| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-23 11:32 -0400 (Sat, 23 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 1854/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RMassBank 3.22.0 (landing page) RMassBank at Eawag
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 3.22.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank |
| StartedAt: 2026-05-22 19:53:44 -0400 (Fri, 22 May 2026) |
| EndedAt: 2026-05-22 20:00:51 -0400 (Fri, 22 May 2026) |
| EllapsedTime: 427.5 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 [2026-05-22 19:54:53] Loaded compoundlist successfully
INFO [2026-05-22 19:54:53] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%INFO [2026-05-22 19:54:59] msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 19:55:17] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2026-05-22 19:55:18] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-05-22 19:55:18] msmsWorkflow: Done.
INFO [2026-05-22 19:56:21] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-05-22 19:56:27] msmsWorkflow: Done.
INFO [2026-05-22 19:56:27] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-05-22 19:56:27] msmsWorkflow: Done.
INFO [2026-05-22 19:56:28] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 19:56:46] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2026-05-22 19:56:46] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 19:58:29] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2026-05-22 19:58:30] msmsWorkflow: Done.
INFO [2026-05-22 19:58:30] mbWorkflow: Step 1. Gather info from several databases
Quitting from RMassBank.Rmd:432-434 [unnamed-chunk-22]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `fromJSON()`:
! not all data was parsed (3 chars were parsed out of a total of 18 chars)
---
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::getCtsRecord(inchikey_split)
7. └─rjson::fromJSON(data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RMassBank.Rmd' failed with diagnostics:
not all data was parsed (3 chars were parsed out of a total of 18 chars)
--- failed re-building ‘RMassBank.Rmd’
--- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown
INFO [2026-05-22 19:59:57] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-05-22 20:00:01] msmsWorkflow: Done.
INFO [2026-05-22 20:00:04] Loaded compoundlist successfully
INFO [2026-05-22 20:00:04] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%INFO [2026-05-22 20:00:11] msmsWorkflow: Done.
INFO [2026-05-22 20:00:11] msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 20:00:13] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2026-05-22 20:00:13] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-05-22 20:00:14] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 20:00:16] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2026-05-22 20:00:16] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 20:00:27] msmsWorkflow: Done.
INFO [2026-05-22 20:00:27] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%INFO [2026-05-22 20:00:34] msmsWorkflow: Done.
INFO [2026-05-22 20:00:34] msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 20:00:36] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2026-05-22 20:00:36] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2026-05-22 20:00:36] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 20:00:38] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2026-05-22 20:00:38] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2026-05-22 20:00:49] msmsWorkflow: Done.
INFO [2026-05-22 20:00:49] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2026-05-22 20:00:49] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’
SUMMARY: processing the following file failed:
‘RMassBank.Rmd’
Error: Vignette re-building failed.
Execution halted