ADaCGH2

Package: ADaCGH2
Version: 2.12.0
Date: 2016-04-29
Title: Analysis of big data from aCGH experiments using parallel
computing and ff objects
Author: Ramon Diaz-Uriarte <rdiaz02@gmail.com> and Oscar M. Rueda <rueda.om@gmail.com>. Wavelet-based aCGH smoothing code from Li Hsu <lih@fhcrc.org> and Douglas Grove <dgrove@fhcrc.org>. Imagemap code from Barry Rowlingson <B.Rowlingson@lancaster.ac.uk>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>.
Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
Depends: R (>= 3.2.0), parallel, ff, GLAD
Imports: bit, ffbase, DNAcopy, tilingArray, waveslim, cluster, aCGH,
snapCGH
Suggests: CGHregions, Cairo, limma
Enhances: Rmpi
Description: Analysis and plotting of array CGH data. Allows usage of
Circular Binary Segementation, wavelet-based smoothing
(both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar),
HMM, BioHMM, GLAD, CGHseg. Most computations are
parallelized (either via forking or with clusters, including
MPI and sockets clusters) and use ff for storing data.
biocViews: Microarray, CopyNumberVariants
LazyLoad: Yes
License: GPL (>= 3)
URL: https://github.com/rdiaz02/adacgh2
NeedsCompilation: yes
Packaged: 2016-05-04 03:48:32 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ADaCGH2' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c r_haarseg.c -o r_haarseg.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o ADaCGH2.so init.o r_haarseg.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/ADaCGH2/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ADaCGH2'
    finding HTML links ... done
    cutFile                                 html  
    inputEx                                 html  
    inputToADaCGH                           html  
Rd warning: /tmp/Rtmpn8NNnY/R.INSTALL5b9555fa0e02/ADaCGH2/man/inputToADaCGH.Rd:45: missing file link 'as.MAList'
Rd warning: /tmp/Rtmpn8NNnY/R.INSTALL5b9555fa0e02/ADaCGH2/man/inputToADaCGH.Rd:46: missing file link 'dim.SegList'
    outputToCGHregions                      html  
    pChromPlot                              html  
Rd warning: /tmp/Rtmpn8NNnY/R.INSTALL5b9555fa0e02/ADaCGH2/man/pChromPlot.Rd:142: missing file link 'clusterApplyLB'
    pSegment                                html  
Rd warning: /tmp/Rtmpn8NNnY/R.INSTALL5b9555fa0e02/ADaCGH2/man/pSegment.Rd:174: missing file link 'clusterApplyLB'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ADaCGH2)
Making 'packages.html' ... done