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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MSstatsBioNet
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* checking for file ‘MSstatsBioNet/DESCRIPTION’ ... OK
* preparing ‘MSstatsBioNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MSstatsBioNet.Rmd’ using rmarkdown

Quitting from MSstatsBioNet.Rmd:108-116 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `statement$data`:
! $ operator is invalid for atomic vectors
---
Backtrace:
    ▆
 1. └─MSstatsBioNet::getSubnetworkFromIndra(...)
 2.   └─MSstatsBioNet:::.filterIndraResponse(...)
 3.     └─base::Filter(...)
 4.       ├─base::unlist(lapply(x, f))
 5.       └─base::lapply(x, f)
 6.         └─MSstatsBioNet (local) FUN(X[[i]], ...)
 7.           └─statement$data$stmt_type %in% interaction_types
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MSstatsBioNet.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘MSstatsBioNet.Rmd’

--- re-building ‘PTM-Analysis.Rmd’ using rmarkdown

Quitting from PTM-Analysis.Rmd:65-69 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `statement$data`:
! $ operator is invalid for atomic vectors
---
Backtrace:
    ▆
 1. └─MSstatsBioNet::getSubnetworkFromIndra(...)
 2.   └─MSstatsBioNet:::.filterIndraResponse(...)
 3.     └─base::Filter(...)
 4.       ├─base::unlist(lapply(x, f))
 5.       └─base::lapply(x, f)
 6.         └─MSstatsBioNet (local) FUN(X[[i]], ...)
 7.           └─statement$data$stmt_type %in% interaction_types
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PTM-Analysis.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘PTM-Analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘MSstatsBioNet.Rmd’ ‘PTM-Analysis.Rmd’

Error: Vignette re-building failed.
Execution halted