Multiple platform build/check report for BioC 3.23 - BUILD results for PSMatch on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4957
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4686
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4627
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*

BUILD results for PSMatch on kunpeng2

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.

raw results

Summary

Package: PSMatch

Version: 1.15.3

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data PSMatch

StartedAt: 2026-04-17 01:17:37 -0000 (Fri, 17 Apr 2026)

EndedAt: 2026-04-17 01:18:34 -0000 (Fri, 17 Apr 2026)

EllapsedTime: 57.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data PSMatch
###
##############################################################################
##############################################################################


* 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