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BioC 3.5: CHECK report for networkBMA on tokay2

This page was generated on 2017-10-18 14:21:58 -0400 (Wed, 18 Oct 2017).

Package 897/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.16.1
Ka Yee Yeung
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/networkBMA
Branch: RELEASE_3_5
Last Commit: 224c810
Last Changed Date: 2017-10-08 18:00:26 -0400 (Sun, 08 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: networkBMA
Version: 2.16.1
Command: rm -rf networkBMA.buildbin-libdir networkBMA.Rcheck && mkdir networkBMA.buildbin-libdir networkBMA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=networkBMA.buildbin-libdir networkBMA_2.16.1.tar.gz >networkBMA.Rcheck\00install.out 2>&1 && cp networkBMA.Rcheck\00install.out networkBMA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=networkBMA.buildbin-libdir --install="check:networkBMA-install.out" --force-multiarch --no-vignettes --timings networkBMA_2.16.1.tar.gz
StartedAt: 2017-10-18 01:43:30 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:47:23 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 233.6 seconds
RetCode: 0
Status:  OK  
CheckDir: networkBMA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf networkBMA.buildbin-libdir networkBMA.Rcheck && mkdir networkBMA.buildbin-libdir networkBMA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=networkBMA.buildbin-libdir networkBMA_2.16.1.tar.gz >networkBMA.Rcheck\00install.out 2>&1 && cp networkBMA.Rcheck\00install.out networkBMA-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=networkBMA.buildbin-libdir --install="check:networkBMA-install.out" --force-multiarch --no-vignettes --timings networkBMA_2.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'networkBMA/DESCRIPTION' ... OK
* this is package 'networkBMA' version '2.16.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'networkBMA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.buildbin-libdir/networkBMA/libs/i386/networkBMA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck/00check.log'
for details.

networkBMA.Rcheck/00install.out:


install for i386

* installing *source* package 'networkBMA' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=core2 -c MurmurHash3.cpp -o MurmurHash3.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -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-3.5-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-3.5-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-3.5-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-3.5-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˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -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++ -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˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.buildbin-libdir/networkBMA/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'networkBMA' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=core2 -c MurmurHash3.cpp -o MurmurHash3.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -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-3.5-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-3.5-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-3.5-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-3.5-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˜1.5-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -fopenmp -std=gnu++11   -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++ -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˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.buildbin-libdir/networkBMA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'networkBMA' as networkBMA_2.16.1.zip
* DONE (networkBMA)

networkBMA.Rcheck/examples_i386/networkBMA-Ex.timings:

nameusersystemelapsed
ScanBMA0.190.000.19
ScanBMAcontrol3.920.033.95
contabs1.350.021.36
contabs.netwBMA000
contabs.prelim000
fastBMAcontrol0.070.000.08
fastgControl0.110.000.11
gControl3.920.003.92
iBMAcontrolLM1.300.011.38
iterateBMAlm0.90.00.9
networkBMA0.320.000.32
roc0.780.000.78
scores0.610.000.61
summary.networkBMA0.260.020.28
varord0.170.030.20
vignette3.750.003.75
writeEdges0.520.000.52

networkBMA.Rcheck/examples_x64/networkBMA-Ex.timings:

nameusersystemelapsed
ScanBMA0.180.010.20
ScanBMAcontrol4.640.024.66
contabs1.810.001.82
contabs.netwBMA000
contabs.prelim000
fastBMAcontrol0.080.000.07
fastgControl0.110.010.13
gControl4.910.004.91
iBMAcontrolLM1.650.022.39
iterateBMAlm0.820.010.82
networkBMA0.310.000.32
roc0.780.000.78
scores0.840.020.86
summary.networkBMA0.250.020.26
varord0.160.030.19
vignette3.450.003.45
writeEdges0.610.010.63