TPP 5.0 - InteractParser - buffer overflow detected

LabKey Support Forum
TPP 5.0 - InteractParser - buffer overflow detected toan nguyen  2018-01-05 11:28
Status: Closed
 
Hi,

  It appears InteractParser in TPP 5 is not working well.
  InteractParser in TPP 4.3 is working fine.

Thanks
Toan


running: "/usr/local/tpp/bin/InteractParser 'xxxxxxxxxxxxxx_msprefix.pep.xml' 'xxxxxxxxxxxxxx_raw.pep.xml' -L'7'"
 file 1: xxxxxxxxxxxxxxxxxxx_msprefix_raw.pep.xml
SUCCESS: CORRECTED data file /20171221-7339800375367778709.work/xxxxxxxxxxxxxxx_msprefix.mzXML in msms_run_summary tag ...
SUCCESS: CORRECTED data file /20171221-7339800375367778709.work/xxxxxxxxxxxxxxx_msprefix.mzXML in msms_run_summary tag ...
 processed altogether 5147 results
*** buffer overflow detected ***: /usr/local/tpp/bin/InteractParser terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f2e805f47e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f2e8069611c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117120)[0x7f2e80694120]
/lib/x86_64-linux-gnu/libc.so.6(+0x116689)[0x7f2e80693689]
/lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0x80)[0x7f2e805f86b0]
/lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0xc90)[0x7f2e805cae00]
/lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7f2e80693714]
/lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7f2e8069366d]
/usr/local/tpp/bin/InteractParser[0x414e4e]
/usr/local/tpp/bin/InteractParser[0x40e1a0]
/usr/local/tpp/bin/InteractParser[0x40abca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f2e8059d830]
/usr/local/tpp/bin/InteractParser[0x40ca29]
======= Memory map: ========
00400000-0064b000 r-xp 00000000 08:01 393493 /usr/local/tpp/bin/InteractParser
0084b000-00876000 r--p 0024b000 08:01 393493 /usr/local/tpp/bin/InteractParser
00876000-008b5000 rw-p 00276000 08:01 393493 /usr/local/tpp/bin/InteractParser
008b5000-008ba000 rw-p 00000000 00:00 0
010e7000-0254b000 rw-p 00000000 00:00 0 [heap]
7f2e7fac9000-7f2e80488000 r--p 00000000 08:01 141861 /usr/lib/locale/locale-archive
7f2e8057d000-7f2e8073d000 r-xp 00000000 08:01 7054 /lib/x86_64-linux-gnu/libc-2.23.so
7f2e8073d000-7f2e8093d000 ---p 001c0000 08:01 7054 /lib/x86_64-linux-gnu/libc-2.23.so
7f2e8093d000-7f2e80941000 r--p 001c0000 08:01 7054 /lib/x86_64-linux-gnu/libc-2.23.so
7f2e80941000-7f2e80943000 rw-p 001c4000 08:01 7054 /lib/x86_64-linux-gnu/libc-2.23.so
7f2e80943000-7f2e80947000 rw-p 00000000 00:00 0
7f2e80947000-7f2e8095d000 r-xp 00000000 08:01 7092 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2e8095d000-7f2e80b5c000 ---p 00016000 08:01 7092 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2e80b5c000-7f2e80b5d000 rw-p 00015000 08:01 7092 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2e80b5d000-7f2e80c65000 r-xp 00000000 08:01 7124 /lib/x86_64-linux-gnu/libm-2.23.so
7f2e80c65000-7f2e80e64000 ---p 00108000 08:01 7124 /lib/x86_64-linux-gnu/libm-2.23.so
7f2e80e64000-7f2e80e65000 r--p 00107000 08:01 7124 /lib/x86_64-linux-gnu/libm-2.23.so
7f2e80e65000-7f2e80e66000 rw-p 00108000 08:01 7124 /lib/x86_64-linux-gnu/libm-2.23.so
7f2e80e66000-7f2e80fd8000 r-xp 00000000 08:01 134315 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2e80fd8000-7f2e811d8000 ---p 00172000 08:01 134315 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2e811d8000-7f2e811e2000 r--p 00172000 08:01 134315 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2e811e2000-7f2e811e4000 rw-p 0017c000 08:01 134315 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2e811e4000-7f2e811e8000 rw-p 00000000 00:00 0
7f2e811e8000-7f2e811ef000 r-xp 00000000 08:01 7208 /lib/x86_64-linux-gnu/librt-2.23.so
7f2e811ef000-7f2e813ee000 ---p 00007000 08:01 7208 /lib/x86_64-linux-gnu/librt-2.23.so
7f2e813ee000-7f2e813ef000 r--p 00006000 08:01 7208 /lib/x86_64-linux-gnu/librt-2.23.so
7f2e813ef000-7f2e813f0000 rw-p 00007000 08:01 7208 /lib/x86_64-linux-gnu/librt-2.23.so
7f2e813f0000-7f2e81408000 r-xp 00000000 08:01 7200 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2e81408000-7f2e81607000 ---p 00018000 08:01 7200 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2e81607000-7f2e81608000 r--p 00017000 08:01 7200 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2e81608000-7f2e81609000 rw-p 00018000 08:01 7200 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2e81609000-7f2e8160d000 rw-p 00000000 00:00 0
7f2e8160d000-7f2e81626000 r-xp 00000000 08:01 7245 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2e81626000-7f2e81825000 ---p 00019000 08:01 7245 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2e81825000-7f2e81826000 r--p 00018000 08:01 7245 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2e81826000-7f2e81827000 rw-p 00019000 08:01 7245 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2e81827000-7f2e8184d000 r-xp 00000000 08:01 7026 /lib/x86_64-linux-gnu/ld-2.23.so
7f2e81937000-7f2e81a33000 rw-p 00000000 00:00 0
7f2e81a42000-7f2e81a43000 rw-p 00000000 00:00 0
7f2e81a43000-7f2e81a4a000 r--s 00000000 08:01 267771 /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f2e81a4a000-7f2e81a4c000 rw-p 00000000 00:00 0
7f2e81a4c000-7f2e81a4d000 r--p 00025000 08:01 7026 /lib/x86_64-linux-gnu/ld-2.23.so
7f2e81a4d000-7f2e81a4e000 rw-p 00026000 08:01 7026 /lib/x86_64-linux-gnu/ld-2.23.so
7f2e81a4e000-7f2e81a4f000 rw-p 00000000 00:00 0
7ffc78071000-7ffc78092000 rw-p 00000000 00:00 0 [stack]
7ffc78160000-7ffc78162000 r--p 00000000 00:00 0 [vvar]
7ffc78162000-7ffc78164000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
 
 
jeckels responded:  2018-01-05 17:53
Hi Toan,

This looks like a bug in InteractParser itself. I'd suggest posting this on the TPP support forum:

https://groups.google.com/forum/#!forum/spctools-discuss

It's possible that there is something that we could do differently to pass alternative arguments to avoid the crash, but there's not enough to go on in the error to immediately know what might avoid the problem.

Thanks,
Josh