Re: tophat: Help needed with boost

[Christian Kastner <debian@kvr.at>]

On 2014-03-18 14:19, Andreas Tille wrote:
> segment_juncs.o: In function `boost::thread::get_id() const':
> /usr/include/boost/thread/detail/thread.hpp:730: undefined reference to `boost::thread::native_handle()'
> segment_juncs.o: In function `boost::thread::join()':
> /usr/include/boost/thread/detail/thread.hpp:756: undefined reference to `boost::thread::join_noexcept()'
> segment_juncs.o: In function `~thread':
> ...

Looking the command that generates this output, you can see that it's
missing -lboost_thread and -lboost_system:

> g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro -L/usr/lib  -Wl,-z,relro -o segment_juncs segment_juncs.o ../src/libtophat.a   -lbam -l

The generated Makefiles have empty BOOST_THREAD_LIB and BOOST_SYSTEM_LIB
variables. A bit of investigating reveals that it's the location of the
boost libraries that seems to be the problem, because adding the
following to debian/rules seems to fix the issue:

override_dh_auto_configure:
	dh_auto_configure -- \
		--with-boost-libdir=/usr/lib/$(DEB_HOST_MULTIARCH)

I'm not entirely sure that's the correct solution to the problem,
though. Perhaps someone with more Multiarch + autotools experience can
enlighten us.

Christian