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Package 182/658HostnameOS / ArchBUILDCHECKBUILD BIN
DNAcopy 1.33.1
Venkatraman E. Seshan
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DNAcopy
Last Changed Rev: 70775 / Revision: 74774
Last Changed Date: 2012-10-25 13:56:03 -0700 (Thu, 25 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: DNAcopy
Version: 1.33.1
Command: rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.33.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DNAcopy.buildbin-libdir
StartedAt: 2013-03-25 05:23:08 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 05:23:18 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 9.6 seconds
RetCode: 0
Status:  OK 
PackageFile: DNAcopy_1.33.1.tgz
PackageFileSize: 407.8 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.33.1.tar.gz'
>>>>>>> 

* installing *source* package 'DNAcopy' ...
** libs
*** arch - i386
gfortran -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 -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 -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c changepoints.f -o changepoints.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c esegment.f -o esegment.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c flchoose.c -o flchoose.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fphyper.c -o fphyper.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fpnorm.c -o fpnorm.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c getbdry.f -o getbdry.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c prune.f -o prune.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c rshared.c -o rshared.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c segmentp.f -o segmentp.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c smoothCNA.f -o smoothCNA.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c tailprobs.f -o tailprobs.o
gcc -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-2.12-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/i386
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DNAcopy.Rnw' 
** 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/3.0/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/3.0/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/3.0/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/3.0/Resources/lib/libreadline.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/i386/DNAcopy.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=DNAcopy.buildbin-libdir --libs-only DNAcopy_1.33.1.tar.gz'
>>>>>>> 

* installing *source* package 'DNAcopy' ...
** libs
*** arch - x86_64
gfortran -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 -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 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c changepoints.f -o changepoints.o
gfortran -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c esegment.f -o esegment.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c flchoose.c -o flchoose.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fphyper.c -o fphyper.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fpnorm.c -o fpnorm.o
gfortran -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c getbdry.f -o getbdry.o
gfortran -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c prune.f -o prune.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c rshared.c -o rshared.o
gfortran -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c segmentp.f -o segmentp.o
gfortran -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c smoothCNA.f -o smoothCNA.o
gfortran -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c tailprobs.f -o tailprobs.o
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 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-2.12-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/x86_64
* DONE (DNAcopy)


>>>>>>> 
>>>>>>> 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/3.0/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/3.0/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/3.0/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/3.0/Resources/lib/libreadline.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/x86_64/DNAcopy.so"