##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r isobar -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data isobar
###
##############################################################################
##############################################################################
* checking for file 'isobar/DESCRIPTION' ... OK
* preparing 'isobar':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Welcome to isobar (v 1.19.0)
'openVignette("isobar")' and '?isobar' provide help on usage.
Attaching package: 'isobar'
The following object is masked from 'package:BiocGenerics':
normalize
The following object is masked from 'package:base':
paste0
Loading required package: ggplot2
ratios 116 vs 114
Warning in .local(x, peptide, ...) :
No spectra for peptide AFVEDSEDEDGAGEGGSSLLQK; modif = iTRAQ4plex_Nterm::::::PHOS::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide APKPPTDGSTSPTSTPSEDQEALGK; modif = iTRAQ4plex_Nterm:::iTRAQ4plex_K::::::::::::::PHOS::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide AQTPPGPSLSGSK; modif = iTRAQ4plex_Nterm:::PHOS::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide ASALLPGVLGSETLSNEVFQESEEEK; modif = iTRAQ4plex_Nterm::PHOS:::::::::PHOS::PHOS:::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide AYSTENYSLESQK; modif = iTRAQ4plex_Nterm:::::::::::PHOS::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK; modif = iTRAQ4plex_Nterm:::::::::::::::PHOS:::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide ESSPLYSPTFSDSTSAVK; modif = iTRAQ4plex_Nterm:::::::::::::::PHOS:::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide ETGTDGLLAGSQEHDPGQGSSSPEQAGSPTEGEGVSTWESFK; modif = iTRAQ4plex_Nterm::::::::::::::::::::::::::::PHOS::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide GHYEVTGSDDETGK; modif = iTRAQ4plex_Nterm::::::::::::PHOS::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide GTEASSGTEAATGLEGEEK; modif = iTRAQ4plex_Nterm::PHOS:::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide KTSPASLDFPESQK; modif = iTRAQ4plex_Nterm:iTRAQ4plex_K:::::::::::PHOS::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide LAQDSQQGGMESPQVEADSGDGDSSEYQDGK; modif = iTRAQ4plex_Nterm:::::PHOS::::::::::::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide LELNDSVNENSDTVGQLVHYLMK; modif = iTRAQ4plex_Nterm::::::PHOS:::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide LNPYMSSPCHLEMLLTEK; modif = iTRAQ4plex_Nterm:::::Oxidation_M::::Cys_CAM::::Oxidation_M:::PHOS::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide LSGGHSLHETSTVLVETVTK; modif = iTRAQ4plex_Nterm::PHOS::::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide MVLQGPSSPQGEAMVTDVLEDQK; modif = iTRAQ4plex_Nterm::::::::::::::Oxidation_M::PHOS:::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide QLHLEGASLELSDDDTESK; modif = iTRAQ4plex_Nterm::::::::PHOS:::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SHLSDQSPLSSK; modif = iTRAQ4plex_Nterm:PHOS:::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SLKYDSLLEQGLVEAALVSK; modif = iTRAQ4plex_Nterm:::iTRAQ4plex_K::::::::::::::::PHOS:iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SLTPPPSSTESK; modif = iTRAQ4plex_Nterm:::::::::::PHOS:iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SPGSPVGEGTGSPPK; modif = iTRAQ4plex_Nterm::::::::::::PHOS:::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SQDADSPGSSGAPENLTFK; modif = iTRAQ4plex_Nterm:::::::::::::::::PHOS::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SQSSDTEQQSPTSGGGK; modif = iTRAQ4plex_Nterm::::::::::PHOS:::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SQSSDTEQQSPTSGGGK; modif = iTRAQ4plex_Nterm::::::::::::PHOS:PHOS::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SRSPSTESQLMSK; modif = iTRAQ4plex_Nterm::::::::::::PHOS:iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SSGHSSSELSPDAVEK; modif = iTRAQ4plex_Nterm::::::::::PHOS::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide SSSSPTEATEK; modif = iTRAQ4plex_Nterm:::::::::PHOS::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide STSFRGGMGSGGLATGLAGGLAGMGGLQNEK; modif = iTRAQ4plex_Nterm:PHOS:::::::Oxidation_M::::::::::::::::Oxidation_M:::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide TASLSSSPSEGTPTVGSYGCTPQSLPK; modif = iTRAQ4plex_Nterm:PHOS:::::::::::::::::::Cys_CAM:::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide TLGGGDDSFNTFFSETGAGK; modif = iTRAQ4plex_Nterm:PHOS:::::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide TPVQYSQQQNSPQK; modif = iTRAQ4plex_Nterm:PHOS:::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide VLHFVSGETMEEYSTDEDEVDGLEK; modif = iTRAQ4plex_Nterm::::::PHOS:::PHOS::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide VQGEAVSNLQENTQTPTVQEESEEEEVDETGVEVK; modif = iTRAQ4plex_Nterm:::::::PHOS::::::::::::::::::::::::::::iTRAQ4plex_K:
Warning in .local(x, peptide, ...) :
No spectra for peptide YSPTSPTYSPTSPK; modif = iTRAQ4plex_Nterm::::::::::::PHOS::iTRAQ4plex_K:
Warning: Removed 67 rows containing non-finite values (stat_bin).
Warning in .local(x, peptide, ...) :
not all colnames of peptide [peptide;modif;correct.ratio] in fData(x)
Warning in .local(x, peptide, ...) :
not all colnames of peptide [peptide;modif;correct.ratio] in fData(x)
Warning in .local(x, peptide, ...) :
not all colnames of peptide [peptide;modif;correct.ratio] in fData(x)
Warning in .local(x, peptide, ...) :
not all colnames of peptide [peptide;modif;correct.ratio] in fData(x)
Warning in .local(x, peptide, ...) :
not all colnames of peptide [peptide;modif;correct.ratio] in fData(x)
Warning: Removed 3341 rows containing non-finite values (stat_bin).
LOG: isotopeImpurities.corrected: TRUE
LOG: is.normalized: TRUE
normalizing ibspiked_set1.ibspectra.csv [14991 spectra]
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 114: 0.834
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 115: 0.9252
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 116: 0.9464
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 117: 1
Warning in .local(x, channel1, channel2, ...) : removing 481 NA points
Warning in .local(x, channel1, channel2, ...) : removing 481 NA points
Error: processing vignette 'isobar.Rnw' failed with diagnostics:
chunk 20 (label = calc-noisemodel)
Error in .validate_assayDataElementReplace(obj, value) :
object and replacement value have different dimensions
Execution halted