##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf networkBMA.buildbin-libdir && mkdir networkBMA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh networkBMA_2.17.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R networkBMA.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=networkBMA.buildbin-libdir networkBMA_2.17.0.tar.gz'
>>>>>>>
* installing *source* package ‘networkBMA’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MurmurHash3.cpp -o MurmurHash3.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ScanBMA_full.cpp -o ScanBMA_full.o
ScanBMA_full.cpp:137:21: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:328:19: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:421:21: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:614:19: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
4 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c fastBMAR.cpp -o fastBMAR.o
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:123:30: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
return (array[index/8] >> 7-(index & 0x7)) & 0x1;
˜˜ ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:123:30: note: place parentheses around the '-' expression to silence this warning
return (array[index/8] >> 7-(index & 0x7)) & 0x1;
^
( )
./fastBMA.hpp:126:44: warning: operator '<<' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
array[index/8] = array[index/8] | 1 << 7-(index & 0x7);
˜˜ ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:126:44: note: place parentheses around the '-' expression to silence this warning
array[index/8] = array[index/8] | 1 << 7-(index & 0x7);
^
( )
./fastBMA.hpp:187:62: warning: operator '<<' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
retValue |= ((uint64_t) array[i]) << elementSize-bitsRead-tBits;
˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./fastBMA.hpp:187:62: note: place parentheses around the '-' expression to silence this warning
retValue |= ((uint64_t) array[i]) << elementSize-bitsRead-tBits;
^
( )
./fastBMA.hpp:225:77: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize - (tBits-bitOffset));
˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:225:77: note: place parentheses around the '-' expression to silence this warning
array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize - (tBits-bitOffset));
^
( )
./fastBMA.hpp:229:51: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
array[i]=(T) (value >> elementSize-bitsWritten-tBits);
˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./fastBMA.hpp:229:51: note: place parentheses around the '-' expression to silence this warning
array[i]=(T) (value >> elementSize-bitsWritten-tBits);
^
( )
./fastBMA.hpp:235:29: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
mask= ones >> elementSize-bitsWritten;
˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:235:29: note: place parentheses around the '-' expression to silence this warning
mask= ones >> elementSize-bitsWritten;
^
( )
./fastBMA.hpp:395:12: warning: unused variable 'n' [-Wunused-variable]
const int n=size*(size+1)/2;
^
./fastBMA.hpp:625:12: warning: unused variable 'modelBits' [-Wunused-variable]
uint8_t modelBits=gModelBits;
^
./fastBMA.hpp:626:12: warning: unused variable 'nModels' [-Wunused-variable]
uint8_t nModels=0;
^
./fastBMA.hpp:721:18: warning: '&' within '|' [-Wbitwise-op-parentheses]
return(hash & 0xFFFFFFF0 | size);
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
./fastBMA.hpp:721:18: note: place parentheses around the '&' expression to silence this warning
return(hash & 0xFFFFFFF0 | size);
^
( )
./fastBMA.hpp:723:24: warning: '&' within '|' [-Wbitwise-op-parentheses]
return(k.hashValue & 0xFFFFFFF0 | size);
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
./fastBMA.hpp:723:24: note: place parentheses around the '&' expression to silence this warning
return(k.hashValue & 0xFFFFFFF0 | size);
^
( )
./fastBMA.hpp:762:24: warning: '&' within '|' [-Wbitwise-op-parentheses]
return(k.hashValue & 0xFFFFFFF0 | size);
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
./fastBMA.hpp:762:24: note: place parentheses around the '&' expression to silence this warning
return(k.hashValue & 0xFFFFFFF0 | size);
^
( )
./fastBMA.hpp:1406:10: warning: unused variable 'g0' [-Wunused-variable]
double g0=g;
^
./fastBMA.hpp:1401:6: warning: unused variable 'nIterations' [-Wunused-variable]
int nIterations=0;
^
./fastBMA.hpp:1402:7: warning: unused variable 'doneOptimizing' [-Wunused-variable]
bool doneOptimizing=0;
^
./fastBMA.hpp:1922:14: warning: unused variable 'izero' [-Wunused-variable]
int ione=1,izero=0;
^
fastBMAR.cpp:33:7: warning: unused variable 'colNum' [-Wunused-variable]
