Laurent Gatto
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/PSMatch |
| git_branch: devel |
| git_last_commit: 3ec4d55 |
| git_last_commit_date: 2026-04-28 08:57:58 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 1665/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PSMatch 1.17.0 (landing page) Laurent Gatto
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for PSMatch in R Universe. | ||||||||||||||
|
To the developers/maintainers of the PSMatch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PSMatch.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: PSMatch |
| Version: 1.17.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data PSMatch |
| StartedAt: 2026-05-05 05:14:05 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 05:14:58 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 53.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data PSMatch
###
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* checking for file ‘PSMatch/DESCRIPTION’ ... OK
* preparing ‘PSMatch’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘AdjacencyMatrix.Rmd’ using rmarkdown
Quitting from AdjacencyMatrix.Rmd:42-49 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': error in evaluating the argument 'x' in selecting a method for function 'metadata': there is no package called 'MsDataHub'
---
Backtrace:
▆
1. ├─PSMatch::filterPsmRank(filterPsmDecoy(PSM(MsDataHub::TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid())))
2. │ └─PSMatch::psmVariables(x)
3. │ └─S4Vectors::metadata(object)
4. ├─PSMatch::filterPsmDecoy(PSM(MsDataHub::TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid()))
5. │ └─PSMatch::psmVariables(x)
6. │ └─S4Vectors::metadata(object)
7. ├─PSMatch::PSM(MsDataHub::TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid())
8. ├─base::loadNamespace(x)
9. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
11. │ │ └─base (local) doWithOneRestart(return(expr), restart)
12. │ └─base::stop(cond)
13. ├─base (local) `<fn>`(`<pckgNtFE>`)
14. └─base::.handleSimpleError(...)
15. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'AdjacencyMatrix.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': error in evaluating the argument 'x' in selecting a method for function 'metadata': there is no package called 'MsDataHub'
--- failed re-building ‘AdjacencyMatrix.Rmd’
--- re-building ‘Fragments.Rmd’ using rmarkdown
Quitting from Fragments.Rmd:43-47 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'MsDataHub'
---
Backtrace:
▆
1. └─base::loadNamespace(x)
2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3. └─base (local) withOneRestart(expr, restarts[[1L]])
4. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Fragments.Rmd' failed with diagnostics:
there is no package called 'MsDataHub'
--- failed re-building ‘Fragments.Rmd’
--- re-building ‘PSM.Rmd’ using rmarkdown
Quitting from PSM.Rmd:52-54 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'MsDataHub'
---
Backtrace:
▆
1. └─base::loadNamespace(x)
2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3. └─base (local) withOneRestart(expr, restarts[[1L]])
4. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'PSM.Rmd' failed with diagnostics:
there is no package called 'MsDataHub'
--- failed re-building ‘PSM.Rmd’
SUMMARY: processing the following files failed:
‘AdjacencyMatrix.Rmd’ ‘Fragments.Rmd’ ‘PSM.Rmd’
Error: Vignette re-building failed.
Execution halted