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BioC 3.5: CHECK report for networkBMA on toluca2

This page was generated on 2017-04-23 14:36:39 -0400 (Sun, 23 Apr 2017).

Package 894/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.14.1
Ka Yee Yeung
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/networkBMA
Last Changed Rev: 129004 / Revision: 129046
Last Changed Date: 2017-04-21 10:41:02 -0400 (Fri, 21 Apr 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
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: 2.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings networkBMA_2.14.1.tar.gz
StartedAt: 2017-04-23 07:24:31 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 07:26:42 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 131.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: networkBMA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings networkBMA_2.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘networkBMA/DESCRIPTION’ ... OK
* this is package ‘networkBMA’ version ‘2.14.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘src’ contains:
  bmaNoMPI.hpp config.h.in fastBMA.hpp my_sort.hpp
These are unlikely file names for src files.
* 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 ... NOTE
Found the following warnings:
  ./fastBMA.hpp:282:2: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck/00install.out’ for details.
* 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
ScanBMAcontrol 6.342  0.056   6.600
gControl       6.138  0.050   6.343
vignette       5.050  0.035   5.166
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck/00check.log’
for details.

networkBMA.Rcheck/00install.out:

* installing *source* package ‘networkBMA’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c MurmurHash3.cpp -o MurmurHash3.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c ScanBMA_full.cpp -o ScanBMA_full.o
ScanBMA_full.cpp:137:21: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
  arma::uvec pord = sort_index(priorProbs, 1);
                    ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:328:19: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
                  ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:421:21: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
  arma::uvec pord = sort_index(priorProbs, 1);
                    ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:614:19: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
                  ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
4 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c fastBMAR.cpp -o fastBMAR.o
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:123:30: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
  return (array[index/8] >> 7-(index & 0x7)) & 0x1;
                         ˜˜ ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:123:30: note: place parentheses around the '-' expression to silence this warning
  return (array[index/8] >> 7-(index & 0x7)) & 0x1;
                             ^
                            (              )
./fastBMA.hpp:126:44: warning: operator '<<' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
  array[index/8] = array[index/8] |  1 << 7-(index & 0x7);
                                       ˜˜ ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:126:44: note: place parentheses around the '-' expression to silence this warning
  array[index/8] = array[index/8] |  1 << 7-(index & 0x7);
                                           ^
                                          (              )
./fastBMA.hpp:187:62: warning: operator '<<' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
                 retValue |=  ((uint64_t) array[i]) << elementSize-bitsRead-tBits;
                                                    ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./fastBMA.hpp:187:62: note: place parentheses around the '-' expression to silence this warning
                 retValue |=  ((uint64_t) array[i]) << elementSize-bitsRead-tBits;
                                                                           ^
                                                       (                         )
./fastBMA.hpp:225:77: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
                        array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize  - (tBits-bitOffset));
                                                                                 ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:225:77: note: place parentheses around the '-' expression to silence this warning
                        array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize  - (tBits-bitOffset));
                                                                                                 ^
                                                                                    (                               )
./fastBMA.hpp:229:51: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
                                array[i]=(T) (value >> elementSize-bitsWritten-tBits);
                                                    ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./fastBMA.hpp:229:51: note: place parentheses around the '-' expression to silence this warning
                                array[i]=(T) (value >> elementSize-bitsWritten-tBits);
                                                                              ^
                                                       (                            )
./fastBMA.hpp:235:29: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses]
                        mask= ones >> elementSize-bitsWritten;
                                   ˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./fastBMA.hpp:235:29: note: place parentheses around the '-' expression to silence this warning
                        mask= ones >> elementSize-bitsWritten;
                                                 ^
                                      (                      )
./fastBMA.hpp:395:12: warning: unused variable 'n' [-Wunused-variable]
        const int n=size*(size+1)/2;
                  ^
./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:721:18: warning: '&' within '|' [-Wbitwise-op-parentheses]
                   return(hash & 0xFFFFFFF0 | size);
                          ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
./fastBMA.hpp:721:18: note: place parentheses around the '&' expression to silence this warning
                   return(hash & 0xFFFFFFF0 | size);
                               ^
                          (                )
./fastBMA.hpp:723:24: warning: '&' within '|' [-Wbitwise-op-parentheses]
                         return(k.hashValue & 0xFFFFFFF0 | size);      
                                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
./fastBMA.hpp:723:24: note: place parentheses around the '&' expression to silence this warning
                         return(k.hashValue & 0xFFFFFFF0 | size);      
                                            ^
                                (                       )
