sci-mathematics/octave-3.8.2 USE="X curl glpk imagemagick java opengl qhull qrupdate readline sparse zlib -doc -fftw -gnuplot -gui -hdf5 -jit -postscript -static-libs" "octave" just segfaults. ldd does not show libpthread. Editing the ebuild to do "filter-flags -Wl,--as-needed" fixes the issue. I first reduced the problem to the vanilla octave-3.8.2.tar.bz2, just export LDFLAGS="-Wl,--as-needed" and "./configure --disable-gui --without-magick && make" This can probably be fixed in the octave build system. Reproducible: Always
Please provide a full backtrace as described below: https://wiki.gentoo.org/wiki/Bugzilla_HOWTO#Debugging_using_GDB
octave => "Segmentation fault" LD_PRELOAD="/lib64/libpthread.so.0" octave => works Backtrace with gdb ("thread apply all bt full"): Thread 1 (process 7420): #0 0x0000000000000000 in ?? () No symbol table info available. #1 0x00007ffff7d37361 in std::locale::_S_initialize() () from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 No symbol table info available. #2 0x00007ffff7d373a3 in std::locale::locale() () from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 No symbol table info available. #3 0x00007ffff7d341a4 in std::ios_base::Init::Init() () from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 No symbol table info available. #4 0x000000000040198e in __static_initialization_and_destruction_0 (__initialize_p=1, __priority=65535) at /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/include/g++-v4/iostream:74 No locals. #5 _GLOBAL__sub_I__Z17display_availableRSs () at main.cc:655 No locals. #6 0x0000000000402015 in __libc_csu_init (argc=argc@entry=1, argv=argv@entry=0x7fffffffdae8, envp=0x7fffffffdaf8) at elf-init.c:88 i = 1 #7 0x00007ffff7944f1f in __libc_start_main (main=0x400fa0 <main(int, char**)>, argc=1, argv=0x7fffffffdae8, init=0x401fd0 <__libc_csu_init>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdad8) at libc-start.c:245 result = <optimized out> unwind_buf = {cancel_jmp_buf = {{jmp_buf = {4200870, 140737351973808, 140737351513312, 140737347170105, 140737351760912, 1, 1, 140737351950442}, mask_was_saved = -1}}, priv = {pad = {0x1, 0x1c, 0x401fd0 <__libc_csu_init>, 0x7fffffffdae8}, data = {prev = 0x1, cleanup = 0x1c, canceltype = 4202448}}} not_first_call = <optimized out> #8 0x00000000004019cf in _start () No symbol table info available.
LD_DEBUG=all octave ... 24930: initialize program: octave 24930: 24930: symbol=_ZNSt8ios_base4InitC1Ev; lookup in file=octave [0] 24930: symbol=_ZNSt8ios_base4InitC1Ev; lookup in file=/usr/lib64/libX11.so.6 [0] 24930: symbol=_ZNSt8ios_base4InitC1Ev; lookup in file=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 [0] 24930: binding file octave [0] to /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 [0]: normal symbol `_ZNSt8ios_base4InitC1Ev' [GLIBCXX_3.4] 24930: symbol=_ZNSt6localeC1Ev; lookup in file=octave [0] 24930: symbol=_ZNSt6localeC1Ev; lookup in file=/usr/lib64/libX11.so.6 [0] 24930: symbol=_ZNSt6localeC1Ev; lookup in file=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 [0] 24930: binding file /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 [0] to /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 [0]: normal symbol `_ZNSt6localeC1Ev' [GLIBCXX_3.4] 24930: symbol=pthread_once; lookup in file=octave [0] 24930: symbol=pthread_once; lookup in file=/usr/lib64/libX11.so.6 [0] 24930: symbol=pthread_once; lookup in file=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libstdc++.so.6 [0] 24930: symbol=pthread_once; lookup in file=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.2/libgcc_s.so.1 [0] 24930: symbol=pthread_once; lookup in file=/lib64/libc.so.6 [0] 24930: symbol=pthread_once; lookup in file=/usr/lib64/libxcb.so.1 [0] 24930: symbol=pthread_once; lookup in file=/lib64/libdl.so.2 [0] 24930: symbol=pthread_once; lookup in file=/lib64/libm.so.6 [0] 24930: symbol=pthread_once; lookup in file=/lib64/ld-linux-x86-64.so.2 [0] 24930: symbol=pthread_once; lookup in file=/usr/lib64/libXau.so.6 [0] 24930: symbol=pthread_once; lookup in file=/usr/lib64/libXdmcp.so.6 [0] Segmentation fault Notice "pthread_once" is not bound.
Markus, could you please retry emerging sci-mathematics/octave-3.8.2, this time with LDFLAGS set to LDFLAGS="-Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--no-undefined" and see if fails in the linking steps? A missing pthread link would cause the compile phase to fail with -Wl,--no-undefined in shared object files.
Just tried the vanilla ebuild from portage. But after like ten month I dont get that error anymore. The system evolved, so I have no clue what could have caused that.
