Compiling error

[tangerzhang]

Hello, I am trying to installl LACHESIS in our linux server (centos6.2) with gcc4.9, boost1.61 and samtools v0.19.
I think I have installed all the dependency correctly, however, I still got error when compiling HMM.c.
Could you please help me solve this problem? Thanks so much!
Please see below for error details:

make[2]: Leaving directory /home/zhangxt/software/LACHESIS-master/include/gtools' make -C markov make[2]: Entering directory/home/zhangxt/software/LACHESIS-master/include/markov'
g++ -c TestMarkovModel.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c SymbolSet.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c WDAG.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c MarkovModel.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c MarkovChain.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c HMM.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
HMM.cc: In member function 'bool HMM::AdjustProbsToBaumWelch(const WDAG&)':
HMM.cc:422:38: error: call of overloaded 'isnan(gnu_cxx::__alloc_traitsstd::allocator::value_type&)' is ambiguous
if ( isnan( new_trans_probs[S1][S2] ) )
^
HMM.cc:422:38: note: candidates are:
In file included from /home/zhangxt/include/features.h:358:0,
from /home/zhangxt/include/c++/4.9.0/x86_64-unknown-linux-gnu/bits/os_defines.h:39,
from /home/zhangxt/include/c++/4.9.0/x86_64-unknown-linux-gnu/bits/c++config.h:430,
from /home/zhangxt/include/c++/4.9.0/bits/stl_algobase.h:59,
from /home/zhangxt/include/c++/4.9.0/vector:60,
from MarkovModel.h:46,
from HMM.h:57,
from HMM.cc:18:
/home/zhangxt/include/bits/mathcalls.h:235:1: note: int isnan(double)
__MATHDECL_1 (int,isnan,, (Mdouble __value)) __attribute ((const));
^
In file included from WDAG.h:28:0,
from HMM.h:58,
from HMM.cc:18:
/home/zhangxt/include/c++/4.9.0/cmath:626:3: note: constexpr bool std::isnan(long double)
isnan(long double __x)
^
/home/zhangxt/include/c++/4.9.0/cmath:622:3: note: constexpr bool std::isnan(double)
isnan(double __x)
^
/home/zhangxt/include/c++/4.9.0/cmath:618:3: note: constexpr bool std::isnan(float)
isnan(float __x)
^
make[2]: *** [HMM.o] Error 1
make[2]: Leaving directory /home/zhangxt/software/LACHESIS-master/include/markov' make[1]: *** [libJmarkov.a] Error 2 make[1]: Leaving directory/home/zhangxt/software/LACHESIS-master/include'
make: *** [libs] Error 2

[zorg-it]

I came across same issue, solved removing -std=c++11 option from CFLAGS in Makefile, only in the Makefile of include/markov folder.
Hope could help.

[tangerzhang]

Thanks for your message.
Yes, I also solved the problem by simply removing the flag.

2016年10月3日星期一，zorg-it notifications@github.com 写道：

I came across same issue, solved removing -std=c++11 option from CFLAGS in
Makefile, only in the Makefile of include/markov folder.
Hope could help.

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