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