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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL networkBMA
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘networkBMA’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c MurmurHash3.cpp -o MurmurHash3.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c ScanBMA_full.cpp -o ScanBMA_full.o
ScanBMA_full.cpp: In function ‘const List ScanBMA_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double)’:
ScanBMA_full.cpp:137:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
sort_index
^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:328:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
sort_index
^
ScanBMA_full.cpp: In function ‘const List ScanBMA_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, double)’:
ScanBMA_full.cpp:421:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
sort_index
^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:614:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
sort_index
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c fastBMAR.cpp -o fastBMAR.o
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp: In member function ‘unsigned char BitArray::getBit(size_t)’:
fastBMA.hpp:123:30: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
return (array[index/8] >> 7-(index & 0x7)) & 0x1;
^
fastBMA.hpp: In member function ‘unsigned char BitArray::setBit(size_t)’:
fastBMA.hpp:126:44: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses]
array[index/8] = array[index/8] | 1 << 7-(index & 0x7);
^
fastBMA.hpp: In member function ‘uint_fast32_t std::hash<CompactModelIndices<long unsigned int> >::operator()(const CompactModelIndices<long unsigned int>&) const’:
fastBMA.hpp:721:18: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
return(hash & 0xFFFFFFF0 | size);
^
fastBMA.hpp:723:24: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
return(k.hashValue & 0xFFFFFFF0 | size);
^
fastBMA.hpp: In member function ‘uint_fast32_t std::hash<ModelIndicesHash<unsigned int> >::operator()(const ModelIndicesHash<unsigned int>&) const’:
fastBMA.hpp:762:24: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
return(k.hashValue & 0xFFFFFFF0 | size);
^
fastBMA.hpp: In member function ‘float EdgeList::dijkstra_limit(int, int, float, float**, float)’:
fastBMA.hpp:1107:6: warning: variable ‘path_found’ set but not used [-Wunused-but-set-variable]
int path_found=0;
^
fastBMA.hpp: In member function ‘float* EdgeList::cutter_prune_edges(float, float)’:
fastBMA.hpp:1226:31: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
if (((*((unsigned int*)&val) & 2147483648u)) or (val >= upper_threshold) )adjMatrix[i] = 2.0f;
^
fastBMA.hpp: In function ‘void mtrv(int, int, double*, int, double*, double*)’:
fastBMA.hpp:1922:14: warning: unused variable ‘izero’ [-Wunused-variable]
int ione=1,izero=0;
^
fastBMAR.cpp: In function ‘const List fastBMA_g(Rcpp::NumericMatrix, int, Rcpp::NumericMatrix, double, int, double, Rcpp::CharacterVector, int, int, int, int, int, bool, bool, bool, double, double, double, double)’:
fastBMAR.cpp:33:7: warning: unused variable ‘colNum’ [-Wunused-variable]
int colNum = x.ncol();
^
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp: In instantiation of ‘uint64_t PackedBitArray<T>::get(uint8_t, size_t) [with T = long unsigned int; uint64_t = long unsigned int; uint8_t = unsigned char; size_t = long unsigned int]’:
fastBMA.hpp:719:50: required from here
fastBMA.hpp:186:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=startIndex+1;i<endIndex;i++){
^
fastBMA.hpp:187:39: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses]
retValue |= ((uint64_t) array[i]) << elementSize-bitsRead-tBits;
^
In file included from fastBMAR.cpp:4:0:
bmaNoMPI.hpp: In instantiation of ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’:
fastBMAR.cpp:150:2: required from here
bmaNoMPI.hpp:121:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k=0;k<evalSubset.size();k++){
^
bmaNoMPI.hpp:145:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<thChildren[th].size();j++){
^
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp: In instantiation of ‘void initRegressParms(T*, T*, T**, int, int, int, int, int&, int, bool) [with T = double]’:
bmaNoMPI.hpp:102:21: required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2: required from here
fastBMA.hpp:1701:7: warning: value computed is not used [-Wunused-value]
*dest++;
^
fastBMA.hpp: In instantiation of ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’:
fastBMA.hpp:1757:26: required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28: required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2: required from here
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: In instantiation of ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’:
fastBMA.hpp:1414:19: required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26: required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28: required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2: required from here
fastBMA.hpp:1661:5: warning: unused variable ‘rvalue’ [-Wunused-variable]
T rvalue=0;
^
fastBMA.hpp: In instantiation of ‘CompactModelIndices<T>::CompactModelIndices() [with T = long unsigned int]’:
fastBMA.hpp:781:63: required from ‘ModelSet<T>::ModelSet(ModelIndices, T, T, double) [with T = double]’
fastBMA.hpp:1430:3: required from ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’
fastBMA.hpp:1414:19: required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26: required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28: required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2: required from here
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: In instantiation of ‘CompactModelIndices<T>::CompactModelIndices(ModelIndices&) [with T = long unsigned int]’:
fastBMA.hpp:782:16: required from ‘ModelSet<T>::ModelSet(ModelIndices, T, T, double) [with T = double]’
fastBMA.hpp:1430:3: required from ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’
fastBMA.hpp:1414:19: required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26: required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28: required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2: required from here
fastBMA.hpp:621:19: warning: ‘CompactModelIndices<long unsigned int>::nModels’ will be initialized after [-Wreorder]
uint8_t nModels=0; //never more than 256 variables in a model
^
fastBMA.hpp:619:17: warning: ‘uint_fast32_t CompactModelIndices<long unsigned int>::hashValue’ [-Wreorder]
uint_fast32_t hashValue;
^
fastBMA.hpp:662:3: warning: when initialized here [-Wreorder]
CompactModelIndices( ModelIndices &mind): nModels(mind.nModels),hashValue(mind.hashValue){
^
fastBMA.hpp: In instantiation of ‘void PackedBitArray<T>::set(uint8_t, size_t, uint64_t) [with T = long unsigned int; uint8_t = unsigned char; size_t = long unsigned int; uint64_t = long unsigned int]’:
fastBMA.hpp:668:6: required from ‘CompactModelIndices<T>::CompactModelIndices(ModelIndices&) [with T = long unsigned int]’
fastBMA.hpp:782:16: required from ‘ModelSet<T>::ModelSet(ModelIndices, T, T, double) [with T = double]’
fastBMA.hpp:1430:3: required from ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’
fastBMA.hpp:1414:19: required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26: required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28: required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2: required from here
fastBMA.hpp:212:48: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
array[startIndex]=array[startIndex] & ˜mask | ((T) value << (tBits- bitOffset -elementSize));
^
fastBMA.hpp:225:61: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize - (tBits-bitOffset));
^
fastBMA.hpp:228:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=startIndex+1;i<endIndex;i++){
^
fastBMA.hpp:229:25: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
array[i]=(T) (value >> elementSize-bitsWritten-tBits);
^
fastBMA.hpp:235:15: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
mask= ones >> elementSize-bitsWritten;
^
fastBMA.hpp:236:43: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
array[endIndex]=array[endIndex] & mask | (T) (value << (tBits-(elementSize-bitsWritten)));
^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/networkBMA/libs
** R
** data
** 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
* DONE (networkBMA)