int colNum = x.ncol();
^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:1701:7: warning: expression result unused [-Wunused-value]
*dest++;
^˜˜˜˜˜˜
./bmaNoMPI.hpp:102:2: note: in instantiation of function template specialization 'initRegressParms<double>' requested here
initRegressParms<T>(A,ATA,data,nGenes,nRows,nSamples,nTimes,nVars,nThreads,timeSeries);
^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
findEdges(
^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:1408:10: warning: unused variable 'r2' [-Wunused-variable]
Result r2 = boost::math::tools::brent_find_minima(BMAoptimizeFunction<T>(ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR), (T) 1, (T)nRows, optimizeBits, max_iter);
^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles);
^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
findEdges(
^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:1661:5: warning: unused variable 'rvalue' [-Wunused-variable]
T rvalue=0;
^
./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here
chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR);
^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles);
^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
findEdges(
^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:662:45: warning: field 'nModels' will be initialized after field 'hashValue' [-Wreorder]
CompactModelIndices( ModelIndices &mind): nModels(mind.nModels),hashValue(mind.hashValue){
^
./fastBMA.hpp:782:17: note: in instantiation of member function 'CompactModelIndices<unsigned long long>::CompactModelIndices' requested here
modelIndices=CompactModelIndices<uint64_t>(mInd);
^
./fastBMA.hpp:1430:23: note: in instantiation of member function 'ModelSet<double>::ModelSet' requested here
activeModels.insert(ModelSet<T>(modelIndices, 0, 0, 0));
^
./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here
chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR);
^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles);
^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
findEdges(
^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:282:2: warning: control may reach end of non-void function [-Wreturn-type]
}
^
./fastBMA.hpp:657:28: note: in instantiation of member function 'BitIndex<unsigned long long>::compare' requested here
bool retvalue=bitIndex.compare(b.list,modelBits,nModels);
^
./fastBMA.hpp:829:84: note: in instantiation of member function 'CompactModelIndices<unsigned long long>::operator==' requested here
bool operator<(const ModelSet& b) const { return (bic < b.bic) && ! (modelIndices == b.modelIndices); }
^
/usr/local/clang4/bin/../include/c++/v1/__functional_base:61:21: note: in instantiation of member function 'ModelSet<double>::operator<' requested here
{return __x < __y;}
^
/usr/local/clang4/bin/../include/c++/v1/__tree:1978:17: note: in instantiation of member function 'std::__1::less<ModelSet<double> >::operator()' requested here
if (value_comp()(__v, __nd->__value_))
^
/usr/local/clang4/bin/../include/c++/v1/__tree:2102:36: note: in instantiation of function template specialization 'std::__1::__tree<ModelSet<double>, std::__1::less<ModelSet<double> >, std::__1::allocator<ModelSet<double> > >::__find_equal<ModelSet<double> >' requested here
__node_base_pointer& __child = __find_equal(__parent, __k);
^
/usr/local/clang4/bin/../include/c++/v1/__tree:1264:16: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
return __emplace_unique_key_args(_NodeTypes::__get_key(__v), _VSTD::move(__v));
^
./fastBMA.hpp:1430:16: note: in instantiation of member function 'std::__1::set<ModelSet<double>, std::__1::less<ModelSet<double> >, std::__1::allocator<ModelSet<double> > >::insert' requested here
activeModels.insert(ModelSet<T>(modelIndices, 0, 0, 0));
^
./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here
chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR);
^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles);
^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
findEdges(
^
22 warnings generated.
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 networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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-3.6-bioc/meat/networkBMA.buildbin-libdir/networkBMA/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 (networkBMA)
>>>>>>>
>>>>>>> FIXING LINKS FOR networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.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" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.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" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
