TitanCNA

Package: TitanCNA
Type: Package
Title: Subclonal copy number and LOH prediction from whole genome
sequencing of tumours
Version: 1.10.0
Date: 2016-03-09
Author: Gavin Ha, Sohrab P Shah
Maintainer: Gavin Ha <gavinha@broadinstitute.org>, Sohrab P Shah <sshah@bccrc.ca>
Depends: R (>= 3.2.0), foreach (>= 1.4.2), IRanges (>= 2.2.4),
GenomicRanges (>= 1.20.5), Rsamtools (>= 1.20.4), GenomeInfoDb
(>= 1.4.0)
Description: Hidden Markov model to segment and predict regions of
subclonal copy number alterations (CNA) and loss of
heterozygosity (LOH), and estimate cellular prevalenece of
clonal clusters in tumour whole genome sequencing data.
License: GPL-3
biocViews: Sequencing, WholeGenome, DNASeq, ExomeSeq,
StatisticalMethod, CopyNumberVariation, HiddenMarkovModel,
Genetics, GenomicVariation
URL: https://github.com/gavinha/TitanCNA
NeedsCompilation: yes
Packaged: 2016-05-04 05:26:30 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TitanCNA' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c getPositionOverlapC.c -o getPositionOverlapC.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c register.c -o register.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o TitanCNA.so fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/TitanCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TitanCNA'
    finding HTML links ... done
    TitanCNA-dataset                        html  
    TitanCNA-output                         html  
    TitanCNA-package                        html  
    TitanCNA-plotting                       html  
    computeSDbwIndex                        html  
    correctReadDepth                        html  
Rd warning: /tmp/Rtmpajfz7U/R.INSTALL76b133e4c3b5/TitanCNA/man/correctReadDepth.Rd:16: missing file link 'wigToRangedData'
Rd warning: /tmp/Rtmpajfz7U/R.INSTALL76b133e4c3b5/TitanCNA/man/correctReadDepth.Rd:57: missing file link 'wigToRangedData'
    extractAlleleReadCounts                 html  
Rd warning: /tmp/Rtmpajfz7U/R.INSTALL76b133e4c3b5/TitanCNA/man/extractAlleleReadCounts.Rd:31: missing file link 'PileupParam'
Rd warning: /tmp/Rtmpajfz7U/R.INSTALL76b133e4c3b5/TitanCNA/man/extractAlleleReadCounts.Rd:59: missing file link 'PileupParam'
    filterData                              html  
    getPositionOverlap                      html  
    loadAlleleCounts                        html  
    loadDefaultParameters                   html  
    removeEmptyClusters                     html  
    runEMclonalCN                           html  
    finding level-2 HTML links ... done

    viterbiClonalCN                         html  
    wigToRangedData                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TitanCNA)
Making 'packages.html' ... done