| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| 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 262/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BUSpaRse 1.23.2 (landing page) Lambda Moses
| 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 | ||||||||||
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To the developers/maintainers of the BUSpaRse package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSpaRse.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: BUSpaRse |
| Version: 1.23.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BUSpaRse |
| StartedAt: 2025-09-21 16:32:46 -0400 (Sun, 21 Sep 2025) |
| EndedAt: 2025-09-21 16:35:19 -0400 (Sun, 21 Sep 2025) |
| EllapsedTime: 153.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BUSpaRse
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* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* preparing ‘BUSpaRse’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘sparse-matrix.Rmd’ using rmarkdown
Quitting from sparse-matrix.Rmd:42-46 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sort_tr2g()`:
! Some transcripts in the kallisto index are absent from tr2g.
---
Backtrace:
▆
1. └─BUSpaRse::transcript2gene(...)
2. └─BUSpaRse::sort_tr2g(tr2g, kallisto_out_path = kallisto_out_path)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sparse-matrix.Rmd' failed with diagnostics:
Some transcripts in the kallisto index are absent from tr2g.
--- failed re-building ‘sparse-matrix.Rmd’
--- re-building ‘tr2g.Rmd’ using rmarkdown
--- finished re-building ‘tr2g.Rmd’
SUMMARY: processing the following file failed:
‘sparse-matrix.Rmd’
Error: Vignette re-building failed.
Execution halted