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CHECK report for networkBMA on malbec1

This page was generated on 2019-04-16 11:49:41 -0400 (Tue, 16 Apr 2019).

Package 1055/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.22.0
Ka Yee Yeung
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/networkBMA
Branch: RELEASE_3_8
Last Commit: 3e29256
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: networkBMA
Version: 2.22.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings networkBMA_2.22.0.tar.gz
StartedAt: 2019-04-16 01:46:13 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:47:31 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 78.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: networkBMA.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings networkBMA_2.22.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/networkBMA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘networkBMA/DESCRIPTION’ ... OK
* this is package ‘networkBMA’ version ‘2.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘networkBMA’ can be installed ... WARNING
Found the following significant warnings:
  fastBMA.hpp:621:19: warning: ‘CompactModelIndices<long unsigned int>::nModels’ will be initialized after [-Wreorder]
  fastBMA.hpp:619:17: warning:   ‘uint_fast32_t CompactModelIndices<long unsigned int>::hashValue’ [-Wreorder]
  fastBMA.hpp:662:3: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.8-bioc/meat/networkBMA.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.6Mb
* 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
* 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 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vignette 5.908  0.000   6.173
gControl 5.708  0.004   5.715
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/networkBMA.Rcheck/00check.log’
for details.

Installation output

networkBMA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL networkBMA
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘networkBMA’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c MurmurHash3.cpp -o MurmurHash3.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c ScanBMA_full.cpp -o ScanBMA_full.o
ScanBMA_full.cpp: In function ‘const List ScanBMA_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double)’:
ScanBMA_full.cpp:137:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:328:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List ScanBMA_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, double)’:
ScanBMA_full.cpp:421:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:614:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:453:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c fastBMAR.cpp -o fastBMAR.o
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp: In member function ‘unsigned char BitArray::getBit(size_t)’:
fastBMA.hpp:123:30: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
   return (array[index/8] >> 7-(index & 0x7)) & 0x1;
                              ^
fastBMA.hpp: In member function ‘unsigned char BitArray::setBit(size_t)’:
fastBMA.hpp:126:44: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses]
   array[index/8] = array[index/8] |  1 << 7-(index & 0x7);
                                            ^
fastBMA.hpp: In member function ‘uint_fast32_t std::hash<CompactModelIndices<long unsigned int> >::operator()(const CompactModelIndices<long unsigned int>&) const’:
fastBMA.hpp:721:18: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
      return(hash & 0xFFFFFFF0 | size);
                  ^
fastBMA.hpp:723:24: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
     return(k.hashValue & 0xFFFFFFF0 | size);      
                        ^
fastBMA.hpp: In member function ‘uint_fast32_t std::hash<ModelIndicesHash<unsigned int> >::operator()(const ModelIndicesHash<unsigned int>&) const’:
fastBMA.hpp:762:24: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
     return(k.hashValue & 0xFFFFFFF0 | size);      
                        ^
fastBMA.hpp: In member function ‘float EdgeList::dijkstra_limit(int, int, float, float**, float)’:
fastBMA.hpp:1107:6: warning: variable ‘path_found’ set but not used [-Wunused-but-set-variable]
  int path_found=0;
      ^
fastBMA.hpp: In member function ‘float* EdgeList::cutter_prune_edges(float, float)’:
fastBMA.hpp:1226:31: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
    if (((*((unsigned int*)&val) & 2147483648u))   or   (val >= upper_threshold)  )adjMatrix[i] = 2.0f;
                               ^
fastBMA.hpp: In function ‘void mtrv(int, int, double*, int, double*, double*)’:
fastBMA.hpp:1922:14: warning: unused variable ‘izero’ [-Wunused-variable]
   int ione=1,izero=0;
              ^
fastBMAR.cpp: In function ‘const List fastBMA_g(Rcpp::NumericMatrix, int, Rcpp::NumericMatrix, double, int, double, Rcpp::CharacterVector, int, int, int, int, int, bool, bool, bool, double, double, double, double)’:
fastBMAR.cpp:33:7: warning: unused variable ‘colNum’ [-Wunused-variable]
   int colNum = x.ncol();
       ^
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp: In instantiation of ‘uint64_t PackedBitArray<T>::get(uint8_t, size_t) [with T = long unsigned int; uint64_t = long unsigned int; uint8_t = unsigned char; size_t = long unsigned int]’:
fastBMA.hpp:719:50:   required from here
fastBMA.hpp:186:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=startIndex+1;i<endIndex;i++){
                           ^
fastBMA.hpp:187:39: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses]
    retValue |=  ((uint64_t) array[i]) << elementSize-bitsRead-tBits;
                                       ^
In file included from fastBMAR.cpp:4:0:
bmaNoMPI.hpp: In instantiation of ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’:
fastBMAR.cpp:150:2:   required from here
bmaNoMPI.hpp:121:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k=0;k<evalSubset.size();k++){
               ^
bmaNoMPI.hpp:145:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j=0;j<thChildren[th].size();j++){
                ^
In file included from fastBMAR.cpp:3:0:
