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CNAV log file (build_win64)

Wed Jul 23 22:30:17 2014: Building binary for package CNAV (SVN revision 23)
using R version 3.1.1 Patched (2014-07-20 r66220) ...

* installing to library 'R:/lib/local/3.1'
* installing *source* package 'CNAV' ...
** libs

*** arch - i386
g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG    -I"R:/lib/local/3.1/Rcpp/include" -I"R:/lib/local/3.1/RcppArmadillo/include" -I"R:/lib/local/3.1/BH/include" -I"R:/base/local215/include"  -IR:/lib/local/3.1/Rcpp/include -I"R:/lib/local/3.1/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c HMM2Rinterface.cpp -o HMM2Rinterface.o
In file included from HMMgibbs.hpp:31:0,
                 from HMM2Rinterface.cpp:9:
HMMparticle.hpp: In constructor 'HMMparticle::HMMparticle(HMMdataSet&, arma::mat, arma::umat, arma::uword, double, arma::uword, arma::uword, arma::uword)':
HMMparticle.hpp:64:13: warning: 'HMMparticle::emission_matrix' will be initialized after [-Wreorder]
HMMparticle.hpp:61:9: warning:   'double HMMparticle::lambda' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:61:9: warning: 'HMMparticle::lambda' will be initialized after [-Wreorder]
HMMparticle.hpp:60:14: warning:   'arma::uword HMMparticle::lambda_ref' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:60:14: warning: 'HMMparticle::lambda_ref' will be initialized after [-Wreorder]
HMMparticle.hpp:57:25: warning:   'boost::random::mt19937 HMMparticle::central_generator' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:57:25: warning: 'HMMparticle::central_generator' will be initialized after [-Wreorder]
HMMparticle.hpp:53:14: warning:   'arma::uword HMMparticle::MAXDEPTH' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
In file included from HMMgibbs.hpp:33:0,
                 from HMM2Rinterface.cpp:9:
HMMchib.hpp: In member function 'HMMchib::IDRefSequenceCountTuple HMMchib::produce_random_sequence(const mat&)':
HMMchib.hpp:58:9: warning: unused variable 'refGenotype' [-Wunused-variable]
HMMchib.hpp: In constructor 'HMMchib::HMMchib(arma::uword, const umat&, const mat&, arma::uword, HMMdataSet&)':
HMMchib.hpp:151:17: warning: 'HMMchib::data_set' will be initialized after [-Wreorder]
HMMchib.hpp:38:37: warning:   'BasicTypes::base_generator_type HMMchib::common_rgen' [-Wreorder]
HMMchib.hpp:156:2: warning:   when initialized here [-Wreorder]
HMM2Rinterface.cpp: In function 'SEXPREC* HMMinterface(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
HMM2Rinterface.cpp:46:10: warning: unused variable 'bcollapsed' [-Wunused-variable]
In file included from R:/lib/local/3.1/BH/include/boost/thread/shared_mutex.hpp:18:0,
                 from R:/lib/local/3.1/BH/include/boost/thread/detail/thread_group.hpp:9,
                 from R:/lib/local/3.1/BH/include/boost/thread/thread.hpp:13,
                 from R:/lib/local/3.1/BH/include/boost/thread.hpp:13,
                 from HMMkernelwrapper.hpp:41,
                 from HMMgibbs.hpp:32,
                 from HMM2Rinterface.cpp:9:
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:124:103:   instantiated from here
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG    -I"R:/lib/local/3.1/Rcpp/include" -I"R:/lib/local/3.1/RcppArmadillo/include" -I"R:/lib/local/3.1/BH/include" -I"R:/base/local215/include"  -IR:/lib/local/3.1/Rcpp/include -I"R:/lib/local/3.1/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c HMMdataSet.cpp -o HMMdataSet.o
g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG    -I"R:/lib/local/3.1/Rcpp/include" -I"R:/lib/local/3.1/RcppArmadillo/include" -I"R:/lib/local/3.1/BH/include" -I"R:/base/local215/include"  -IR:/lib/local/3.1/Rcpp/include -I"R:/lib/local/3.1/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c HMMgibbs.cpp -o HMMgibbs.o
