#33 buffer overflow in libmuscle under linux

[Joel Berendzen]

libmuscle from svn, repository at revision 4462.
libmuscle 3.7 also shows this effect. So does Edgar's 3.7 and 3.6.
Problem appeared with glibc's improved buffer overflow detection in (I think) glibc-2.10.
Problem seems to be in progress reporting, workaround is to use -quiet.

> muscle -in in.fa -out out.fa
in 280 seqs, max length 190, avg length 150
*** buffer overflow detected ***: muscle terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x37)[0x31834fd597]
/lib/libc.so.6[0x31834fb3f0]
/lib/libc.so.6[0x31834fa759]
/lib/libc.so.6(_IO_vfprintf+0x51ed)[0x318344a0ad]
/lib/libc.so.6(__vsprintf_chk+0x9d)[0x31834fa7fd]
/lib/libc.so.6(__sprintf_chk+0x7f)[0x31834fa73f]
/usr/lib/libMUSCLE-3.7.so.1(_ZN6muscle8MemToStrEd+0x7d)[0x7f398e63c10d]
/usr/lib/libMUSCLE-3.7.so.1(_ZN6muscle8ProgressEjj+0x64)[0x7f398e63c294]
/usr/lib/libMUSCLE-3.7.so.1(_ZN6muscle11DistKmer6_6ERKNS_7SeqVectERNS_8DistFuncE+0x681)[0x7f398e609b41]
/usr/lib/libMUSCLE-3.7.so.1(_ZN6muscle13DistUnalignedERKNS_7SeqVectENS_8DISTANCEERNS_8DistFuncE+0x36b)[0x7f398e60767b]
/usr/lib/libMUSCLE-3.7.so.1(_ZN6muscle15TreeFromSeqVectERKNS_7SeqVectERNS_4TreeENS_7CLUSTERENS_8DISTANCEENS_4ROOTEPKc+0x41)[0x7f398e606ee1]
/usr/lib/libMUSCLE-3.7.so.1(_ZN6muscle8DoMuscleEv+0xd73)[0x7f398e601a23]
/usr/lib/libMUSCLE-3.7.so.1(_ZN6muscle3RunEv+0x149)[0x7f398e601cd9]
muscle[0x400f85]
/lib/libc.so.6(__libc_start_main+0xfd)[0x318341ebbd]
muscle[0x400e49]
======= Memory map: ========
00400000-00402000 r-xp 00000000 fd:03 1073745184 /usr/bin/muscle
00601000-00602000 r--p 00001000 fd:03 1073745184 /usr/bin/muscle
00602000-00603000 rw-p 00002000 fd:03 1073745184 /usr/bin/muscle
00956000-009fb000 rw-p 00000000 00:00 0 [heap]
3183000000-3183020000 r-xp 00000000 fd:03 2148011593 /lib64/ld-2.11.so
318321f000-3183220000 r--p 0001f000 fd:03 2148011593 /lib64/ld-2.11.so
3183220000-3183221000 rw-p 00020000 fd:03 2148011593 /lib64/ld-2.11.so
3183221000-3183222000 rw-p 00000000 00:00 0
3183400000-318356a000 r-xp 00000000 fd:03 2148016071 /lib64/libc-2.11.so
318356a000-318376a000 ---p 0016a000 fd:03 2148016071 /lib64/libc-2.11.so
318376a000-318376e000 r--p 0016a000 fd:03 2148016071 /lib64/libc-2.11.so
318376e000-318376f000 rw-p 0016e000 fd:03 2148016071 /lib64/libc-2.11.so
318376f000-3183774000 rw-p 00000000 00:00 0
3183800000-3183882000 r-xp 00000000 fd:03 2148016106 /lib64/libm-2.11.so
3183882000-3183a81000 ---p 00082000 fd:03 2148016106 /lib64/libm-2.11.so
3183a81000-3183a82000 r--p 00081000 fd:03 2148016106 /lib64/libm-2.11.so
3183a82000-3183a83000 rw-p 00082000 fd:03 2148016106 /lib64/libm-2.11.so
3184800000-3184816000 r-xp 00000000 fd:03 2148016109 /lib64/libgcc_s.so.1
3184816000-3184a15000 ---p 00016000 fd:03 2148016109 /lib64/libgcc_s.so.1
3184a15000-3184a16000 r--p 00015000 fd:03 2148016109 /lib64/libgcc_s.so.1
3184a16000-3184a17000 rw-p 00016000 fd:03 2148016109 /lib64/libgcc_s.so.1Aborted