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Package 126/467HostnameOS / ArchBUILDCHECKBUILD BIN
DNAcopy 1.26.0
Venkatraman E. Seshan
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/DNAcopy
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: DNAcopy
Version: 1.26.0
Command: rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R DNAcopy.buildbin-libdir
StartedAt: 2011-10-20 18:09:52 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 18:10:04 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 12.1 seconds
RetCode: 0
Status:  OK 
PackageFile: DNAcopy_1.26.0.tgz
PackageFileSize: 466.4 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=DNAcopy.buildbin-libdir DNAcopy_1.26.0.tar.gz'
>>>>>>> 

* installing *source* package 'DNAcopy' ...
** libs
*** arch - i386
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function 'wtmaxo':
cbsWtstats.f:17: warning: 'tmaxj' may be used uninitialized in this function
cbsWtstats.f:17: warning: 'tmaxi' may be used uninitialized in this function
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c cbststats.f -o cbststats.o
cbststats.f: In function 'tmaxo':
cbststats.f:11: warning: 'sxmxi' may be used uninitialized in this function
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c changepoints.f -o changepoints.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c esegment.f -o esegment.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c flchoose.c -o flchoose.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c fphyper.c -o fphyper.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c fpnorm.c -o fpnorm.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c getbdry.f -o getbdry.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c prune.f -o prune.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rshared.c -o rshared.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c segmentp.f -o segmentp.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c smoothCNA.f -o smoothCNA.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -pedantic -c tailprobs.f -o tailprobs.o
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 DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/i386
*** arch - ppc
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function 'wtmaxo':
cbsWtstats.f:17: warning: 'tmaxj' may be used uninitialized in this function
cbsWtstats.f:17: warning: 'tmaxi' may be used uninitialized in this function
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c cbststats.f -o cbststats.o
cbststats.f: In function 'tmaxo':
cbststats.f:11: warning: 'sxmxi' may be used uninitialized in this function
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c changepoints.f -o changepoints.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c esegment.f -o esegment.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c flchoose.c -o flchoose.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c fphyper.c -o fphyper.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c fpnorm.c -o fpnorm.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c getbdry.f -o getbdry.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c prune.f -o prune.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rshared.c -o rshared.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c segmentp.f -o segmentp.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c smoothCNA.f -o smoothCNA.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -pedantic -c tailprobs.f -o tailprobs.o
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 DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/ppc
*** arch - x86_64
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function 'wtmaxo':
cbsWtstats.f:17: warning: 'tmaxj' may be used uninitialized in this function
cbsWtstats.f:17: warning: 'tmaxi' may be used uninitialized in this function
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c cbststats.f -o cbststats.o
cbststats.f: In function 'tmaxo':
cbststats.f:11: warning: 'sxmxi' may be used uninitialized in this function
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c changepoints.f -o changepoints.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c esegment.f -o esegment.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c flchoose.c -o flchoose.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c fphyper.c -o fphyper.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c fpnorm.c -o fpnorm.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c getbdry.f -o getbdry.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c prune.f -o prune.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rshared.c -o rshared.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c segmentp.f -o segmentp.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c smoothCNA.f -o smoothCNA.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic -c tailprobs.f -o tailprobs.o
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 DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/x86_64
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (DNAcopy)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/i386/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/i386/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/i386/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/i386/DNAcopy.so"


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/ppc/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/ppc/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/ppc/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/ppc/DNAcopy.so"


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/x86_64/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/x86_64/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/x86_64/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/x86_64/DNAcopy.so"