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BUILD BIN report for BHC on celaya2

This page was generated on 2019-04-09 12:59:09 -0400 (Tue, 09 Apr 2019).

Package 128/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BHC 1.35.0
Rich Savage
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BHC
Branch: master
Last Commit: 72f0953
Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: BHC
Version: 1.35.0
Command: rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BHC_1.35.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BHC.buildbin-libdir
StartedAt: 2019-04-09 06:42:34 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:43:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 54.4 seconds
RetCode: 0
Status:  OK 
PackageFile: BHC_1.35.0.tgz
PackageFileSize: 229.6 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BHC_1.35.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BHC.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BHC.buildbin-libdir BHC_1.35.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BHC’ ...
** using staged installation
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for clang option to support OpenMP... unsupported
configure: WARNING: No OpenMP support. If using GCC, upgrade to >= 4.2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.cpp:15:
In file included from ./BlockCovarianceMatrix.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from CubicSplineTimecourseDataSet.cpp:15:
In file included from ./CubicSplineTimecourseDataSet.h:20:
In file included from ./TimecourseDataSet.h:20:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
In file included from CubicSplineTimecourseDataSet.cpp:15:
./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual]
  double GetMLIINoise(const vector<int>& itemIndex);
         ^
./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector<int>' vs 'const vector<int> &')
  double GetMLIINoise(vector<int> itemIndex);
         ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c DataSet.cpp -o DataSet.o
In file included from DataSet.cpp:13:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
DataSet.cpp:36:48: warning: if statement has empty body [-Wempty-body]
    if(!system("PAUSE")) /* could not pause */ ;
                                               ^
DataSet.cpp:36:48: note: put the semicolon on a separate line to silence this warning
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.cpp:15:
In file included from ./DirichletProcessMixture.h:4:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from MultinomialDataSet.cpp:1:
In file included from ./MultinomialDataSet.h:4:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
In file included from MultinomialDataSet.cpp:1:
./MultinomialDataSet.h:19:10: warning: 'MultinomialDataSet::SingleClusterLogEvidence' hides overloaded virtual function [-Woverloaded-virtual]
  double SingleClusterLogEvidence(vector<int> itemIndex);  // returns the log-evidence for a cluster that contains data items defined by itemIndex
         ^
./DataSet.h:29:18: note: hidden overloaded virtual function 'DataSet::SingleClusterLogEvidence' declared here: different number of parameters (5 vs 1)
  virtual double SingleClusterLogEvidence(const vector<int>& itemIndex,
                 ^
MultinomialDataSet.cpp:77:43: warning: if statement has empty body [-Wempty-body]
    if(!system("PAUSE"))/* didn't pause */;
                                          ^
MultinomialDataSet.cpp:77:43: note: put the semicolon on a separate line to silence this warning
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c Node.cpp -o Node.o
In file included from Node.cpp:13:
In file included from ./Node.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from RobustCubicSplineTimecourseDataSet.cpp:15:
In file included from ./RobustCubicSplineTimecourseDataSet.h:20:
In file included from ./CubicSplineTimecourseDataSet.h:20:
In file included from ./TimecourseDataSet.h:20:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
In file included from RobustCubicSplineTimecourseDataSet.cpp:15:
In file included from ./RobustCubicSplineTimecourseDataSet.h:20:
./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual]
  double GetMLIINoise(const vector<int>& itemIndex);
         ^
./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector<int>' vs 'const vector<int> &')
  double GetMLIINoise(vector<int> itemIndex);
         ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from RobustSquaredExponentialTimecourseDataSet.cpp:15:
In file included from ./RobustSquaredExponentialTimecourseDataSet.h:20:
In file included from ./SquaredExponentialTimecourseDataSet.h:20:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.cpp:15:
In file included from ./SquaredExponentialTimecourseDataSet.h:20:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from TimecourseDataSet.cpp:13:
In file included from ./TimecourseDataSet.h:20:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
TimecourseDataSet.cpp:80:40: warning: if statement has empty body [-Wempty-body]
    if(!system("PAUSE"))/*didn't work*/;
                                       ^
TimecourseDataSet.cpp:80:40: note: put the semicolon on a separate line to silence this warning
TimecourseDataSet.cpp:143:40: warning: if statement has empty body [-Wempty-body]
    if(!system("PAUSE"))/*didn't work*/;
                                       ^
TimecourseDataSet.cpp:143:40: note: put the semicolon on a separate line to silence this warning
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
In file included from bhc.cpp:20:
./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual]
  double GetMLIINoise(const vector<int>& itemIndex);
         ^
./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector<int>' vs 'const vector<int> &')
  double GetMLIINoise(vector<int> itemIndex);
         ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c gammaln.cpp -o gammaln.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c header.cpp -o header.o
In file included from header.cpp:1:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c multinomial_binevidence.cpp -o multinomial_binevidence.o
clang++ -std=gnu++11 -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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/BHC.buildbin-libdir/00LOCK-BHC/00new/BHC/libs
** R
** 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 (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/3.6/Resources/lib/libgcc_s.1.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/lib/libreadline.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "BHC.buildbin-libdir/BHC/libs//BHC.so"