RMassBank at Eawag
| Snapshot Date: 2025-12-04 13:40 -0500 (Thu, 04 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/RMassBank |
| git_branch: devel |
| git_last_commit: c946a1f |
| git_last_commit_date: 2025-10-29 10:11:40 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-05 11:35 -0500 (Fri, 05 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1790/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RMassBank 3.21.0 (landing page) RMassBank at Eawag
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 3.21.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank |
| StartedAt: 2025-12-04 19:40:26 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 19:47:29 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 423.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank
###
##############################################################################
##############################################################################
* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* preparing ‘RMassBank’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘RMassBank.Rmd’ using rmarkdown
INFO [2025-12-04 19:41:33] Loaded compoundlist successfully
INFO [2025-12-04 19:41:33] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%INFO [2025-12-04 19:41:39] msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:41:58] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-12-04 19:41:58] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-12-04 19:41:59] msmsWorkflow: Done.
INFO [2025-12-04 19:43:04] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-12-04 19:43:09] msmsWorkflow: Done.
INFO [2025-12-04 19:43:09] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-12-04 19:43:09] msmsWorkflow: Done.
INFO [2025-12-04 19:43:10] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:43:28] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-12-04 19:43:28] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:45:10] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-12-04 19:45:12] msmsWorkflow: Done.
INFO [2025-12-04 19:45:12] mbWorkflow: Step 1. Gather info from several databases
INFO [2025-12-04 19:45:29] 2819: smiles
INFO [2025-12-04 19:45:29] mbWorkflow: Step 2. Export infolist (if required)
INFO [2025-12-04 19:45:29] The file ./Narcotics_infolist.csv was generated with new compound information. Please check and edit the table, and add it to your infolist folder.
INFO [2025-12-04 19:45:29] mbWorkflow: Step 1. Gather info from several databases
INFO [2025-12-04 19:45:29] mbWorkflow: Step 2. Export infolist (if required)
INFO [2025-12-04 19:45:29] No new data added.
INFO [2025-12-04 19:45:29] mbWorkflow: Step 3. Data reformatting
INFO [2025-12-04 19:45:29] mbWorkflow: Step 4. Spectra compilation
INFO [2025-12-04 19:45:29] Compiling: 1-(3-Chlorophenyl)piperazine
INFO [2025-12-04 19:45:32] Compiling: 1-(3-Trifluoromethylphenyl)-piperazine
INFO [2025-12-04 19:45:33] mbWorkflow: [Legacy Step 5. Flattening records] ignored
INFO [2025-12-04 19:45:33] mbWorkflow: Step 6. Generate molfiles
Quitting from RMassBank.Rmd:470-472 [unnamed-chunk-25]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `strsplit()`:
! non-character argument
---
Backtrace:
▆
1. └─RMassBank::mbWorkflow(mb)
2. ├─BiocGenerics::lapply(mb@compiled_ok, function(c) createMolfile(as.numeric(c@id)))
3. └─base::lapply(mb@compiled_ok, function(c) createMolfile(as.numeric(c@id)))
4. └─RMassBank (local) FUN(X[[i]], ...)
5. └─RMassBank::createMolfile(as.numeric(c@id))
6. └─RMassBank::getCactus(smiles, "sdf")
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 [2025-12-04 19:46:39] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-12-04 19:46:43] msmsWorkflow: Done.
INFO [2025-12-04 19:46:46] Loaded compoundlist successfully
INFO [2025-12-04 19:46:46] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%INFO [2025-12-04 19:46:51] msmsWorkflow: Done.
INFO [2025-12-04 19:46:51] msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:46:53] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-12-04 19:46:53] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-12-04 19:46:54] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:46:56] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-12-04 19:46:56] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:47:06] msmsWorkflow: Done.
INFO [2025-12-04 19:47:07] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%INFO [2025-12-04 19:47:13] msmsWorkflow: Done.
INFO [2025-12-04 19:47:13] msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:47:14] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-12-04 19:47:14] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-12-04 19:47:15] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:47:16] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-12-04 19:47:16] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-12-04 19:47:27] msmsWorkflow: Done.
INFO [2025-12-04 19:47:27] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-12-04 19:47:28] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’
SUMMARY: processing the following file failed:
‘RMassBank.Rmd’
Error: Vignette re-building failed.
Execution halted