| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-09 11:58 -0500 (Mon, 09 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4888 |
| 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 1812/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RMassBank 3.20.0 (landing page) RMassBank at Eawag
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for RMassBank in R Universe. | ||||||||||||||
|
To the developers/maintainers of the RMassBank package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RMassBank.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: RMassBank |
| Version: 3.20.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 RMassBank |
| StartedAt: 2026-02-05 19:44:51 -0500 (Thu, 05 Feb 2026) |
| EndedAt: 2026-02-05 19:52:17 -0500 (Thu, 05 Feb 2026) |
| EllapsedTime: 446.4 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 RMassBank
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* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* preparing ‘RMassBank’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RMassBank.Rmd’ using rmarkdown
INFO [2026-02-05 19:45:58] Loaded compoundlist successfully
INFO [2026-02-05 19:45:58] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
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|================================================================| 100%INFO [2026-02-05 19:46:05] msmsWorkflow: Step 2. First analysis pre recalibration
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INFO [2026-02-05 19:46:23] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2026-02-05 19:46:23] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-02-05 19:46:24] msmsWorkflow: Done.
INFO [2026-02-05 19:47:27] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-02-05 19:47:33] msmsWorkflow: Done.
INFO [2026-02-05 19:47:33] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-02-05 19:47:33] msmsWorkflow: Done.
INFO [2026-02-05 19:47:34] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
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INFO [2026-02-05 19:47:52] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2026-02-05 19:47:52] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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INFO [2026-02-05 19:49:38] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2026-02-05 19:49:39] msmsWorkflow: Done.
INFO [2026-02-05 19:49:40] mbWorkflow: Step 1. Gather info from several databases
Quitting from RMassBank.Rmd:432-434 [unnamed-chunk-22]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `strsplit()`:
! non-character argument
---
Backtrace:
▆
1. └─RMassBank::mbWorkflow(mb, infolist_path = "./Narcotics_infolist.csv")
2. ├─BiocGenerics::lapply(...)
3. └─base::lapply(...)
4. └─RMassBank (local) FUN(X[[i]], ...)
5. └─RMassBank::gatherData(id)
6. └─RMassBank::getCactus(inchikey_split, "chemspider_id")
7. ├─base::unlist(strsplit(ret, "\n"))
8. └─base::strsplit(ret, "\n")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RMassBank.Rmd' failed with diagnostics:
non-character argument
--- failed re-building ‘RMassBank.Rmd’
--- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown
INFO [2026-02-05 19:51:27] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-02-05 19:51:31] msmsWorkflow: Done.
INFO [2026-02-05 19:51:34] Loaded compoundlist successfully
INFO [2026-02-05 19:51:34] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
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|================================================================| 100%INFO [2026-02-05 19:51:39] msmsWorkflow: Done.
INFO [2026-02-05 19:51:39] msmsWorkflow: Step 2. First analysis pre recalibration
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INFO [2026-02-05 19:51:41] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2026-02-05 19:51:41] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-02-05 19:51:41] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
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INFO [2026-02-05 19:51:43] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2026-02-05 19:51:43] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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|================================================================| 100%
INFO [2026-02-05 19:51:54] msmsWorkflow: Done.
INFO [2026-02-05 19:51:54] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
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|================================ | 50%
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|================================================================| 100%INFO [2026-02-05 19:52:01] msmsWorkflow: Done.
INFO [2026-02-05 19:52:01] msmsWorkflow: Step 2. First analysis pre recalibration
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|================================ | 50%
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|================================================================| 100%
INFO [2026-02-05 19:52:02] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2026-02-05 19:52:02] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-02-05 19:52:02] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
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|================================================================| 100%
INFO [2026-02-05 19:52:04] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2026-02-05 19:52:04] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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|================================================================| 100%
INFO [2026-02-05 19:52:15] msmsWorkflow: Done.
INFO [2026-02-05 19:52:15] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2026-02-05 19:52:15] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’
SUMMARY: processing the following file failed:
‘RMassBank.Rmd’
Error: Vignette re-building failed.
Execution halted