Please x86 and amd64 at least.
Martin, To properly file a stabilization request, include the keyword STABLEREQ in the Keywords field.
Please go ahead arch teams.
amd64 stable
I guess this isn't supposed to be happening (on x86): muscle -in agc.fst -out agc_aligned.fst MUSCLE v3.7 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. agc 3 seqs, max length 1722, avg length 1637 *** buffer overflow detected ***: muscle terminated ======= Backtrace: ========= /lib/libc.so.6(__fortify_fail+0x50)[0xb768d780] /lib/libc.so.6(+0xe17da)[0xb768b7da] /lib/libc.so.6(+0xe0ea8)[0xb768aea8] /lib/libc.so.6(_IO_default_xsputn+0x9e)[0xb7613d9e] /lib/libc.so.6(_IO_vfprintf+0x61a)[0xb75e708a] /lib/libc.so.6(__vsprintf_chk+0xa7)[0xb768af57] /lib/libc.so.6(__sprintf_chk+0x2d)[0xb768ae9d] muscle[0x806f19c] ======= Memory map: ======== 08048000-0808b000 r-xp 00000000 08:01 2722915 /usr/bin/muscle 0808b000-0808c000 r--p 00042000 08:01 2722915 /usr/bin/muscle 0808c000-08098000 rw-p 00043000 08:01 2722915 /usr/bin/muscle 08098000-080f5000 rw-p 00000000 00:00 0 08f59000-08f7a000 rw-p 00000000 00:00 0 [heap] b6da7000-b75aa000 rw-p 00000000 00:00 0 b75aa000-b76e9000 r-xp 00000000 08:01 6853113 /lib/libc-2.11.1.so b76e9000-b76ea000 ---p 0013f000 08:01 6853113 /lib/libc-2.11.1.so b76ea000-b76ec000 r--p 0013f000 08:01 6853113 /lib/libc-2.11.1.so b76ec000-b76ed000 rw-p 00141000 08:01 6853113 /lib/libc-2.11.1.so b76ed000-b76f0000 rw-p 00000000 00:00 0 b76f0000-b770c000 r-xp 00000000 08:01 3802800 /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libgcc_s.so.1 b770c000-b770d000 r--p 0001b000 08:01 3802800 /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libgcc_s.so.1 b770d000-b770e000 rw-p 0001c000 08:01 3802800 /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libgcc_s.so.1 b770e000-b7732000 r-xp 00000000 08:01 6853402 /lib/libm-2.11.1.so b7732000-b7733000 r--p 00023000 08:01 6853402 /lib/libm-2.11.1.so b7733000-b7734000 rw-p 00024000 08:01 6853402 /lib/libm-2.11.1.so b7734000-b7818000 r-xp 00000000 08:01 3802635 /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libstdc++.so.6.0.13 b7818000-b781c000 r--p 000e4000 08:01 3802635 /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libstdc++.so.6.0.13 b781c000-b781d000 rw-p 000e8000 08:01 3802635 /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libstdc++.so.6.0.13 b781d000-b7824000 rw-p 00000000 00:00 0 b7847000-b7849000 rw-p 00000000 00:00 0 b7849000-b784a000 r-xp 00000000 00:00 0 [vdso] b784a000-b7866000 r-xp 00000000 08:01 6853649 /lib/ld-2.11.1.so b7866000-b7867000 r--p 0001b000 08:01 6853649 /lib/ld-2.11.1.so b7867000-b7868000 rw-p 0001c000 08:01 6853649 /lib/ld-2.11.1.so bfc7c000-bfc9d000 rw-p 00000000 00:00 0 [stack] Aborted
(In reply to comment #4) > I guess this isn't supposed to be happening (on x86): For me it works fine on ~x86: # ldd /usr/bin/muscle linux-gate.so.1 => (0xb77c3000) libstdc++.so.6 => /usr/lib/gcc/i686-pc-linux-gnu/4.4.4/libstdc++.so.6 (0xb76a8000) libm.so.6 => /lib/libm.so.6 (0xb7682000) libgcc_s.so.1 => /usr/lib/gcc/i686-pc-linux-gnu/4.4.4/libgcc_s.so.1 (0xb7666000) libc.so.6 => /lib/libc.so.6 (0xb7520000) /lib/ld-linux.so.2 (0xb77c4000) # I have glibc-2.11.2-r0. I am not saying there is not bug in the code at some printf call which is probably trapped now by libc for 'convenience'. Please contact upstream author to inspect the code. Most probably, you should recompile muscle before that and allow for extra debugging code, to find the line in the sources where the bug appears. Read http://www.gentoo.org/proj/en/qa/backtraces.xml to adjust you system setup for that.
Seems to be the same as bug #309341
Added patch from bug #309341. Please test
Oops.
The developer of muscle suggested to test 3.8. That fixed the problem.
(In reply to comment #9) > The developer of muscle suggested to test 3.8. That fixed the problem. > I backported the changes from 3.8* to 3.7.
The patch you applied to 3.7 from bug #309341 also worked. You decide what's best.
It (In reply to comment #11) > The patch you applied to 3.7 from bug #309341 also worked. You decide what's > best. > It is basicaly the same patch but the muscle maintainer are using a different size for the buffer.
Retested on x86, builds and runs fine (also from within seaview), please mark stable for x86.
stable x86, thanks Myckel
Marked ppc stable. Closing since we're the last arch.
