Last data update: 2014.03.03
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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
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