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BioC 3.5: BUILD BIN report for DNAcopy on veracruz2

This page was generated on 2017-10-18 14:27:31 -0400 (Wed, 18 Oct 2017).

Package 360/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.50.1
Venkatraman E. Seshan
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/DNAcopy
Branch: RELEASE_3_5
Last Commit: a201530
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: DNAcopy
Version: 1.50.1
Command: rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.50.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DNAcopy.buildbin-libdir
StartedAt: 2017-10-18 10:48:48 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 10:48:54 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 6.6 seconds
RetCode: 0
Status:  OK 
PackageFile: DNAcopy_1.50.1.tgz
PackageFileSize: 373.6 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.50.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DNAcopy.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.50.1.tar.gz'
>>>>>>> 

* installing *source* package ‘DNAcopy’ ...
** libs
gfortran   -fPIC  -g -O2  -c cbsWtstats.f -o cbsWtstats.o
gfortran   -fPIC  -g -O2  -c cbststats.f -o cbststats.o
gfortran   -fPIC  -g -O2  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran   -fPIC  -g -O2  -c changepoints.f -o changepoints.o
gfortran   -fPIC  -g -O2  -c esegment.f -o esegment.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c flchoose.c -o flchoose.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fphyper.c -o fphyper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fpnorm.c -o fpnorm.o
gfortran   -fPIC  -g -O2  -c getbdry.f -o getbdry.o
gfortran   -fPIC  -g -O2  -c prune.f -o prune.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rshared.c -o rshared.o
gfortran   -fPIC  -g -O2  -c segmentp.f -o segmentp.o
gfortran   -fPIC  -g -O2  -c smoothCNA.f -o smoothCNA.o
gfortran   -fPIC  -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-3.5-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs//DNAcopy.so"