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BioC 3.3: BUILD BIN report for CoGAPS on oaxaca

This page was generated on 2016-10-13 12:57:20 -0700 (Thu, 13 Oct 2016).

Package 225/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 2.6.0
Elana J. Fertig
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/CoGAPS
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: CoGAPS
Version: 2.6.0
Command: rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CoGAPS_2.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CoGAPS.buildbin-libdir
StartedAt: 2016-10-13 07:29:19 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 07:30:18 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 59.4 seconds
RetCode: 0
Status:  OK 
PackageFile: CoGAPS_2.6.0.tgz
PackageFileSize: 835.7 KiB

Command output

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##############################################################################
###
### Running command:
###
###   rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CoGAPS_2.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CoGAPS.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_2.6.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CoGAPS’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c AtomicSupport.cc -o AtomicSupport.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GAPSNorm.cpp -o GAPSNorm.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GibbsSampler.cpp -o GibbsSampler.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Matrix.cpp -o Matrix.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cogapsR.cpp -o cogapsR.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cogapsmapR.cpp -o cogapsmapR.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cogapsmaptestR.cpp -o cogapsmaptestR.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cogapstestR.cpp -o cogapstestR.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c randgen.cpp -o randgen.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c sub_func.cpp -o sub_func.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 CoGAPS.so AtomicSupport.o GAPSNorm.o GibbsSampler.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o cogapsmaptestR.o cogapstestR.o randgen.o sub_func.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CoGAPS)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"