HMMcopy

Package: HMMcopy
Type: Package
Title: Copy number prediction with correction for GC and mappability
bias for HTS data
Version: 1.14.0
Date: 2012-08-27
Author: Daniel Lai, Gavin Ha, Sohrab Shah
Maintainer: Daniel Lai <jujubix@cs.ubc.ca>, Gavin Ha <gha@bccrc.ca>,
Sohrab Shah <sshah@bccrc.ca>
Import: IRanges
Depends: R (>= 2.10.0), IRanges (>= 1.4.16), geneplotter (>= 1.24.0)
Description: Corrects GC and mappability biases for readcounts (i.e.
coverage) in non-overlapping windows of fixed length for single
whole genome samples, yielding a rough estimate of copy number
for furthur analysis. Designed for rapid correction of high
coverage whole genome tumour and normal samples.
License: GPL-3
biocViews: Sequencing, Preprocessing, Visualization,
CopyNumberVariation, Microarray
NeedsCompilation: yes
Packaged: 2016-05-04 04:44:45 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'HMMcopy' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c forward_backward.c -o forward_backward.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 viterbi.c -o viterbi.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o HMMcopy.so forward_backward.o register.o viterbi.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/HMMcopy/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'HMMcopy'
    finding HTML links ... done
    HMMcopy-dataset                         html  
    HMMcopy-input                           html  
    HMMcopy-internal                        html  
    HMMcopy-output                          html  
    HMMcopy-package                         html  
    HMMcopy-visualize                       html  
    HMMsegment                              html  
    correctReadcount                        html  
    wigsToRangedData                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HMMcopy)
Making 'packages.html' ... done