MSnID

Package: MSnID
Type: Package
Title: Utilities for Exploration and Assessment of Confidence of LC-MSn
Proteomics Identifications.
Version: 1.6.0
Author: Vlad Petyuk with contributions from Laurent Gatto
Maintainer: Vlad Petyuk <petyuk@gmail.com>
Description: Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or
text files. After collating the search results from multiple datasets it
assesses their identification quality and optimize filtering criteria to
achieve the maximum number of identifications while not exceeding a
specified false discovery rate. Also contains a number of utilities to
explore the MS/MS results and assess missed and irregular enzymatic
cleavages, mass measurement accuracy, etc.
License: Artistic-2.0
Depends: R (>= 2.10), Rcpp
Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach,
doParallel, parallel, reshape2, methods, iterators, data.table,
Biobase, ProtGenerics
Suggests: BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics
LazyData: yes
biocViews: Proteomics, MassSpectrometry
NeedsCompilation: no
Packaged: 2016-05-04 05:46:21 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MSnID' ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Warning: replacing previous import 'reshape2::melt' by 'data.table::melt' when loading 'MSnID'
Warning: replacing previous import 'reshape2::dcast' by 'data.table::dcast' when loading 'MSnID'
Creating a generic function for 'update' from package 'stats' in package 'MSnID'
** help
*** installing help indices
  converting help for package 'MSnID'
    finding HTML links ... done
    MSnID-class                             html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/MSnID-class.Rd:65: missing file link 'R.cache'
Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/MSnID-class.Rd:81: missing file link 'R.cache'
Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/MSnID-class.Rd:102: missing file link 'proteins'
Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/MSnID-class.Rd:188: missing file link 'MSnSet'
    MSnID-package                           html  
    MSnIDFilter-class                       html  
Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/MSnIDFilter-class.Rd:86: missing file link 'MSnSet'
    accessions                              html  
    apply_filter                            html  
Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/apply_filter.Rd:20: missing file link 'MSnIDFilter'
    assess_missed_cleavages                 html  
    assess_termini                          html  
    correct_peak_selection                  html  
    data                                    html  
    evaluate_filter                         html  
    id_quality                              html  
    mass_measurement_error                  html  
    optimize_filter                         html  
Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/optimize_filter.Rd:67: missing file link 'R.cache'
    peptides                                html  
    psms                                    html  
    read_mzIDs                              html  
Rd warning: /tmp/RtmpaReUGj/R.INSTALL7954157eb471/MSnID/man/read_mzIDs.Rd:11: missing file link 'R.cache'
    recalibrate                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'reshape2::melt' by 'data.table::melt' when loading 'MSnID'
Warning: replacing previous import 'reshape2::dcast' by 'data.table::dcast' when loading 'MSnID'
* DONE (MSnID)
Making 'packages.html' ... done