--with-oniguruma は付けてないです。付けて試してみたほうがいいですかね？バックトレースはこんな感じです。
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 805b021c0 (LWP 100240)]
0x000000080595e386 in strlen () from /lib/libc.so.7
(gdb) bt
#0 0x000000080595e386 in strlen () from /lib/libc.so.7
#1 0x00000008058a132d in realpath () from /lib/libc.so.7
#2 0x0000000000492deb in CACHE::get_realpath (path=Variable "path" is not available.
) at cache.cpp:1111
#3 0x000000000047b1a4 in CORE::Core::exec_command (this=0x805ea1800)
at core.cpp:2974
#4 0x000000000047ba91 in CORE::Core::callback_dispatch (this=0x805ea1800)
at core.cpp:2811
#5 0x00000000004b1d6d in CORE::DispatchManager::slot_dispatch (this=0x0)
at dispatchmanager.cpp:98
#6 0x0000000801c287c3 in Glib::DispatchNotifier::pipe_io_handler ()
from /usr/local/lib/libglibmm-2.4.so.1
#7 0x0000000801c28b09 in sigc::internal::slot_call1<sigc::bound_mem_functor1<bool, Glib::DispatchNotifier, Glib::IOCondition>, bool, Glib::IOCondition>::call_it () from /usr/local/lib/libglibmm-2.4.so.1
#8 0x0000000801c2b4f7 in Glib::IOSource::dispatch ()
from /usr/local/lib/libglibmm-2.4.so.1
#9 0x0000000801c2ac57 in Glib::Source::dispatch_vfunc ()
from /usr/local/lib/libglibmm-2.4.so.1
#10 0x00000008043fbec2 in g_main_context_dispatch ()
from /usr/local/lib/libglib-2.0.so.0
#11 0x00000008043ff09e in g_main_context_check ()
from /usr/local/lib/libglib-2.0.so.0
#12 0x00000008043ff389 in g_main_loop_run ()
from /usr/local/lib/libglib-2.0.so.0
#13 0x00000008016081c3 in gtk_main () from /usr/local/lib/libgtk-x11-2.0.so.0
#14 0x0000000800e479dc in Gtk::Main::run ()
from /usr/local/lib/libgtkmm-2.4.so.1
#15 0x000000000042ab2e in main (argc=1, argv=0x7fffffffe930) at main.cpp:580