./fastBMA.hpp:762:24: warning: '&' within '|' [-Wbitwise-op-parentheses]
                         return(k.hashValue & 0xFFFFFFF0 | size);      
                                ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
./fastBMA.hpp:762:24: note: place parentheses around the '&' expression to silence this warning
                         return(k.hashValue & 0xFFFFFFF0 | size);      
                                            ^
                                (                       )
./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:1922:14: warning: unused variable 'izero' [-Wunused-variable]
  int ione=1,izero=0;
             ^
fastBMAR.cpp:33:7: warning: unused variable 'colNum' [-Wunused-variable]
  int colNum = x.ncol();
      ^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:1701:7: warning: expression result unused [-Wunused-value]
                                                *dest++;
                                                ^˜˜˜˜˜˜
./bmaNoMPI.hpp:102:2: note: in instantiation of function template specialization 'initRegressParms<double>' requested here
        initRegressParms<T>(A,ATA,data,nGenes,nRows,nSamples,nTimes,nVars,nThreads,timeSeries);
        ^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
        findEdges(
        ^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:1408:10: warning: unused variable 'r2' [-Wunused-variable]
                Result r2 = boost::math::tools::brent_find_minima(BMAoptimizeFunction<T>(ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR), (T) 1, (T)nRows, optimizeBits, max_iter);
                       ^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
        int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); 
                   ^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
                int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
                           ^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
        findEdges(
        ^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:1661:5: warning: unused variable 'rvalue' [-Wunused-variable]
                T rvalue=0;
                  ^
./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here
                chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR);
                ^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
        int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); 
                   ^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
                int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
                           ^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
        findEdges(
        ^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:662:45: warning: field 'nModels' will be initialized after field 'hashValue' [-Wreorder]
         CompactModelIndices( ModelIndices &mind): nModels(mind.nModels),hashValue(mind.hashValue){
                                                   ^
./fastBMA.hpp:782:17: note: in instantiation of member function 'CompactModelIndices<unsigned long long>::CompactModelIndices' requested here
   modelIndices=CompactModelIndices<uint64_t>(mInd);
                ^
./fastBMA.hpp:1430:23: note: in instantiation of member function 'ModelSet<double>::ModelSet' requested here
  activeModels.insert(ModelSet<T>(modelIndices, 0, 0, 0));
                      ^
./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here
                chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR);
                ^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
        int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); 
                   ^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
                int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
                           ^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
        findEdges(
        ^
In file included from fastBMAR.cpp:3:
./fastBMA.hpp:282:2: warning: control may reach end of non-void function [-Wreturn-type]
        }                                
        ^
./fastBMA.hpp:657:28: note: in instantiation of member function 'BitIndex<unsigned long long>::compare' requested here
                  bool retvalue=bitIndex.compare(b.list,modelBits,nModels);
                                         ^
./fastBMA.hpp:829:84: note: in instantiation of member function 'CompactModelIndices<unsigned long long>::operator==' requested here
 bool operator<(const ModelSet& b) const { return (bic < b.bic) && ! (modelIndices == b.modelIndices); }
                                                                                   ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__functional_base:63:21: note: in instantiation of member function 'ModelSet<double>::operator<' requested here
        {return __x < __y;}
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__tree:1613:17: note: in instantiation of member function 'std::__1::less<ModelSet<double> >::operator()' requested here
            if (value_comp()(__v, __nd->__value_))
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__tree:1923:36: note: in instantiation of function template specialization 'std::__1::__tree<ModelSet<double>, std::__1::less<ModelSet<double> >, std::__1::allocator<ModelSet<double> > >::__find_equal<ModelSet<double> >' requested here
    __node_base_pointer& __child = __find_equal(__parent, __nd->__value_);
                                   ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__tree:1805:32: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
    pair<iterator, bool> __r = __node_insert_unique(__h.get());
                               ^
./fastBMA.hpp:1430:16: note: in instantiation of member function 'std::__1::set<ModelSet<double>, std::__1::less<ModelSet<double> >, std::__1::allocator<ModelSet<double> > >::insert' requested here
  activeModels.insert(ModelSet<T>(modelIndices, 0, 0, 0));
               ^
./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here
                chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR);
                ^
./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here
        int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); 
                   ^
./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here
                int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes);
                           ^
fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here
        findEdges(
        ^
22 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck/networkBMA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (networkBMA)

networkBMA.Rcheck/networkBMA-Ex.timings:

nameusersystemelapsed
ScanBMA0.2310.0150.254
ScanBMAcontrol6.3420.0566.600
contabs2.1970.0242.254
contabs.netwBMA0.0010.0000.001
contabs.prelim0.0010.0000.002
fastBMAcontrol0.0700.0090.080
fastgControl0.1580.0100.171
gControl6.1380.0506.343
iBMAcontrolLM1.4320.0181.477
iterateBMAlm0.9930.0161.017
networkBMA0.3570.0090.367
roc0.9670.0150.989
scores0.9580.0150.978
summary.networkBMA0.3490.0120.364
varord0.2030.0110.215
vignette5.0500.0355.166
writeEdges0.8620.0160.899