crlmm

Package: crlmm
Type: Package
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Version: 1.30.0
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
Ruczinski, Rafael A Irizarry
Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie
<mritchie@wehi.EDU.AU>
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
arrays, as well as a copy number tool specific to 5.0, 6.0, and
Illumina platforms
License: Artistic-2.0
Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
1.17.7)
LinkingTo: preprocessCore (>= 1.17.7)
Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
matrixStats, VGAM, parallel
Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
RUnit
Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R
snprma-functions.R utils.R zzz.R test_crlmm_package.R
LazyLoad: yes
## Local Variables:
## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
## End:
biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation
NeedsCompilation: yes
Packaged: 2016-05-04 03:14:37 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'crlmm' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c gtypeCaller.c -o gtypeCaller.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c init.c -o init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c trimmed.c -o trimmed.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c utils.c -o utils.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/crlmm/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'crlmm'
    finding HTML links ... done
    ABpanel                                 html  
Rd warning: /tmp/RtmpAIqcki/R.INSTALL5c63d59b66b/crlmm/man/ABpanel.Rd:57: missing file link 'lpolygon'
    AssayData-methods                       html  
    finding level-2 HTML links ... done

    CNSet-methods                           html  
    ListClassConstructors                   html  
    PredictionRegion-class                  html  
    batchStatisticAccessors                 html  
    calculateRBaf                           html  
    celfile-utils                           html  
    cnSetExample                            html  
    cnrmaAffy                               html  
    constructAffyCNSet                      html  
    constructInf                            html  
    copynumberAccessors                     html  
    crlmm-package                           html  
    crlmm                                   html  
    crlmmCopynumber                         html  
    crlmmIllumina                           html  
    crlmmIlluminaV2                         html  
    genotype.Illumina                       html  
Rd warning: /tmp/RtmpAIqcki/R.INSTALL5c63d59b66b/crlmm/man/genotype.Illumina.Rd:135: missing file link 'ocSamples'
    genotype                                html  
Rd warning: /tmp/RtmpAIqcki/R.INSTALL5c63d59b66b/crlmm/man/genotype.Rd:88: missing file link 'ocSamples'
    genotypeAffy                            html  
    genotypeInf                             html  
    genotypes                               html  
    posteriorProbability                    html  
    predictionRegion                        html  
    preprocessInf                           html  
    readGenCallOutput                       html  
    readIdatFiles                           html  
    snprma                                  html  
    snprmaAffy                              html  
    validCdfNames                           html  
    xyplot                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (crlmm)
Making 'packages.html' ... done