In file included from HMMgibbs.hpp:31:0,
                 from HMMgibbs.cpp:23:
HMMparticle.hpp: In constructor 'HMMparticle::HMMparticle(HMMdataSet&, arma::mat, arma::umat, arma::uword, double, arma::uword, arma::uword, arma::uword)':
HMMparticle.hpp:64:13: warning: 'HMMparticle::emission_matrix' will be initialized after [-Wreorder]
HMMparticle.hpp:61:9: warning:   'double HMMparticle::lambda' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:61:9: warning: 'HMMparticle::lambda' will be initialized after [-Wreorder]
HMMparticle.hpp:60:14: warning:   'arma::uword HMMparticle::lambda_ref' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:60:14: warning: 'HMMparticle::lambda_ref' will be initialized after [-Wreorder]
HMMparticle.hpp:57:25: warning:   'boost::random::mt19937 HMMparticle::central_generator' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:57:25: warning: 'HMMparticle::central_generator' will be initialized after [-Wreorder]
HMMparticle.hpp:53:14: warning:   'arma::uword HMMparticle::MAXDEPTH' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
In file included from HMMgibbs.hpp:33:0,
                 from HMMgibbs.cpp:23:
HMMchib.hpp: In member function 'HMMchib::IDRefSequenceCountTuple HMMchib::produce_random_sequence(const mat&)':
HMMchib.hpp:58:9: warning: unused variable 'refGenotype' [-Wunused-variable]
HMMchib.hpp: In constructor 'HMMchib::HMMchib(arma::uword, const umat&, const mat&, arma::uword, HMMdataSet&)':
HMMchib.hpp:151:17: warning: 'HMMchib::data_set' will be initialized after [-Wreorder]
HMMchib.hpp:38:37: warning:   'BasicTypes::base_generator_type HMMchib::common_rgen' [-Wreorder]
HMMchib.hpp:156:2: warning:   when initialized here [-Wreorder]
HMMgibbs.cpp: In constructor 'Gibbs_Sampling::Gibbs_Sampling(HMMdataSet&, const vec&, const mat&, const umat&, arma::uword, arma::uword, arma::uword, arma::uword, arma::uword)':
HMMgibbs.cpp:50:14: warning: unused variable 'nid' [-Wunused-variable]
In file included from R:/lib/local/3.1/BH/include/boost/thread/shared_mutex.hpp:18:0,
                 from R:/lib/local/3.1/BH/include/boost/thread/detail/thread_group.hpp:9,
                 from R:/lib/local/3.1/BH/include/boost/thread/thread.hpp:13,
                 from R:/lib/local/3.1/BH/include/boost/thread.hpp:13,
                 from HMMkernelwrapper.hpp:41,
                 from HMMgibbs.hpp:32,
                 from HMMgibbs.cpp:23:
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:124:103:   instantiated from here
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
R:/lib/local/3.1/BH/include/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from HMMgibbs.hpp:32:0,
                 from HMMgibbs.cpp:23:
HMMkernelwrapper.hpp: In constructor 'HMMkernelwrapper::HMMkernelwrapper(arma::uword, arma::uword, arma::uword) [with KernelType = HMMlongjump_squirrelKernel, bool CollapsedVersion = true, arma::uword = unsigned int]':
HMMgibbs.cpp:100:119:   instantiated from here
HMMkernelwrapper.hpp:134:13: warning: 'HMMkernelwrapper::MCMCkernel' will be initialized after [-Wreorder]
HMMkernelwrapper.hpp:184:62: warning:   base 'kernel_monitor_class' [-Wreorder]
HMMkernelwrapper.hpp:183:2: warning:   when initialized here [-Wreorder]
HMMkernelwrapper.hpp: In constructor 'HMMkernelwrapper::HMMkernelwrapper(arma::uword, arma::uword, arma::uword) [with bool CollapsedVersion = false, arma::uword = unsigned int]':
HMMgibbs.cpp:101:122:   instantiated from here
HMMkernelwrapper.hpp:258:11: warning: 'HMMkernelwrapper::countdown_start' will be initialized after [-Wreorder]
HMMkernelwrapper.hpp:423:63: warning:   base 'kernel_monitor_class' [-Wreorder]
HMMkernelwrapper.hpp:422:2: warning:   when initialized here [-Wreorder]
