[Debian-med-packaging] Bug#753190: ncbi-blast+: FTBFS: shared_ptr_base.h:479:39: error: must #include <typeinfo> before using typeid

[David Suárez]

Source: ncbi-blast+
Version: 2.2.29-1
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20140628 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> /usr/bin/g++  -std=gnu++11 -c -Wall -Wno-format-y2k  -pthread -fopenmp -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC    -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -D_FORTIFY_SOURCE=2 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/BUILD/inc -I/build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include  /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/src/corelib/ncbi_os_unix.cpp -o ncbi_os_unix.o 
> In file included from /usr/include/c++/4.9/bits/shared_ptr.h:52:0,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbistl.hpp:219,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbistre.hpp:40,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbi_stack.hpp:35,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbidiag.hpp:42,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/error_codes.hpp:38,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/src/corelib/ncbi_os_unix.cpp:33:
> /usr/include/c++/4.9/bits/shared_ptr_base.h: In member function 'virtual void* std::_Sp_counted_deleter<_Ptr, _Deleter, _Alloc, _Lp>::_M_get_deleter(const std::type_info&)':
> /usr/include/c++/4.9/bits/shared_ptr_base.h:479:39: error: must #include <typeinfo> before using typeid
>          return __ti == typeid(_Deleter) ? &_M_impl._M_del() : nullptr;
>                                        ^
> /usr/include/c++/4.9/bits/shared_ptr_base.h: In member function 'virtual void* std::_Sp_counted_ptr_inplace<_Tp, _Alloc, _Lp>::_M_get_deleter(const std::type_info&)':
> /usr/include/c++/4.9/bits/shared_ptr_base.h:543:40: error: must #include <typeinfo> before using typeid
>   if (__ti == typeid(_Sp_make_shared_tag))
>                                         ^
> /usr/include/c++/4.9/bits/shared_ptr_base.h: In constructor 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...)':
> /usr/include/c++/4.9/bits/shared_ptr_base.h:1094:50: error: must #include <typeinfo> before using typeid
>     void* __p = _M_refcount._M_get_deleter(typeid(__tag));
>                                                   ^
> In file included from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbistl.hpp:219:0,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbistre.hpp:40,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbi_stack.hpp:35,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/ncbidiag.hpp:42,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/include/corelib/error_codes.hpp:38,
>                  from /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/src/corelib/ncbi_os_unix.cpp:33:
> /usr/include/c++/4.9/bits/shared_ptr.h: In function '_Del* std::get_deleter(const std::__shared_ptr<_Tp2, _Lp>&)':
> /usr/include/c++/4.9/bits/shared_ptr.h:79:63: error: must #include <typeinfo> before using typeid
>        return static_cast<_Del*>(__p._M_get_deleter(typeid(_Del)));
>                                                                ^
> /build/ncbi-blast+-zNoIe0/ncbi-blast+-2.2.29/c++/BUILD/build/Makefile.rules:50: recipe for target 'ncbi_os_unix.o' failed
> make[3]: *** [ncbi_os_unix.o] Error 1

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2014/06/28/ncbi-blast+_2.2.29-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.