MSnbase

Package: MSnbase
Title: Base Functions and Classes for MS-based Proteomics
Version: 1.20.7
Description: Basic plotting, data manipulation and processing
of MS-based Proteomics data.
Authors@R: c(person(given = "Laurent", family = "Gatto",
email = "lg390@cam.ac.uk",
role = c("aut","cre")),
person(given = "Guangchuang", family ="Yu",
email = "guangchuangyu@gmail.com",
role = "ctb"),
person(given = "Samuel", family ="Wieczorek",
email = "samuel.wieczorek@cea.fr",
role = "ctb"),
person(given = "Vasile-Cosmin", family ="Lazar",
email = "v.cosmin.lazar@googlemail.com",
role = "ctb"),
person(given = "Vladislav", family ="Petyuk",
email = "petyuk@gmail.com",
role = "ctb"),
person(given = "Thomas", family ="Naake",
email = "tn299@cam.ac.uk",
role = "ctb"),
person(given = "Richie", family ="Cotton",
email = "richierocks@gmail.com",
role = "ctb"),
person(given = "Martina", family ="Fischer",
email = "FischerM@rki.de",
role = "ctb"),
person(given = "Gibb", family ="Sebastian",
email = "mail@sebastiangibb.de",
role = "ctb"))
Author: Laurent Gatto <lg390@cam.ac.uk> with contributions from
Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar,
Vladislav Petyuk, Thomas Naake, Richie Cotton, Martina Fisher
and Sebastian Gibb.
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
Depends: R (>= 3.1), methods, BiocGenerics (>= 0.7.1), Biobase (>=
2.15.2), mzR, BiocParallel, ProtGenerics (>= 1.3.1)
Imports: plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4,
affy, impute, pcaMethods, mzID (>= 1.5.2), MALDIquant (>=
1.12), digest, lattice, ggplot2, S4Vectors, Rcpp
Suggests: testthat, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc,
pRolocdata (>= 1.7.1), msdata, roxygen2, rgl, BiocStyle,
imputeLCMD, norm, gplots, shiny
LinkingTo: Rcpp
License: Artistic-2.0
LazyData: yes
VignetteBuilder: knitr
BugReports: https://github.com/lgatto/MSnbase/issues
URL: https://github.com/lgatto/MSnbase
biocViews: Infrastructure, Proteomics, MassSpectrometry,
QualityControl, DataImport
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-26 02:50:18 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MSnbase' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o MSnbase.so RcppExports.o imp_neighbour_avg.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for 'smooth' in package 'MSnbase'
Creating a new generic function for 'trimws' in package 'MSnbase'
Creating a generic function for 't' from package 'base' in package 'MSnbase'
Creating a generic function for 'scale' from package 'base' in package 'MSnbase'
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
Creating a generic function for 'split' from package 'base' in package 'MSnbase'
** inst
** preparing package for lazy loading
Creating a new generic function for 'smooth' in package 'MSnbase'
Creating a new generic function for 'trimws' in package 'MSnbase'
Creating a generic function for 't' from package 'base' in package 'MSnbase'
Creating a generic function for 'scale' from package 'base' in package 'MSnbase'
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
Creating a generic function for 'split' from package 'base' in package 'MSnbase'
** help
*** installing help indices
  converting help for package 'MSnbase'
    finding HTML links ... done
    FeatComp-class                          html  
    FeaturesOfInterest-class                html  
    finding level-2 HTML links ... done

    MIAPE-class                             html  
    MSmap-class                             html  
    MSnExp-class                            html  
    MSnProcess-class                        html  
    MSnSet-class                            html  
Rd warning: /tmp/Rtmp5pR5PW/R.INSTALL38f2631d54c/MSnbase/man/MSnSet-class.Rd:416: missing file link 'write.exprs'
    MSnSetList-class                        html  
    MSnbase-package                         html  
    MzTab-class                             html  
    NAnnotatedDataFrame-class               html  
    ReporterIons-class                      html  
    Spectrum-class                          html  
    Spectrum1-class                         html  
    Spectrum2-class                         html  
    TMT6                                    html  
    addIdentificationData-methods           html  
    averageMSnSet                           html  
    bin-methods                             html  
    calculateFragments-methods              html  
    chromatogram-methods                    html  
    clean-methods                           html  
    combineFeatures                         html  
    commonFeatureNames                      html  
    compareMSnSets                          html  
    compareSpectra-methods                  html  
    defunct                                 html  
    estimateNoise-method                    html  
Rd warning: /tmp/Rtmp5pR5PW/R.INSTALL38f2631d54c/MSnbase/man/estimateNoise-method.Rd:45: missing file link 'estimateNoise'
    exprsToRatios-methods                   html  
    extractPrecSpectra-methods              html  
    featureCV                               html  
    fillUp                                  html  
    formatRt                                html  
    get.amino.acids                         html  
    get.atomic.mass                         html  
    getVariableName                         html  
    grepEcols                               html  
    iPQF                                    html  
    iTRAQ4                                  html  
    imageNA2                                html  
    impute-methods                          html  
    itraqdata                               html  
    listOf                                  html  
    makeNaData                              html  
    missing-data                            html  
    nQuants                                 html  
    naplot                                  html  
    normalise-methods                       html  
    npcv                                    html  
    pSet-class                              html  
    pickPeaks-method                        html  
    plot-methods                            html  
    plot2d-methods                          html  
    plotDensity-methods                     html  
    plotMzDelta-methods                     html  
    plotNA-methods                          html  
    plotSpectrumSpectrum-methods            html  
    precSelection                           html  
    purityCorrect-methods                   html  
    quantify-methods                        html  
    readMSData                              html  
    readMSnSet                              html  
    readMgfData                             html  
    readMzTabData                           html  
    readMzTabData_v0.9                      html  
    removeNoId-methods                      html  
    removePeaks-methods                     html  
    removeReporters-methods                 html  
    selectFeatureData                       html  
    smooth-methods                          html  
    trimMz-methods                          html  
    writeMgfData-methods                    html  
    xic-methods                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)
Making 'packages.html' ... done