* checking for file 'snapCGH/DESCRIPTION' ... OK
* preparing 'snapCGH':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* installing *source* package 'snapCGH' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -fpic -g -O2 -c optimizer.c -o optimizer.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o snapCGH.so optimizer.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /tmp/Rinst929868891/snapCGH/libs
** R
** data
** inst
** preparing package for lazy loading
**************************************************************************
The data format for the CNA object will be changed in version 1.23.0
Instead of a data frame it will be a list of 3 (or more) objects
chrom and maploc will be vectors and CN/LOH data will be a matrix
**************************************************************************
######################################################################################
Have fun with GLAD
For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002)
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008)
If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)
If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)
For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg
######################################################################################
New options are available in daglad: see help for details.
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (snapCGH)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'snapCGH_1.18.0.tar.gz'