| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1219/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methodical 1.2.0 (landing page) Richard Heery
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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To the developers/maintainers of the methodical package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methodical.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: methodical |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 methodical |
| StartedAt: 2024-12-19 17:51:55 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 17:52:56 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 61.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 methodical ### ############################################################################## ############################################################################## * checking for file ‘methodical/DESCRIPTION’ ... OK * preparing ‘methodical’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘calculating_methylation_transcription_correlations.Rmd’ using rmarkdown Quitting from lines 51-56 [unnamed-chunk-3] (calculating_methylation_transcription_correlations.Rmd) Error: processing vignette 'calculating_methylation_transcription_correlations.Rmd' failed with diagnostics: This RangedSummarizedExperiment object contains out-of-memory data so cannot be serialized reliably. Please use saveHDF5SummarizedExperiment() from the HDF5Array package instead. Alternatively you can call base::saveRDS() on it but only if you know what you are doing. See '?containsOutOfMemoryData' in the BiocGenerics package for more information. --- failed re-building ‘calculating_methylation_transcription_correlations.Rmd’ --- re-building ‘identifying_tmrs.Rmd’ using rmarkdown Quitting from lines 68-82 [unnamed-chunk-4] (identifying_tmrs.Rmd) Error: processing vignette 'identifying_tmrs.Rmd' failed with diagnostics: unused arguments (expand_upstream = 5000, expand_downstream = 5000) --- failed re-building ‘identifying_tmrs.Rmd’ --- re-building ‘working_with_meth_rses.Rmd’ using rmarkdown Quitting from lines 46-48 [unnamed-chunk-2] (working_with_meth_rses.Rmd) Error: processing vignette 'working_with_meth_rses.Rmd' failed with diagnostics: This RangedSummarizedExperiment object contains out-of-memory data so cannot be serialized reliably. Please use saveHDF5SummarizedExperiment() from the HDF5Array package instead. Alternatively you can call base::saveRDS() on it but only if you know what you are doing. See '?containsOutOfMemoryData' in the BiocGenerics package for more information. --- failed re-building ‘working_with_meth_rses.Rmd’ SUMMARY: processing the following files failed: ‘calculating_methylation_transcription_correlations.Rmd’ ‘identifying_tmrs.Rmd’ ‘working_with_meth_rses.Rmd’ Error: Vignette re-building failed. Execution halted