##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r CluMSID -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data CluMSID
###
##############################################################################
##############################################################################


* checking for file 'CluMSID/DESCRIPTION' ... OK
* preparing 'CluMSID':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'CluMSID_DI-MSMS.Rmd' using rmarkdown
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
Quitting from lines 78-80 (CluMSID_DI-MSMS.Rmd) 
Error: processing vignette 'CluMSID_DI-MSMS.Rmd' failed with diagnostics:
'arg' should be one of "pwiz", "netCDF"
--- failed re-building 'CluMSID_DI-MSMS.Rmd'

--- re-building 'CluMSID_GC-EI-MS.Rmd' using rmarkdown
Loading required package: CAMERA
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.21.6 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws


This is xcms version 3.17.3 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "CluMSID GC-EI-MS Tutorial", and the latter is "Clustering Mass Spectra from Low Resolution GC-EI-MS Data Using CluMSID". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building 'CluMSID_GC-EI-MS.Rmd'

--- re-building 'CluMSID_MTBLS.Rmd' using rmarkdown
Quitting from lines 108-123 (CluMSID_MTBLS.Rmd) 
Error: processing vignette 'CluMSID_MTBLS.Rmd' failed with diagnostics:
'arg' should be one of "pwiz", "netCDF"
--- failed re-building 'CluMSID_MTBLS.Rmd'

--- re-building 'CluMSID_lowres-LC-MSMS.Rmd' using rmarkdown
Quitting from lines 97-99 (CluMSID_lowres-LC-MSMS.Rmd) 
Error: processing vignette 'CluMSID_lowres-LC-MSMS.Rmd' failed with diagnostics:
'arg' should be one of "pwiz", "netCDF"
--- failed re-building 'CluMSID_lowres-LC-MSMS.Rmd'

--- re-building 'CluMSID_tutorial.Rmd' using rmarkdown
Quitting from lines 218-225 (CluMSID_tutorial.Rmd) 
Error: processing vignette 'CluMSID_tutorial.Rmd' failed with diagnostics:
'arg' should be one of "pwiz", "netCDF"
--- failed re-building 'CluMSID_tutorial.Rmd'

SUMMARY: processing the following files failed:
  'CluMSID_DI-MSMS.Rmd' 'CluMSID_MTBLS.Rmd'
  'CluMSID_lowres-LC-MSMS.Rmd' 'CluMSID_tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted