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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 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
2025-03-21 17:53:01.146 R[57983:777250247] XType: Using static font registry.

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