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Package 427/472HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.23.0
John Marioni
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snapCGH
Last Changed Rev: 54810 / Revision: 56351
Last Changed Date: 2011-04-13 18:14:51 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: snapCGH
Version: 1.23.0
Command: mkdir snapCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snapCGH_1.23.0.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R snapCGH.buildbin-libdir
StartedAt: 2011-06-22 06:32:55 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 06:33:12 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 17.3 seconds
RetCode: 0
Status:  OK 
PackageFile: snapCGH_1.23.0.tgz
PackageFileSize: 1.093 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=snapCGH.buildbin-libdir snapCGH_1.23.0.tar.gz'
>>>>>>> 

* installing *source* package ‘snapCGH’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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-4.2 -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-2.9-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/i386
*** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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-4.2 -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-2.9-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/ppc
*** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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-4.2 -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-2.9-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************



######################################################################################



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 ...
*** tangling vignette sources ...
   ‘snapCGHguide.Rnw’ 
** testing if installed package can be loaded

* DONE (snapCGH)


>>>>>>> 
>>>>>>> FIXING LINKS FOR snapCGH.buildbin-libdir/snapCGH/libs/i386/snapCGH.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/i386/snapCGH.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/i386/snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/i386/snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/i386/snapCGH.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR snapCGH.buildbin-libdir/snapCGH/libs/ppc/snapCGH.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/ppc/snapCGH.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/ppc/snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/ppc/snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/ppc/snapCGH.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR snapCGH.buildbin-libdir/snapCGH/libs/x86_64/snapCGH.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/x86_64/snapCGH.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/x86_64/snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/x86_64/snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/x86_64/snapCGH.so"