fastBMA.hpp: In instantiation of ‘void initRegressParms(T*, T*, T**, int, int, int, int, int&, int, bool) [with T = double]’:
bmaNoMPI.hpp:102:21:   required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2:   required from here
fastBMA.hpp:1701:7: warning: value computed is not used [-Wunused-value]
       *dest++;
       ^
fastBMA.hpp: In instantiation of ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’:
fastBMA.hpp:1757:26:   required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28:   required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2:   required from here
fastBMA.hpp:1406:10: warning: unused variable ‘g0’ [-Wunused-variable]
   double g0=g; 
          ^
fastBMA.hpp:1401:6: warning: unused variable ‘nIterations’ [-Wunused-variable]
  int nIterations=0;
      ^
fastBMA.hpp:1402:7: warning: unused variable ‘doneOptimizing’ [-Wunused-variable]
  bool doneOptimizing=0;
       ^
fastBMA.hpp: In instantiation of ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’:
fastBMA.hpp:1414:19:   required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26:   required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28:   required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2:   required from here
fastBMA.hpp:1661:5: warning: unused variable ‘rvalue’ [-Wunused-variable]
   T rvalue=0;
     ^
fastBMA.hpp: In instantiation of ‘CompactModelIndices<T>::CompactModelIndices() [with T = long unsigned int]’:
fastBMA.hpp:781:63:   required from ‘ModelSet<T>::ModelSet(ModelIndices, T, T, double) [with T = double]’
fastBMA.hpp:1430:3:   required from ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’
fastBMA.hpp:1414:19:   required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26:   required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28:   required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2:   required from here
fastBMA.hpp:625:12: warning: unused variable ‘modelBits’ [-Wunused-variable]
    uint8_t modelBits=gModelBits; 
            ^
fastBMA.hpp:626:12: warning: unused variable ‘nModels’ [-Wunused-variable]
    uint8_t nModels=0;
            ^
fastBMA.hpp: In instantiation of ‘CompactModelIndices<T>::CompactModelIndices(ModelIndices&) [with T = long unsigned int]’:
fastBMA.hpp:782:16:   required from ‘ModelSet<T>::ModelSet(ModelIndices, T, T, double) [with T = double]’
fastBMA.hpp:1430:3:   required from ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’
fastBMA.hpp:1414:19:   required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26:   required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28:   required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2:   required from here
fastBMA.hpp:621:19: warning: ‘CompactModelIndices<long unsigned int>::nModels’ will be initialized after [-Wreorder]
   uint8_t nModels=0; //never more than 256 variables in a model
                   ^
fastBMA.hpp:619:17: warning:   ‘uint_fast32_t CompactModelIndices<long unsigned int>::hashValue’ [-Wreorder]
   uint_fast32_t hashValue;
                 ^
fastBMA.hpp:662:3: warning:   when initialized here [-Wreorder]
   CompactModelIndices( ModelIndices &mind): nModels(mind.nModels),hashValue(mind.hashValue){
   ^
fastBMA.hpp: In instantiation of ‘void PackedBitArray<T>::set(uint8_t, size_t, uint64_t) [with T = long unsigned int; uint8_t = unsigned char; size_t = long unsigned int; uint64_t = long unsigned int]’:
fastBMA.hpp:668:6:   required from ‘CompactModelIndices<T>::CompactModelIndices(ModelIndices&) [with T = long unsigned int]’
fastBMA.hpp:782:16:   required from ‘ModelSet<T>::ModelSet(ModelIndices, T, T, double) [with T = double]’
fastBMA.hpp:1430:3:   required from ‘T chooseBestModels(double, T*, int, int, int, int*, T*, T, T, double*, int*, int*, double*, double) [with T = double]’
fastBMA.hpp:1414:19:   required from ‘int fastScanBMA_g(T*, T*, T, T, int, T*, bool, double*, int*, int, int, int, double, double, int, int) [with T = double]’
fastBMA.hpp:1757:26:   required from ‘int findRegulators(T, int, int, float, float, int, int, bool, int, T**, T**, int*, double*, T*, T*, int, int, int, int, int, int) [with T = double]’
bmaNoMPI.hpp:127:28:   required from ‘void findEdges(BMARetStruct*, T**, T**, std::vector<std::__cxx11::basic_string<char> >&, int, int, int, bool, bool, bool, int, int, int, int, float, float, float, float, float, float, int, int) [with T = double]’
fastBMAR.cpp:150:2:   required from here
fastBMA.hpp:212:48: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
    array[startIndex]=array[startIndex] & ˜mask | ((T) value << (tBits- bitOffset -elementSize));
                                                ^
fastBMA.hpp:225:61: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
    array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize  - (tBits-bitOffset));
                                                             ^
fastBMA.hpp:228:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int i=startIndex+1;i<endIndex;i++){
                            ^
fastBMA.hpp:229:25: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
     array[i]=(T) (value >> elementSize-bitsWritten-tBits);
                         ^
fastBMA.hpp:235:15: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
    mask= ones >> elementSize-bitsWritten;
               ^
fastBMA.hpp:236:43: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
    array[endIndex]=array[endIndex] & mask | (T) (value << (tBits-(elementSize-bitsWritten)));    
                                           ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/networkBMA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (networkBMA)

Tests output

Example timings

networkBMA.Rcheck/networkBMA-Ex.timings

nameusersystemelapsed
ScanBMA0.1160.0080.139
ScanBMAcontrol4.7840.0204.810
contabs1.7000.0121.713
contabs.netwBMA000
contabs.prelim000
fastBMAcontrol0.0920.0000.092
fastgControl0.0920.0000.093
gControl5.7080.0045.715
iBMAcontrolLM0.6920.0000.692
iterateBMAlm1.2040.0161.223
networkBMA0.3840.0080.389
roc0.6640.0040.670
scores0.6880.0000.689
summary.networkBMA0.3320.0000.332
varord0.220.000.22
vignette5.9080.0006.173
writeEdges0.7920.0000.796