Multiple platform build/check report for BioC 3.22 - BUILD results for synapter on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 beta (2025-04-02 r88102) -- "How About a Twenty-Six"	4737
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-03 r88103 ucrt) -- "How About a Twenty-Six"	4524
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 synapter on nebbiolo2

To the developers/maintainers of the synapter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/synapter.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.

raw results

Summary

Package: synapter

Version: 2.31.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 synapter

StartedAt: 2025-04-08 19:35:33 -0400 (Tue, 08 Apr 2025)

EndedAt: 2025-04-08 19:38:05 -0400 (Tue, 08 Apr 2025)

EllapsedTime: 152.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 synapter
###
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* checking for file ‘synapter/DESCRIPTION’ ... OK
* preparing ‘synapter’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘fragmentmatching.Rmd’ using rmarkdown

Quitting from fragmentmatching.Rmd:106-113 [filterfragments]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
---
Backtrace:
     ▆
  1. ├─synapter::filterFragments(...)
  2. └─synapter::filterFragments(...)
  3.   └─synapter (local) .local(object, ...)
  4.     └─object$filterFragments(...)
  5.       └─synapter:::.filterIntensity(...)
  6.         ├─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
  7.         └─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
  8.           └─MSnbase (local) .local(object, t, ...)
  9.             └─MSnbase:::removePeaks_MSnExp(object, t, verbose)
 10.               └─methods::validObject(object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'fragmentmatching.Rmd' failed with diagnostics:
invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
--- failed re-building ‘fragmentmatching.Rmd’

--- re-building ‘synapter.Rmd’ using rmarkdown
--- finished re-building ‘synapter.Rmd’

--- re-building ‘synapter2.Rmd’ using rmarkdown

Quitting from synapter2.Rmd:178-185 [filterfragments]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
---
Backtrace:
     ▆
  1. ├─synapter::filterFragments(...)
  2. └─synapter::filterFragments(...)
  3.   └─synapter (local) .local(object, ...)
  4.     └─object$filterFragments(...)
  5.       └─synapter:::.filterIntensity(...)
  6.         ├─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
  7.         └─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
  8.           └─MSnbase (local) .local(object, t, ...)
  9.             └─MSnbase:::removePeaks_MSnExp(object, t, verbose)
 10.               └─methods::validObject(object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'synapter2.Rmd' failed with diagnostics:
invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
--- failed re-building ‘synapter2.Rmd’

SUMMARY: processing the following files failed:
  ‘fragmentmatching.Rmd’ ‘synapter2.Rmd’

Error: Vignette re-building failed.
Execution halted