isobar 1.6.0
Florian P Breitwieser
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/isobar | | Last Changed Rev: 76007 / Revision: 76155 | | Last Changed Date: 2013-04-24 12:21:49 -0700 (Wed, 24 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | ERROR | skipped | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ERROR | skipped | skipped |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | ERROR | skipped | skipped |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | [ ERROR ] | skipped | skipped |
* checking for file 'isobar/DESCRIPTION' ... OK
* preparing 'isobar':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... 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 object is masked from 'package:stats':
xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: plyr
Welcome to isobar (v 1.6.0)
'openVignette("isobar")' and '?isobar' provide help on usage.
Attaching package: 'isobar'
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 in .local(x, peptide, ...) :
don't know how to handle matrix with 3 columns! expecting 2.
Warning in .local(x, peptide, ...) :
don't know how to handle matrix with 3 columns! expecting 2.
Warning in .local(x, peptide, ...) :
don't know how to handle matrix with 3 columns! expecting 2.
Warning in .local(x, peptide, ...) :
don't know how to handle matrix with 3 columns! expecting 2.
Warning in .local(x, peptide, ...) :
don't know how to handle matrix with 3 columns! expecting 2.
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: 0.7861
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 115: 0.9305
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 116: 0.9657
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 12 (label = calc-noisemodel)
Error in as.data.frame.default(proteinGroup(x)) :
cannot coerce class "structure("ProteinGroup", package = "isobar")" to a data.frame
Execution halted