beadarray

Package: beadarray
Title: Quality assessment and low-level analysis for Illumina BeadArray
data
Version: 2.22.2
Date: 2015-04-09
Author: Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie
Maintainer: Mark Dunning <Mark.Dunning@cruk.cam.ac.uk>
Description: The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8),
methods, ggplot2
Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio
Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
License: GPL-2
biocViews: Microarray, OneChannel, QualityControl, Preprocessing
LazyData: yes
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-05-16 01:41:02 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'beadarray' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BASH.c -o BASH.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c HULK.c -o HULK.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c findAllOutliers.c -o findAllOutliers.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c imageProcessing.c -o imageProcessing.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'beadarray'
    finding HTML links ... done
    BASH                                    html  
    BASHCompact                             html  
    BASHDiffuse                             html  
    BASHExtended                            html  
    GEO                                     html  
    GEOtemplate                             html  
    HULK                                    html  
    addFeatureData                          html  
    annotationInterface                     html  
    backgroundCorrectSingleSection          html  
    beadarray-package                       html  
    beadarrayUsersGuide                     html  
    boxplot                                 html  
    calculateDetection                      html  
    calculateOutlierStats                   html  
    checkRegistration                       html  
    class-BeadLevelList                     html  
    class-ExpressionSetIllumina             html  
    class-beadLevelData                     html  
    class-beadRegistrationData              html  
    class-illuminaChannel                   html  
    class-limmaResults                      html  
    combine                                 html  
    controlProbeDetection                   html  
    convertBeadLevelList                    html  
    createTargetsFile                       html  
    deprecatedFunctions                     html  
    dim                                     html  
    expressionQCPipeline                    html  
    generateNeighbours                      html  
    getBeadData                             html  
    identifyControlBeads                    html  
    illuminaOutlierMethod                   html  
    imageProcessing                         html  
    imageplot                               html  
    insertBeadData                          html  
    insertSectionData                       html  
    limmaDE                                 html  
Rd warning: /tmp/RtmpUfyKxx/R.INSTALL7f6e254f6a3c/beadarray/man/limmaDE.Rd:32: missing file link 'eBayes'
    makeControlProfile                      html  
    makeQCTable                             html  
    maplots                                 html  
    medianNormalise                         html  
    metrics                                 html  
    noOutlierMethod                         html  
    normaliseIllumina                       html  
    numBeads                                html  
    outlierplot                             html  
    platformSigs                            html  
    plotBeadIntensities                     html  
    plotBeadLocations                       html  
    plotChipLayout                          html  
    plotMAXY                                html  
    plotTIFF                                html  
    poscontPlot                             html  
    processSwathData                        html  
    quickSummary                            html  
    readBeadSummaryData                     html  
    readIdatFiles                           html  
    readIllumina                            html  
    readLocsFile                            html  
    readTIFF                                html  
    sampleSheet                             html  
    sectionNames                            html  
    setWeights                              html  
    show                                    html  
    showArrayMask                           html  
    squeezedVarOutlierMethod                html  
    summarize                               html  
    transformationFunctions                 html  
    weightsOutlierMethod                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beadarray)
Making 'packages.html' ... done