Back to "Blame Jeroen" build/check report for BioC 3.11

BUILD report for MSnbase on tokay2

This page was generated on 2020-04-15 03:20:15 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE MSnbase PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 55/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.13.6
Laurent Gatto
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/MSnbase
Branch: master
Last Commit: 6d41fd1
Last Changed Date: 2020-04-14 10:17:32 -0400 (Tue, 14 Apr 2020)
tokay2 Windows Server 2012 R2 Standard / x64  OK [ ERROR ] skipped  skipped 

Summary

Package: MSnbase
Version: 2.13.6
Command: chmod a+r MSnbase -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MSnbase
StartedAt: 2020-04-14 20:21:11 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 20:33:29 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 738.2 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r MSnbase -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MSnbase
###
##############################################################################
##############################################################################


* checking for file 'MSnbase/DESCRIPTION' ... OK
* preparing 'MSnbase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'v01-MSnbase-demo.Rmd' using rmarkdown
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/mapheat-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/map3d-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/map3d2-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/spectrumPlot-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/msnexpPlot-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/chromPlot-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/idvis-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/fragplot-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/spectrum-clean-plot-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/preprocPlot-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v01-MSnbase-demo_files/figure-html/quantitationPlot-1.png" but not available.
Warning: file MRM-standmix-5.mzML.gz contains multiple chromatograms with identical polarity, precursor and product m/z values
Quitting from lines 1060-1067 (v01-MSnbase-demo.Rmd) 
Error: processing vignette 'v01-MSnbase-demo.Rmd' failed with diagnostics:
there is no package called 'Rdisop'
--- failed re-building 'v01-MSnbase-demo.Rmd'

--- re-building 'v02-MSnbase-io.Rmd' using rmarkdown
--- finished re-building 'v02-MSnbase-io.Rmd'

--- re-building 'v03-MSnbase-centroiding.Rmd' using rmarkdown
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/serine-plot-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/serine-spectrum24-1.png" but not available.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 632. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 670. Returning empty spectrum.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/simple-pickPeaks-1.png" but not available.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 596. Returning empty spectrum.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/proline-1.png" but not available.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/smoothSG-pp-serine-1.png" but not available.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 597. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/smoothSG-pp-proline-1.png" but not available.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 596. Returning empty spectrum.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/proline-rtsmooth-1.png" but not available.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 669. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/refineMz-serine-1.png" but not available.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 632. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 670. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 639. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 640. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 106.039871 and 106.059871 for spectrum with
acquisition number 669. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 597. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 597. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/refineMz-proline-1.png" but not available.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 596. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 597. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 592. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 593. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 594. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 595. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 116.060608 and 116.080608 for spectrum with
acquisition number 597. Returning empty spectrum.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
Warning in smooth_Spectrum(x, method = match.arg(method), halfWindowSize = halfWindowSize,  :
  Negative intensities generated. Replaced by zeros.
--- finished re-building 'v03-MSnbase-centroiding.Rmd'

--- re-building 'v04-benchmarking.Rmd' using rmarkdown
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpmQxcoC/Rbuild1ee457d2287f/MSnbase/vignettes/v04-benchmarking_files/figure-html/plot1-1.png" but not available.
--- finished re-building 'v04-benchmarking.Rmd'

--- re-building 'v05-MSnbase-development.Rmd' using rmarkdown
--- finished re-building 'v05-MSnbase-development.Rmd'

SUMMARY: processing the following file failed:
  'v01-MSnbase-demo.Rmd'

Error: Vignette re-building failed.
Execution halted