7. └─BSgenome::getSeq(x, unlisted_names, as.character = as.character) 8. └─BSgenome (local) .local(x, ...) 9. ├─base::merge(seqinfo(x), seqinfo(names)) 10. └─Seqinfo::merge(seqinfo(x), seqinfo(names)) 11. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...) 12. └─Seqinfo:::.merge_two_Seqinfo_objects(x, y) 13. └─Seqinfo:::mergeNamedAtomicVectors(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Introduction_to_MutationalPatterns.Rmd' failed with diagnostics: sequence chrMT has incompatible circularity flags: - in 'x': TRUE - in 'y': FALSE --- failed re-building ‘Introduction_to_MutationalPatterns.Rmd’ SUMMARY: processing the following file failed: ‘Introduction_to_MutationalPatterns.Rmd’ Error: Vignette re-building failed. Execution halted