error building isaac2

[lindenb]

Hi illumina, I've started installing isaac2. ./configure is OK but when i type make i receive the following error:

In file included from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Threads.hpp:26,
                 from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/bgzf/BgzfReader.hh:29,
                 from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp:25:
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:23:18: error: atomic: No such file or direc
tory
In file included from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Threads.hpp:26,
                 from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/bgzf/BgzfReader.hh:29,
                 from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp:25:
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:145: error: 'atomic_int' in namespace 'std'
 does not name a type
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh: In constructor 'isaac::common::detail::Cer
rBlocker::CerrBlocker()':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:149: error: 'cerrBlocked_' was not declared
 in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh: In static member function 'static bool isa
ac::common::detail::CerrBlocker::blocked()':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:158: error: 'cerrBlocked_' was not declared
 in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh: In destructor 'isaac::common::detail::Cerr
Blocker::~CerrBlocker()':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:188: error: 'cerrBlocked_' was not declared
 in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:189: error: 'cerrBlocked_' was not declared
 in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp: In member function 'void isaac::bgzf::Para
llelBgzfReader::open(const boost::filesystem::path&)':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp:145: error: no match for 'operator<<' in '(
((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<bo
ost::iostreams::output, char, std::char_traits<char>, std::allocator<char>, boost::iostreams::public_>(((const boost::iostreams::null_sink&)((const b
oost::iostreams::null_sink*)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stre
am<boost::iostreams::output, char, std::char_traits<char>, std::allocator<char>, boost::iostreams::public_>(((std::basic_ostream<char, std::char_trai
ts<char> >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::bas
ic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>& (*)(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits 
= std::char_traits<char>]
(...)

gcc version

]$ g++ -v      
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-16) (GCC) 

$ uname -a
Linux airain71 2.6.32-573.1.1.el6.Bull.80.x86_64 #1 SMP Fri Jul 31 01:43:22 CEST 2015 x86_64 x86_64 x86_64 GNU/Linux

[kvshams]

Hi lindenb, Your version of GCC is not suitable for isaac2. It need gcc version higher than 4.7 for the compilation. The earliest supported gcc is 4.7.3. Shams

[lindenb]

@kvshams ok thanks, I assumed the gcc version was detected by ./configure.