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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BHC
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘BHC’ ...
** using staged installation
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to support OpenMP... -fopenmp
checking whether OpenMP will work in this package... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.h:16:0,
                 from BlockCovarianceMatrix.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from DataSet.h:16:0,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c DataSet.cpp -o DataSet.o
In file included from DataSet.h:16:0,
                 from DataSet.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.h:4:0,
                 from DirichletProcessMixture.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from DataSet.h:16:0,
                 from MultinomialDataSet.h:4,
                 from MultinomialDataSet.cpp:1:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c Node.cpp -o Node.o
In file included from Node.h:16:0,
                 from Node.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from DataSet.h:16:0,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20:0,
                 from RobustSquaredExponentialTimecourseDataSet.h:20,
                 from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20:0,
                 from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
SquaredExponentialTimecourseDataSet.cpp: In member function ‘void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector<double>, double&, double&, double&, double)’:
SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable ‘gridLogEvidence’ set but not used [-Wunused-but-set-variable]
   double currentLogEvidence, gridLogEvidence,
                              ^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from DataSet.h:16:0,
                 from TimecourseDataSet.h:20,
                 from TimecourseDataSet.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:0:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c gammaln.cpp -o gammaln.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c header.cpp -o header.o
In file included from header.cpp:1:0:
header.h:16:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_binevidence.cpp -o multinomial_binevidence.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/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 -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-BHC/00new/BHC/libs
** R
** 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 (BHC)