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INSTALL report for networkBMA on tokay2

This page was generated on 2018-10-17 08:36:25 -0400 (Wed, 17 Oct 2018).

Package 994/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.20.0
Ka Yee Yeung
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/networkBMA
Branch: RELEASE_3_7
Last Commit: b0c0668
Last Changed Date: 2018-04-30 10:35:26 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: networkBMA
Version: 2.20.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/networkBMA_2.20.0.tar.gz && rm -rf networkBMA.buildbin-libdir && mkdir networkBMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=networkBMA.buildbin-libdir networkBMA_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL networkBMA_2.20.0.zip && rm networkBMA_2.20.0.tar.gz networkBMA_2.20.0.zip
StartedAt: 2018-10-16 19:07:54 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:10:28 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 154.4 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/networkBMA_2.20.0.tar.gz && rm -rf networkBMA.buildbin-libdir && mkdir networkBMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=networkBMA.buildbin-libdir networkBMA_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL networkBMA_2.20.0.zip && rm networkBMA_2.20.0.tar.gz networkBMA_2.20.0.zip
###
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##############################################################################


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100 1318k  100 1318k    0     0  18.5M      0 --:--:-- --:--:-- --:--:-- 20.4M

install for i386

* installing *source* package 'networkBMA' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -c MurmurHash3.cpp -o MurmurHash3.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -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-3.7-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-3.7-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-3.7-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-3.7-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++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -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++ -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˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/networkBMA.buildbin-libdir/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
In R CMD INSTALL

install for x64

* installing *source* package 'networkBMA' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -c MurmurHash3.cpp -o MurmurHash3.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -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-3.7-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-3.7-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-3.7-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-3.7-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++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=generic -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++ -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˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/networkBMA.buildbin-libdir/networkBMA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'networkBMA' as networkBMA_2.20.0.zip
* DONE (networkBMA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'networkBMA' successfully unpacked and MD5 sums checked
In R CMD INSTALL