isobar

Package: isobar
Title: Analysis and quantitation of isobarically tagged MSMS proteomics
data
Description: isobar provides methods for preprocessing, normalization, and
report generation for the analysis of quantitative mass spectrometry
proteomics data labeled with isobaric tags, such as iTRAQ and TMT.
Features modules for integrating and validating PTM-centric datasets
(isobar-PTM). More information on http://www.ms-isobar.org.
Version: 1.18.0
Author: Florian P Breitwieser <florian.bw@gmail.com> and
Jacques Colinge <jacques.colinge@inserm.fr>, with contributions from
Alexey Stukalov <stukalov@biochem.mpg.de>,
Xavier Robin <xavier.robin@unige.ch> and Florent Gluck <florent.gluck@unige.ch>
Maintainer: Florian P Breitwieser <florian.bw@gmail.com>
biocViews: Proteomics, MassSpectrometry, Bioinformatics,
MultipleComparisons, QualityControl
Depends: R (>= 2.10.0), Biobase, stats, methods
Imports: distr, plyr
Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2, RJSONIO, Hmisc,
gplots, RColorBrewer, gridExtra, limma, boot, distr, DBI, MASS
LazyLoad: yes
License: LGPL-2
URL: https://github.com/fbreitwieser/isobar
BugReports: https://github.com/fbreitwieser/isobar/issues
Collate: utils.R ProteinGroup-class.R IBSpectra-class.R isobar-import.R
IBSpectra-plots.R NoiseModel-class.R Tlsd-class.R
ratio-methods.R distr-methods.R sharedpep-methods.R
report-utils-xls.R report-utils-tex.R report-utils.R
metareport-utils.R ptm-methods.R MSnSet-methods.R zzz.R
NeedsCompilation: no
Packaged: 2016-05-04 04:17:45 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'isobar' ...
** R
** data
** inst
** preparing package for lazy loading
in method for 'coerce' with signature '"MSnSet","IBSpectra"': no definition for class "MSnSet"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "MSnSet"
** help
*** installing help indices
  converting help for package 'isobar'
    finding HTML links ... done
    IBSpectra-class                         html  
    finding level-2 HTML links ... done

Rd warning: /tmp/Rtmp7ImFKV/R.INSTALL49c9280319b3/isobar/man/IBSpectra-class.Rd:175: missing file link 'MSnSet'
Rd warning: /tmp/Rtmp7ImFKV/R.INSTALL49c9280319b3/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase'
Rd warning: /tmp/Rtmp7ImFKV/R.INSTALL49c9280319b3/isobar/man/IBSpectra-class.Rd:178: missing file link 'MSnSet'
Rd warning: /tmp/Rtmp7ImFKV/R.INSTALL49c9280319b3/isobar/man/IBSpectra-class.Rd:232: missing file link 'ProteinGroup'
    NoiseModel-class                        html  
    ProteinGroup-class                      html  
Rd warning: /tmp/Rtmp7ImFKV/R.INSTALL49c9280319b3/isobar/man/ProteinGroup-class.Rd:177: missing file link 'IBSpectra'
    TlsParameter-class                      html  
    Tlsd-class                              html  
    calc.delta.score                        html  
    calc.startpos                           html  
    calculate-pvalues                       html  
    calculate.dNSAF                         html  
    calculate.emPAI                         html  
    correct.peptide.ratios                  html  
    distr-methods                           html  
    fit-distr                               html  
Rd warning: /tmp/Rtmp7ImFKV/R.INSTALL49c9280319b3/isobar/man/fit-distr.Rd:28: missing file link 'Cauchy'
Rd warning: /tmp/Rtmp7ImFKV/R.INSTALL49c9280319b3/isobar/man/fit-distr.Rd:28: missing file link 'Norm'
    getPeptideModifContext                  html  
    getPhosphoRSProbabilities               html  
    getPtmInfo                              html  
    groupMemberPeptides                     html  
    human.protein.names                     html  
    isobar-analysis                         html  
    isobar-data                             html  
    isobar-import                           html  
    isobar-log                              html  
    isobar-package                          html  
    isobar-plots                            html  
    isobar-preprocessing                    html  
    isobar-reports                          html  
    maplot.protein                          html  
    number.ranges                           html  
    observedKnownSites                      html  
    peptide.count                           html  
    proteinInfo-methods                     html  
    proteinNameAndDescription               html  
    ratio-summ                              html  
    ratiosReshapeWide                       html  
    reporter.protein-methods                html  
    sanitize                                html  
    shared.ratios                           html  
    shared.ratios.sign                      html  
    specificities                           html  
    spectra.count2                          html  
    subsetIBSpectra                         html  
    utils                                   html  
    writeHscoreData                         html  
    writeIBSpectra                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (isobar)
Making 'packages.html' ... done