Package: DNAcopy

Version: 1.58.0

Command: rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.58.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DNAcopy.buildbin-libdir

StartedAt: 2019-10-16 08:30:03 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 08:30:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 21.0 seconds

RetCode: 0

Status:  OK

PackageFile: DNAcopy_1.58.0.tgz

PackageFileSize: 417.2 KiB

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### Running command:
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###   rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.58.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DNAcopy.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.58.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DNAcopy’ ...
** using staged installation
** libs
gfortran  -fPIC  -Wall -g -O2  -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:283:0:

       iseg(2) = tmaxj
 
Warning: ‘tmaxj’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cbsWtstats.f:282:0:

       iseg(1) = tmaxi
 
Warning: ‘tmaxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fPIC  -Wall -g -O2  -c cbststats.f -o cbststats.o
cbststats.f:258:0:

                      tmaxj = sxmxi + i2j
 
Warning: ‘sxmxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fPIC  -Wall -g -O2  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran  -fPIC  -Wall -g -O2  -c changepoints.f -o changepoints.o
gfortran  -fPIC  -Wall -g -O2  -c esegment.f -o esegment.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c flchoose.c -o flchoose.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fphyper.c -o fphyper.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fpnorm.c -o fpnorm.o
gfortran  -fPIC  -Wall -g -O2  -c getbdry.f -o getbdry.o
gfortran  -fPIC  -Wall -g -O2  -c prune.f -o prune.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c rshared.c -o rshared.o
gfortran  -fPIC  -Wall -g -O2  -c segmentp.f -o segmentp.o
gfortran  -fPIC  -Wall -g -O2  -c smoothCNA.f -o smoothCNA.o
gfortran  -fPIC  -Wall -g -O2  -c tailprobs.f -o tailprobs.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -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 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/DNAcopy.buildbin-libdir/00LOCK-DNAcopy/00new/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DNAcopy)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"