HMMkernelwrapper.hpp: In member function 'HMMparticle::IDRefSequenceCountTuple HMMkernelwrapper::produce_random_sequence(boost::random::mt19937&) [with bool CollapsedVersion = false, HMMparticle::IDRefSequenceCountTuple = boost::tuples::tuple, arma::Mat, bool>, boost::random::mt19937 = boost::random::mersenne_twister_engine]':
HMMkernelwrapper.hpp:357:93:   instantiated from 'void HMMkernelwrapper::cycling_thread(arma::uword) [with bool CollapsedVersion = false, arma::uword = unsigned int]'
HMMkernelwrapper.hpp:433:4:   instantiated from 'HMMkernelwrapper::HMMkernelwrapper(arma::uword, arma::uword, arma::uword) [with bool CollapsedVersion = false, arma::uword = unsigned int]'
HMMgibbs.cpp:101:122:   instantiated from here
HMMkernelwrapper.hpp:283:9: warning: unused variable 'refGenotype' [-Wunused-variable]
g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG    -I"R:/lib/local/3.1/Rcpp/include" -I"R:/lib/local/3.1/RcppArmadillo/include" -I"R:/lib/local/3.1/BH/include" -I"R:/base/local215/include"  -IR:/lib/local/3.1/Rcpp/include -I"R:/lib/local/3.1/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c HMMparticle.cpp -o HMMparticle.o
In file included from HMMparticle.cpp:1:0:
HMMparticle.hpp: In constructor 'HMMparticle::HMMparticle(HMMdataSet&, arma::mat, arma::umat, arma::uword, double, arma::uword, arma::uword, arma::uword)':
HMMparticle.hpp:64:13: warning: 'HMMparticle::emission_matrix' will be initialized after [-Wreorder]
HMMparticle.hpp:61:9: warning:   'double HMMparticle::lambda' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:61:9: warning: 'HMMparticle::lambda' will be initialized after [-Wreorder]
HMMparticle.hpp:60:14: warning:   'arma::uword HMMparticle::lambda_ref' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:60:14: warning: 'HMMparticle::lambda_ref' will be initialized after [-Wreorder]
HMMparticle.hpp:57:25: warning:   'boost::random::mt19937 HMMparticle::central_generator' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
HMMparticle.hpp:57:25: warning: 'HMMparticle::central_generator' will be initialized after [-Wreorder]
HMMparticle.hpp:53:14: warning:   'arma::uword HMMparticle::MAXDEPTH' [-Wreorder]
HMMparticle.hpp:160:2: warning:   when initialized here [-Wreorder]
g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG    -I"R:/lib/local/3.1/Rcpp/include" -I"R:/lib/local/3.1/RcppArmadillo/include" -I"R:/lib/local/3.1/BH/include" -I"R:/base/local215/include"  -IR:/lib/local/3.1/Rcpp/include -I"R:/lib/local/3.1/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c calculate_unnormalized_density.cpp -o calculate_unnormalized_density.o
calculate_unnormalized_density.cpp: In function 'BasicTypes::IDRefSequenceCountTuple produce_random_sequence(const mat&, const umat&, HMMdataSet&, BasicTypes::base_generator_type&, arma::uword)':
calculate_unnormalized_density.cpp:78:8: warning: unused variable 'refGenotype' [-Wunused-variable]
g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG    -I"R:/lib/local/3.1/Rcpp/include" -I"R:/lib/local/3.1/RcppArmadillo/include" -I"R:/lib/local/3.1/BH/include" -I"R:/base/local215/include"  -IR:/lib/local/3.1/Rcpp/include -I"R:/lib/local/3.1/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c generate_random_sequences.cpp -o generate_random_sequences.o
g++ -m32 -shared -s -static-libgcc -o CNAV.dll tmp.def HMM2Rinterface.o HMMdataSet.o HMMgibbs.o HMMparticle.o calculate_unnormalized_density.o generate_random_sequences.o -LR:/lib/R/R-patched/bin/i386 -lRlapack -LR:/lib/R/R-patched/bin/i386 -lRblas -lgfortran -lboost_system -lboost_thread -LR:/base/local215/lib/i386 -LR:/base/local215/lib -LR:/lib/R/R-patched/bin/i386 -lR
r:/base/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lboost_system
r:/base/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lboost_thread
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'CNAV'
* removing 'R:/lib/local/3.1/CNAV'
Run time: 80.03 seconds.