Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 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" | 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 |
Package 1266/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetMashR 1.3.0 (landing page) Gavin Rhys Lloyd
| 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 MetMashR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetMashR.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. |
Package: MetMashR |
Version: 1.3.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 MetMashR |
StartedAt: 2025-09-19 18:33:54 -0400 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 18:37:17 -0400 (Fri, 19 Sep 2025) |
EllapsedTime: 203.2 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 MetMashR ### ############################################################################## ############################################################################## * checking for file ‘MetMashR/DESCRIPTION’ ... OK * preparing ‘MetMashR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Extending_MetMashR.Rmd’ using rmarkdown --- finished re-building ‘Extending_MetMashR.Rmd’ --- re-building ‘annotate_mixtures.Rmd’ using rmarkdown Quitting from annotate_mixtures.Rmd:425-456 [unnamed-chunk-15] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `validObject()`: ! invalid class "annotation_venn_chart" object: The required package "RVenn" is not installed. --- Backtrace: ▆ 1. └─MetMashR::annotation_venn_chart(...) 2. └─struct::new_struct(...) 3. ├─BiocGenerics::do.call(new, L) 4. ├─base::do.call(new, L) 5. └─methods (local) `<fn>`(...) 6. ├─methods::initialize(value, ...) 7. └─methods::initialize(value, ...) 8. └─methods::validObject(.Object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'annotate_mixtures.Rmd' failed with diagnostics: invalid class "annotation_venn_chart" object: The required package "RVenn" is not installed. --- failed re-building ‘annotate_mixtures.Rmd’ --- re-building ‘exploring_mtox.Rmd’ using rmarkdown Quitting from exploring_mtox.Rmd:107-119 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! download failed; see warnings() --- Backtrace: ▆ 1. ├─MetMashR::read_database(MT) 2. └─MetMashR::read_database(MT) 3. └─MetMashR (local) .local(obj, ...) 4. ├─methods::callNextMethod(obj) 5. │ └─base::eval(call, callEnv) 6. │ └─base::eval(call, callEnv) 7. └─MetMashR (local) .nextMethod(obj) 8. └─MetMashR (local) .local(obj, ...) 9. └─MetMashR:::.get_cached_path(obj) 10. ├─BiocFileCache::bfcdownload(...) 11. └─BiocFileCache::bfcdownload(...) 12. └─BiocFileCache:::.util_download_and_rename(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'exploring_mtox.Rmd' failed with diagnostics: download failed; see warnings() --- failed re-building ‘exploring_mtox.Rmd’ --- re-building ‘using_MetMashR.Rmd’ using rmarkdown Quitting from using_MetMashR.Rmd:201-210 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! download failed; see warnings() --- Backtrace: ▆ 1. ├─MetMashR::read_source(MT) 2. └─MetMashR::read_source(MT) 3. └─MetMashR (local) .local(obj, ...) 4. ├─MetMashR::read_database(obj) 5. └─MetMashR::read_database(obj) 6. └─MetMashR (local) .local(obj, ...) 7. ├─methods::callNextMethod(obj) 8. │ └─base::eval(call, callEnv) 9. │ └─base::eval(call, callEnv) 10. └─MetMashR (local) .nextMethod(obj) 11. └─MetMashR (local) .local(obj, ...) 12. └─MetMashR:::.get_cached_path(obj) 13. ├─BiocFileCache::bfcdownload(...) 14. └─BiocFileCache::bfcdownload(...) 15. └─BiocFileCache:::.util_download_and_rename(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'using_MetMashR.Rmd' failed with diagnostics: download failed; see warnings() --- failed re-building ‘using_MetMashR.Rmd’ SUMMARY: processing the following files failed: ‘annotate_mixtures.Rmd’ ‘exploring_mtox.Rmd’ ‘using_MetMashR.Rmd’ Error: Vignette re-building failed. Execution halted