Package: networkBMA

Version: 2.27.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings networkBMA_2.27.0.tar.gz

StartedAt: 2020-01-16 06:59:42 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:02:05 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 143.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: networkBMA.Rcheck

Warnings: 1

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings networkBMA_2.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/networkBMA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘networkBMA/DESCRIPTION’ ... OK
* this is package ‘networkBMA’ version ‘2.27.0’
* 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:
  ScanBMA_full.cpp:137:21: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
  ScanBMA_full.cpp:328:19: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
  ScanBMA_full.cpp:421:21: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
  ScanBMA_full.cpp:614:19: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
  ./fastBMA.hpp:1701:7: warning: expression result unused [-Wunused-value]
  ./fastBMA.hpp:662:45: warning: field 'nModels' will be initialized after field 'hashValue' [-Wreorder]
Found the following additional notes/warnings:
  ./fastBMA.hpp:282:2: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Users/biocbuild/bbs-3.11-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 dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  summary.networkBMA
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 use of PKG_*FLAGS in Makefiles ... NOTE
   PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.in’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
gControl       9.531  0.088  11.238
ScanBMAcontrol 9.033  0.137  10.553
vignette       5.627  0.119   6.288
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/networkBMA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL networkBMA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘networkBMA’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./include -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./include -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c ScanBMA_full.cpp -o ScanBMA_full.o
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from ScanBMA_full.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
ScanBMA_full.cpp:137:21: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
  arma::uvec pord = sort_index(priorProbs, 1);
                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:304:44: note: expanded from macro 'arma_deprecated'
    #define arma_deprecated __attribute__((__deprecated__))
                                           ^
ScanBMA_full.cpp:328:19: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
                  ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:304:44: note: expanded from macro 'arma_deprecated'
    #define arma_deprecated __attribute__((__deprecated__))
                                           ^
ScanBMA_full.cpp:421:21: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
  arma::uvec pord = sort_index(priorProbs, 1);
                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:304:44: note: expanded from macro 'arma_deprecated'
    #define arma_deprecated __attribute__((__deprecated__))
                                           ^
ScanBMA_full.cpp:614:19: warning: 'sort_index<arma::Mat<double> >' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
                  ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:304:44: note: expanded from macro 'arma_deprecated'
    #define arma_deprecated __attribute__((__deprecated__))
                                           ^
21 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./include -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -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:626:12: warning: unused variable 'nModels' [-Wunused-variable]
                uint8_t nModels=0;
                        ^
./fastBMA.hpp:625:12: warning: unused variable 'modelBits' [-Wunused-variable]
                uint8_t modelBits=gModelBits; 
                        ^
./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); }
                                                                                   ^
/usr/local/clang8/bin/../include/c++/v1/__functional_base:55:21: note: in instantiation of member function 'ModelSet<double>::operator<' requested here
        {return __x < __y;}
                    ^
/usr/local/clang8/bin/../include/c++/v1/__tree:2028:17: note: in instantiation of member function 'std::__1::less<ModelSet<double> >::operator()' requested here
            if (value_comp()(__v, __nd->__value_))
                ^
/usr/local/clang8/bin/../include/c++/v1/__tree:2151:36: 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, __k);
                                   ^
/usr/local/clang8/bin/../include/c++/v1/__tree:1276:16: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return __emplace_unique_key_args(_NodeTypes::__get_key(__v), _VSTD::move(__v));
               ^
./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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-networkBMA/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (networkBMA)

name	user	system	elapsed
ScanBMA	0.135	0.021	0.162
ScanBMAcontrol	9.033	0.137	10.553
contabs	2.708	0.078	3.233
contabs.netwBMA	0.000	0.001	0.001
contabs.prelim	0.000	0.000	0.001
fastBMAcontrol	0.085	0.009	0.116
fastgControl	0.088	0.010	0.121
gControl	9.531	0.088	11.238
iBMAcontrolLM	0.932	0.012	1.133
iterateBMAlm	1.268	0.029	1.509
networkBMA	0.502	0.020	0.550
roc	1.499	0.022	1.867
scores	1.453	0.038	1.719
summary.networkBMA	0.438	0.026	0.517
varord	0.244	0.013	0.258
vignette	5.627	0.119	6.288
writeEdges	1.049	0.087	1.135