pRoloc

Package: pRoloc
Type: Package
Title: A unifying bioinformatics framework for spatial proteomics
Version: 1.12.4
Authors@R: c(person(given = "Laurent", family = "Gatto",
email = "lg390@cam.ac.uk",
role = c("aut","cre")),
person(given = "Lisa", family ="Breckels",
email = "lms79@cam.ac.uk",
role = "aut"),
person(given = "Samuel", family ="Wieczorek",
email = "samuel.wieczorek@cea.fr",
role = "ctb"))
Author: Laurent Gatto and Lisa M. Breckels with contributions from
Thomas Burger and Samuel Wieczorek
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
Description: This package implements pattern recognition techniques on
quantitiative mass spectrometry data to infer protein
sub-cellular localisation.
Depends: R (>= 2.15), MSnbase (>= 1.19.20), MLInterfaces (>= 1.37.1),
methods, Rcpp (>= 0.10.3), BiocParallel
Imports: Biobase, mclust (>= 4.3), caret, e1071, sampling, class,
kernlab, lattice, nnet, randomForest, proxy, FNN, BiocGenerics,
stats, RColorBrewer, scales, MASS, knitr, mvtnorm, gtools,
plyr, ggplot2, biomaRt, utils, grDevices, graphics
Suggests: testthat, pRolocdata (>= 1.9.4), roxygen2, synapter, xtable,
tsne, BiocStyle, hpar, dplyr, GO.db, AnnotationDbi
LinkingTo: Rcpp, RcppArmadillo
License: GPL-2
VignetteBuilder: knitr
Video:
https://www.youtube.com/playlist?list=PLvIXxpatSLA2loV5Srs2VBpJIYUlVJ4ow
URL: https://github.com/lgatto/pRoloc
BugReports: https://github.com/lgatto/pRoloc/issues
biocViews: Proteomics, MassSpectrometry, Classification, Clustering,
QualityControl
Collate: AllGenerics.R machinelearning-framework.R
machinelearning-framework-theta.R machinelearning-utils.R
machinelearning-functions-knn.R
machinelearning-functions-ksvm.R machinelearning-functions-nb.R
machinelearning-functions-nnet.R
machinelearning-functions-PerTurbo.R
machinelearning-functions-plsda.R
machinelearning-functions-rf.R machinelearning-functions-svm.R
machinelearning-functions-knntl.R belief.R distances.R
markers.R pRolocmarkers.R chi2.R MLInterfaces.R
clustering-framework.R MSnSet.R clustering-kmeans.R
perTurbo-algorithm.R phenodisco.R plotting.R plotting2.R
environment.R utils.R lopims.R annotation.R goenv.R go.R
makeGoSet.R vis.R MartInterface.R dynamics.R zzz.R
goannotations.R clusterdist-functions.R clusterdist-framework.R
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-06-15 03:40:44 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'pRoloc' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c pRoloc.cpp -o pRoloc.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o pRoloc.so pRoloc.o -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'pRoloc'
    finding HTML links ... done
    AnnotationParams-class                  html  
    ClustDist-class                         html  
    ClustDistList-class                     html  
    GenRegRes-class                         html  
    finding level-2 HTML links ... done

    MLearn-methods                          html  
    MartInstance-class                      html  
    SpatProtVis-class                       html  
    addGoAnnotations                        html  
    addLegend                               html  
    addMarkers                              html  
    checkFeatureNamesOverlap                html  
    checkFvarOverlap                        html  
    chi2-methods                            html  
    classWeights                            html  
    clustDist                               html  
    defunct                                 html  
    empPvalues                              html  
    exprsToRatios-methods                   html  
    fDataToUnknown                          html  
    filterBinMSnSet                         html  
    filterMaxMarkers                        html  
    filterMinMarkers                        html  
    filterZeroCols                          html  
    getGOFromFeatures                       html  
    getMarkerClasses                        html  
    getMarkers                              html  
    getNormDist                             html  
    getPredictions                          html  
    getStockcol                             html  
    goIdToTerm                              html  
    highlightOnPlot                         html  
    knnClassification                       html  
    knnOptimisation                         html  
    knntlClassification                     html  
    knntlOptimisation                       html  
    ksvmClassification                      html  
    ksvmOptimisation                        html  
    lopims                                  html  
Rd warning: /tmp/RtmpGpKWMP/R.INSTALLf7b1a6a7198/pRoloc/man/lopims.Rd:45: missing file link 'synapter'
    makeGoSet                               html  
    markerMSnSet                            html  
    markers                                 html  
    minMarkers                              html  
    move2Ds                                 html  
    nbClassification                        html  
    nbOptimisation                          html  
    nndist-methods                          html  
    nnetClassification                      html  
    nnetOptimisation                        html  
    orderGoAnnotations                      html  
    orgQuants                               html  
    pRoloc-package                          html  
    pRolocmarkers                           html  
    perTurboClassification                  html  
    perTurboOptimisation                    html  
    phenoDisco                              html  
    plot2D                                  html  
    plot2Ds                                 html  
    plotDist                                html  
    plsdaClassification                     html  
    plsdaOptimisation                       html  
    rfClassification                        html  
    rfOptimisation                          html  
    sampleMSnSet                            html  
    showGOEvidenceCodes                     html  
    subsetMarkers                           html  
    svmClassification                       html  
    svmOptimisation                         html  
    testMSnSet                              html  
    testMarkers                             html  
    thetas                                  html  
    undocumented                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pRoloc)
Making 'packages.html' ... done