#1 Cannot compile

[Martin]

I'm having issues when I try to compile muffinec.

Error:

cc1plus: warning: command line option '-std=c99' is valid for C/ObjC but not for C++
In file included from /usr/local/include/assert.h:5:0,
from /home/mberacochea/.linuxbrew/Cellar/gcc/5.4.0/include/c++/5.4.0/cassert:43,
from util.h:32,
from greedygrouping.h:48,
from greedygrouping.cpp:27:
/usr/local/include/except.h:15:32: error: conflicting declaration 'typedef struct Except_Frame_T Except_Frame_T'
typedef struct Except_Frame_T Except_Frame_T;
^
/usr/local/include/except.h:15:16: note: previous declaration as 'struct Except_Frame_T'
typedef struct Except_Frame_T Except_Frame_T;
^
/usr/local/include/except.h:17:18: error: field 'prev' has incomplete type 'Except_Frame_T'
Except_Frame_T prev;
^
cc1plus: warning: command line option '-std=c99' is valid for C/ObjC but not for C++
In file included from /usr/local/include/assert.h:5:0,
from /home/mberacochea/.linuxbrew/Cellar/gcc/5.4.0/include/c++/5.4.0/cassert:43,
from util.h:32,
from greedygrouping.h:48,
from greedygrouping.cpp:27:
/usr/local/include/except.h:15:32: error: conflicting declaration 'typedef struct Except_Frame_T Except_Frame_T'
typedef struct Except_Frame_T Except_Frame_T;
^
/usr/local/include/except.h:15:16: note: previous declaration as 'struct Except_Frame_T'
typedef struct Except_Frame_T Except_Frame_T;
^
/usr/local/include/except.h:17:18: error: field 'prev' has incomplete type 'Except_Frame_T'
Except_Frame_T prev;
^
/usr/local/include/except.h:16:8: note: definition of 'struct Except_Frame_T' is not complete until the closing brace
struct Except_Frame_T {
^
In file included from greedygrouping.cpp:27:0:
greedygrouping.h: In constructor 'upv::i3m::muffinec::GreedyGrouping::GreedyGrouping(const upv::i3m::muffinec::GlobalParams&, upv::i3m::general::FastW&, upv::i3m::general::Fastr&)':
greedygrouping.h:103:14: warning: 'upv::i3m::muffinec::GreedyGrouping::numGenNeighb' will be initialized after [-Wreorder]
uint64_t numGenNeighb;
^
greedygrouping.h:98:14: warning: 'uint64_t upv::i3m::muffinec::GreedyGrouping::numMinKCall' [-Wreorder]
uint64_t numMinKCall;
^
greedygrouping.cpp:41:1: warning: when initialized here [-Wreorder]
upv::i3m::muffinec::GreedyGrouping::GreedyGrouping(/std::string inFPatha, uint32_t kmerSizea,
^
In file included from greedygrouping.cpp:27:0:
greedygrouping.h:113:14: warning: 'upv::i3m::muffinec::GreedyGrouping::readsFile' will be initialized after [-Wreorder]
uint64_t readsFile;
^
greedygrouping.h:109:14: warning: 'uint64_t upv::i3m::muffinec::GreedyGrouping::numTrim' [-Wreorder]
uint64_t numTrim;
^
greedygrouping.cpp:41:1: warning: when initialized here [-Wreorder]
upv::i3m::muffinec::GreedyGrouping::GreedyGrouping(/std::string inFPatha, uint32_t kmerSizea,
^
In file included from greedygrouping.cpp:27:0:
greedygrouping.h:132:11: warning: 'upv::i3m::muffinec::GreedyGrouping::minSizeKmerNeigh' will be initialized after [-Wreorder]
float minSizeKmerNeigh;
^
greedygrouping.h:96:18: warning: 'unsigned int upv::i3m::muffinec::GreedyGrouping::oversNeighb' [-Wreorder]
unsigned int oversNeighb;
^
greedygrouping.cpp:41:1: warning: when initialized here [-Wreorder]
upv::i3m::muffinec::GreedyGrouping::GreedyGrouping(/std::string inFPatha, uint32_t kmerSizea,
^
greedygrouping.cpp: In member function 'void upv::i3m::muffinec::GreedyGrouping::countKmers()':
greedygrouping.cpp:225:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (maxQ < line[idx])
^
greedygrouping.cpp:227:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (minQ > line[idx])
^
In file included from greedygrouping.cpp:27:0:
greedygrouping.h: In member function 'bool upv::i3m::muffinec::GreedyGrouping::isBaseLowQ(int)':
greedygrouping.h:230:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
make: ** [build/greedygrouping.o] Error 1

gcc version:

Reading specs from /home/mberacochea/.linuxbrew/Cellar/gcc/5.4.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.4.0/specs
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/home/mberacochea/.linuxbrew/Cellar/gcc/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/gcc/5.4.0 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/home/linuxbrew/.linuxbrew/opt/gmp --with-mpfr=/home/linuxbrew/.linuxbrew/opt/mpfr --with-mpc=/home/linuxbrew/.linuxbrew/opt/libmpc --with-isl=/home/linuxbrew/.linuxbrew/opt/isl --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 5.4.0' --with-bugurl=https://github.com/Homebrew/homebrew/issues --with-boot-ldflags='-static-libstdc++ -static-libgcc ' --disable-nls --disable-multilib
Thread model: posix
gcc version 5.4.0 (Homebrew gcc 5.4.0)

I'll appreciatte any help.

Regards