BioC 3.1: BUILD BIN report for BHC on petty

Package: BHC

Version: 1.20.0

Command: rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BHC_1.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BHC.buildbin-libdir

StartedAt: 2015-10-09 03:00:45 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:01:16 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 31.3 seconds

RetCode: 0

Status:  OK

PackageFile: BHC_1.20.0.tgz

PackageFileSize: 205.2 KiB

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### Running command:
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###   rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BHC_1.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BHC.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BHC.buildbin-libdir BHC_1.20.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BHC’ ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to support OpenMP... -fopenmp
checking whether OpenMP will work in this package... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.h:16,
                 from BlockCovarianceMatrix.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c DataSet.cpp -o DataSet.o
In file included from DataSet.h:16,
                 from DataSet.cpp:13:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.h:4,
                 from DirichletProcessMixture.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from DataSet.h:16,
                 from MultinomialDataSet.h:4,
                 from MultinomialDataSet.cpp:1:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Node.cpp -o Node.o
In file included from Node.h:16,
                 from Node.cpp:13:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
                 from RobustSquaredExponentialTimecourseDataSet.h:20,
                 from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
                 from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from TimecourseDataSet.cpp:13:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gammaln.cpp -o gammaln.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c header.cpp -o header.o
In file included from header.cpp:1:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_binevidence.cpp -o multinomial_binevidence.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o BHC.so BlockCovarianceMatrix.o CubicSplineTimecourseDataSet.o DataSet.o DirichletProcessMixture.o MultinomialDataSet.o Node.o RobustCubicSplineTimecourseDataSet.o RobustSquaredExponentialTimecourseDataSet.o SquaredExponentialTimecourseDataSet.o TimecourseDataSet.o bhc.o gammaln.o header.o multinomial_CalculateHyperparameters.o multinomial_OutputDendrogramInformation.o multinomial_ReadInData.o multinomial_bayeslink_binf.o multinomial_binevidence.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/BHC.buildbin-libdir/BHC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BHC)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"