RMassBank at Eawag
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/RMassBank |
| git_branch: RELEASE_3_20 |
| git_last_commit: aadbd4c |
| git_last_commit_date: 2024-10-29 09:42:07 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:11 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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 1765/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RMassBank 3.16.0 (landing page) RMassBank at Eawag
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 3.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank |
| StartedAt: 2025-03-18 07:12:03 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 07:20:19 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 495.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data 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 [2025-03-18 07:13:20] Loaded compoundlist successfully
INFO [2025-03-18 07:13:21] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
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|================================================================| 100%INFO [2025-03-18 07:13:27] msmsWorkflow: Step 2. First analysis pre recalibration
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|================================================================| 100%
INFO [2025-03-18 07:13:48] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-03-18 07:13:48] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
2025-03-18 07:13:48.702 R[14333:301961417] XType: Using static font registry.
INFO [2025-03-18 07:13:49] msmsWorkflow: Done.
INFO [2025-03-18 07:14:55] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-18 07:15:01] msmsWorkflow: Done.
INFO [2025-03-18 07:15:01] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-18 07:15:01] msmsWorkflow: Done.
INFO [2025-03-18 07:15:02] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
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INFO [2025-03-18 07:15:22] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-03-18 07:15:22] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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INFO [2025-03-18 07:17:05] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-03-18 07:17:07] msmsWorkflow: Done.
INFO [2025-03-18 07:17:08] 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(identifier = smiles, representation = "stdinchikey")
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 [2025-03-18 07:19:27] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-18 07:19:31] msmsWorkflow: Done.
INFO [2025-03-18 07:19:34] Loaded compoundlist successfully
INFO [2025-03-18 07:19:34] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
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|================================ | 50%
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|================================================================| 100%INFO [2025-03-18 07:19:41] msmsWorkflow: Done.
INFO [2025-03-18 07:19:41] msmsWorkflow: Step 2. First analysis pre recalibration
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| | 0%
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|================================ | 50%
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|================================================================| 100%
INFO [2025-03-18 07:19:43] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-03-18 07:19:43] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-18 07:19:44] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
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|================================ | 50%
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|================================================================| 100%
INFO [2025-03-18 07:19:46] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-03-18 07:19:46] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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| | 0%
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|================================ | 50%
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|================================================================| 100%
INFO [2025-03-18 07:19:56] msmsWorkflow: Done.
INFO [2025-03-18 07:19:57] msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%INFO [2025-03-18 07:20:04] msmsWorkflow: Done.
INFO [2025-03-18 07:20:04] msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-03-18 07:20:06] msmsWorkflow: Step 3. Aggregate all spectra
INFO [2025-03-18 07:20:06] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
INFO [2025-03-18 07:20:06] msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-03-18 07:20:07] msmsWorkflow: Step 6. Aggregate recalibrated results
INFO [2025-03-18 07:20:07] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%
INFO [2025-03-18 07:20:16] msmsWorkflow: Done.
INFO [2025-03-18 07:20:16] msmsWorkflow: Step 8. Peak multiplicity filtering
INFO [2025-03-18 07:20:17] msmsWorkflow: Done.
--- finished re-building ‘RMassBankNonstandard.Rmd’
SUMMARY: processing the following file failed:
‘RMassBank.Rmd’
Error: Vignette re-building failed.
Execution halted