snapCGH 1.18.0
John Marioni
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/snapCGH | | Last Changed Rev: 47149 / Revision: 49923 | | Last Changed Date: 2010-05-26 11:24:55 -0700 (Wed, 26 May 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
INSTALLATION WITH 'R CMD INSTALL --preclean --library=snapCGH.buildbin-libdir snapCGH_1.18.0.tar.gz'
* installing *source* package ‘snapCGH’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c optimizer.c -o optimizer.o
optimizer.c: In function ‘fr_two’:
optimizer.c:26: warning: unused variable ‘temp3’
optimizer.c:26: warning: unused variable ‘temp2’
optimizer.c:26: warning: unused variable ‘denom’
optimizer.c: In function ‘fr_three’:
optimizer.c:195: warning: unused variable ‘temp3’
optimizer.c:195: warning: unused variable ‘temp2’
optimizer.c:195: warning: unused variable ‘denom’
optimizer.c:194: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_four’:
optimizer.c:413: warning: unused variable ‘temp3’
optimizer.c:413: warning: unused variable ‘temp2’
optimizer.c:413: warning: unused variable ‘denom’
optimizer.c:412: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_five’:
optimizer.c:687: warning: unused variable ‘temp3’
optimizer.c:687: warning: unused variable ‘temp2’
optimizer.c:687: warning: unused variable ‘denom’
optimizer.c:686: warning: unused variable ‘alphahat’
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c optimizer.c -o optimizer.o
optimizer.c: In function ‘fr_two’:
optimizer.c:26: warning: unused variable ‘temp3’
optimizer.c:26: warning: unused variable ‘temp2’
optimizer.c:26: warning: unused variable ‘denom’
optimizer.c: In function ‘fr_three’:
optimizer.c:195: warning: unused variable ‘temp3’
optimizer.c:195: warning: unused variable ‘temp2’
optimizer.c:195: warning: unused variable ‘denom’
optimizer.c:194: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_four’:
optimizer.c:413: warning: unused variable ‘temp3’
optimizer.c:413: warning: unused variable ‘temp2’
optimizer.c:413: warning: unused variable ‘denom’
optimizer.c:412: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_five’:
optimizer.c:687: warning: unused variable ‘temp3’
optimizer.c:687: warning: unused variable ‘temp2’
optimizer.c:687: warning: unused variable ‘denom’
optimizer.c:686: warning: unused variable ‘alphahat’
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c optimizer.c -o optimizer.o
optimizer.c: In function ‘fr_two’:
optimizer.c:26: warning: unused variable ‘temp3’
optimizer.c:26: warning: unused variable ‘temp2’
optimizer.c:26: warning: unused variable ‘denom’
optimizer.c: In function ‘fr_three’:
optimizer.c:195: warning: unused variable ‘temp3’
optimizer.c:195: warning: unused variable ‘temp2’
optimizer.c:195: warning: unused variable ‘denom’
optimizer.c:194: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_four’:
optimizer.c:413: warning: unused variable ‘temp3’
optimizer.c:413: warning: unused variable ‘temp2’
optimizer.c:413: warning: unused variable ‘denom’
optimizer.c:412: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_five’:
optimizer.c:687: warning: unused variable ‘temp3’
optimizer.c:687: warning: unused variable ‘temp2’
optimizer.c:687: warning: unused variable ‘denom’
optimizer.c:686: warning: unused variable ‘alphahat’
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x86_64
** 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)