podkat

Package: podkat
Type: Package
Title: Position-Dependent Kernel Association Test
Version: 1.4.2
Date: 2016-04-12
Author: Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Description: This package provides an association test that is capable
of dealing with very rare and even private variants. This is
accomplished by a kernel-based approach that takes the
positions of the variants into account. The test can be used
for pre-processed matrix data, but also directly for variant
data stored in VCF files. Association testing can be performed
whole-genome, whole-exome, or restricted to pre-defined regions
of interest. The test is complemented by tools for analyzing
and visualizing the results.
URL: http://www.bioinf.jku.at/software/podkat/
License: GPL (>= 2)
Depends: R (>= 3.2.0), methods, Rsamtools, GenomicRanges
Imports: Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils,
Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges,
Biostrings, BSgenome (>= 1.32.0)
Suggests: BSgenome.Hsapiens.UCSC.hg38.masked,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
VariantAnnotation, knitr
LinkingTo: Rcpp, Rsamtools
VignetteBuilder: knitr
Collate: AllGenerics.R AllClasses.R inputChecks.R sort-methods.R
show-methods.R print-methods.R summary-methods.R
p.adjust-methods.R c-methods.R access-methods.R
coerce-methods.R resampling.R unmaskedRegions.R
partitionRegions-methods.R genotypeMatrix-methods.R
computeKernel.R computePvalues.R readGenotypeMatrix-methods.R
readVariantInfo-methods.R readSampleNamesFromVcfHeader.R
readRegionsFromBedFile.R weightFuncs.R assocTest-methods.R
nullModel-methods.R qqplot-methods.R plot-methods.R
filterResult-methods.R split-methods.R computeWeights.R
weights-methods.R
biocViews: Genetics, WholeGenome, Annotation, VariantAnnotation,
Sequencing, DataImport
NeedsCompilation: yes
Packaged: 2016-05-16 05:21:25 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'podkat' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c R_init_podkat.cpp -o R_init_podkat.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c bernoulliExact.cpp -o bernoulliExact.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c cumMax.cpp -o cumMax.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c doubleMale.cpp -o doubleMale.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c kernels.cpp -o kernels.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c pValues.cpp -o pValues.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c partitionRegions.cpp -o partitionRegions.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c qfc.cpp -o qfc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c readVariantInfo.cpp -o readVariantInfo.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o podkat.so R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbam.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbcf.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/podkat/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'p.adjust' from package 'stats' in package 'podkat'
Creating a generic function for 'coefficients' from package 'stats' in package 'podkat'
Creating a generic function for 'qqplot' from package 'stats' in package 'podkat'
** help
*** installing help indices
  converting help for package 'podkat'
    finding HTML links ... done
    AssocTestResult-class                   html  
    AssocTestResultRanges-class             html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/AssocTestResultRanges-class.Rd:40: missing file link 'mcols'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/AssocTestResultRanges-class.Rd:40: missing file link 'elementMetadata'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/AssocTestResultRanges-class.Rd:106: missing file link 'print'
    GenotypeMatrix-class                    html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/GenotypeMatrix-class.Rd:56: missing file link 'rownames'
    NullModel-class                         html  
    VariantInfo-class                       html  
    assocTest-methods                       html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/assocTest-methods.Rd:41: missing file link 'TabixFile'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/assocTest-methods.Rd:103: missing file link 'makePSOCKcluster'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/assocTest-methods.Rd:246: missing file link 'TabixFile'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/assocTest-methods.Rd:253: missing file link 'makePSOCKcluster'
    computeKernel                           html  
    filterResult-methods                    html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/filterResult-methods.Rd:62: missing file link 'p.adjust'
    genotypeMatrix-methods                  html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/genotypeMatrix-methods.Rd:33: missing file link 'eSet'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/genotypeMatrix-methods.Rd:149: missing file link 'eSet'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/genotypeMatrix-methods.Rd:150: missing file link 'SnpSet'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/genotypeMatrix-methods.Rd:152: missing file link 'eSet'
    hgA                                     html  
    nullModel-methods                       html  
    p.adjust-methods                        html  
    partitionRegions-methods                html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/partitionRegions-methods.Rd:20: missing file link 'BSgenome'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/partitionRegions-methods.Rd:55: missing file link 'BSgenome'
    plot-methods                            html  
    podkat-package                          html  
    print-methods                           html  
    qqplot-methods                          html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/qqplot-methods.Rd:76: missing file link 'qqplot'
    readGenotypeMatrix-methods              html  
    readRegionsFromBedFile                  html  
    readSampleNamesFromVcfHeader            html  
    readVariantInfo-methods                 html  
    sort-methods                            html  
    split-methods                           html  
    unmasked-datasets                       html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmasked-datasets.Rd:30: missing file link 'pseudoautosomal.hg18'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmasked-datasets.Rd:31: missing file link 'pseudoautosomal.hg19'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmasked-datasets.Rd:32: missing file link 'pseudoautosomal.hg38'
    unmaskedRegions                         html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:6: missing file link 'BSgenome'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:13: missing file link 'BSgenome'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:19: missing file link 'pseudoautosomal.hg18'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:20: missing file link 'pseudoautosomal.hg19'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:21: missing file link 'pseudoautosomal.hg38'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:29: missing file link 'BSgenome'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:34: missing file link 'BSgenome'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:47: missing file link 'BSgenome'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:51: missing file link 'pseudoautosomal.hg18'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:52: missing file link 'pseudoautosomal.hg19'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/unmaskedRegions.Rd:53: missing file link 'pseudoautosomal.hg38'
    weightFuncs                             html  
    weights-methods                         html  
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/weights-methods.Rd:20: missing file link 'TabixFile'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/weights-methods.Rd:65: missing file link 'TabixFile'
Rd warning: /tmp/RtmpyeC9aB/R.INSTALL233a542f8479/podkat/man/weights-methods.Rd:92: missing file link 'TabixFile'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (podkat)
Making 'packages.html' ... done