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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data msPurity
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* checking for file ‘msPurity/DESCRIPTION’ ... OK
* preparing ‘msPurity’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’ using rmarkdown
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.20.4
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
This is xcms version 3.16.1
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Warning in .local(object, ...) :
It looks like this file is in profile mode. centWave can process only centroid mode data !
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 16399 regions of interest ... OK: 9961 found.
Warning in .local(object, ...) :
It looks like this file is in profile mode. centWave can process only centroid mode data !
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 16425 regions of interest ... OK: 9896 found.
Warning in .local(object, ...) :
It looks like this file is in profile mode. centWave can process only centroid mode data !
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 71125 regions of interest ... OK: 32825 found.
Warning in .local(object, ...) :
It looks like this file is in profile mode. centWave can process only centroid mode data !
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 71486 regions of interest ... OK: 32736 found.
Processing 11756 mz slices ... OK
Attaching package: 'magrittr'
The following object is masked from 'package:msPurity':
subtract
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 1996 regions of interest ... OK: 368 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 2104 regions of interest ... OK: 432 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3234 regions of interest ... OK: 1107 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3284 regions of interest ... OK: 1111 found.
Processing 11756 mz slices ... OK
only MS1 data
No MS/MS spectra for file: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/msPurityData/extdata/lcms/mzML/LCMS_1.mzML
only MS1 data
No MS/MS spectra for file: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/msPurityData/extdata/lcms/mzML/LCMS_2.mzML
convert2RawRT == TRUE but retention time alignment not applied to xcmsObj. Using raw retention times for features
Creating a database of fragmentation spectra and LC features
--- finished re-building ‘msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd’
--- re-building ‘msPurity-spectral-database-vignette.Rmd’ using rmarkdown
--- finished re-building ‘msPurity-spectral-database-vignette.Rmd’
--- re-building ‘msPurity-vignette.Rmd’ using rmarkdown
only MS1 data
No MS/MS spectra for file: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/msPurityData/extdata/lcms/mzML/LCMS_1.mzML
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 1996 regions of interest ... OK: 368 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 2104 regions of interest ... OK: 432 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3234 regions of interest ... OK: 1107 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3284 regions of interest ... OK: 1111 found.
Processing 11756 mz slices ... OK
convert2RawRT == TRUE but retention time alignment not applied to xcmsObj. Using raw retention times for features
Sizes of mz and intensity arrays don't match.
Quitting from lines 175-176 (msPurity-vignette.Rmd)
Error: processing vignette 'msPurity-vignette.Rmd' failed with diagnostics:
dims [product 4516] do not match the length of object [2258]
--- failed re-building ‘msPurity-vignette.Rmd’
SUMMARY: processing the following file failed:
‘msPurity-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
