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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/networkBMA_2.26.0.tar.gz && rm -rf networkBMA.buildbin-libdir && mkdir networkBMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=networkBMA.buildbin-libdir networkBMA_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL networkBMA_2.26.0.zip && rm networkBMA_2.26.0.tar.gz networkBMA_2.26.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1324k 100 1324k 0 0 14.0M 0 --:--:-- --:--:-- --:--:-- 14.6M
install for i386
* installing *source* package 'networkBMA' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -c MurmurHash3.cpp -o MurmurHash3.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -c fastBMAR.cpp -o fastBMAR.o
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp:10:0: warning: "USE_RBLAS" redefined
#define USE_RBLAS //for now always use the default RBLAS library
^
<command-line>:0:0: note: this is the location of the previous definition
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 long unsigned int> >::operator()(const CompactModelIndices<long 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 long unsigned int; uint64_t = long long unsigned int; uint8_t = unsigned char; size_t = 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::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:121:2: 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:102:87: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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 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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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 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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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 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 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 long unsigned int; uint8_t = unsigned char; size_t = unsigned int; uint64_t = long long unsigned int]':
fastBMA.hpp:668:6: required from 'CompactModelIndices<T>::CompactModelIndices(ModelIndices&) [with T = long 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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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)));
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o networkBMA.dll tmp.def MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/networkBMA.buildbin-libdir/00LOCK-networkBMA/00new/networkBMA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'networkBMA'
finding HTML links ... done
ScanBMA html
ScanBMAcontrol html
contabs html
contabs.netwBMA html
contabs.prelim html
dream4 html
fastBMAcontrol html
fastgControl html
gControl html
iBMAcontrolLM html
iterateBMAlm html
finding level-2 HTML links ... done
networkBMA-internal html
networkBMA html
roc html
scores html
summary.networkBMA html
varord html
vignette html
writeEdges html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'networkBMA' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -c MurmurHash3.cpp -o MurmurHash3.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
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 (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I. -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=core2 -c fastBMAR.cpp -o fastBMAR.o
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp:10:0: warning: "USE_RBLAS" redefined
#define USE_RBLAS //for now always use the default RBLAS library
^
<command-line>:0:0: note: this is the location of the previous definition
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 long unsigned int> >::operator()(const CompactModelIndices<long 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 long unsigned int; uint64_t = long long unsigned int; uint8_t = unsigned char; size_t = long 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::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:121:2: 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:102:87: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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 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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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 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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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 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 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 long unsigned int; uint8_t = unsigned char; size_t = long long unsigned int; uint64_t = long long unsigned int]':
fastBMA.hpp:668:6: required from 'CompactModelIndices<T>::CompactModelIndices(ModelIndices&) [with T = long 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:1414:109: 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:1757:151: 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:127:217: required from 'void findEdges(BMARetStruct*, T**, T**, std::vector<std::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)));
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o networkBMA.dll tmp.def MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/networkBMA.buildbin-libdir/networkBMA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'networkBMA' as networkBMA_2.26.0.zip
* DONE (networkBMA)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'networkBMA' successfully unpacked and MD5 sums checked
