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epruesse / SINA

SINA - Reference based multiple sequence alignment
https://sina.readthedocs.io
GNU General Public License v3.0
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double free (concurrency bug) #66

Closed epruesse closed 4 years ago

epruesse commented 5 years ago

From https://circleci.com/gh/epruesse/SINA/461

*** glibc detected *** /root/build/src/.libs/lt-sina: double free or corruption (out): 0x00007fb558819390 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x75e5e)[0x7fb569847e5e]
/lib64/libc.so.6(+0x78cf0)[0x7fb56984acf0]
/root/build/src/.libs/libsina.so.0(_ZNSt6vectorIN4sina15aligned_compactINS0_10base_iupacEEESaIS3_EEaSERKS5_+0x151)[0x7fb56a301a11]
/root/build/src/.libs/libsina.so.0(_ZN4sina9query_arb7getCseqERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1bd)[0x7fb56a36b0cd]
/root/build/src/.libs/libsina.so.0(_ZN4sina11kmer_search4impl4findERKNS_14annotated_cseqERSt6vectorINS_6search11result_itemESaIS7_EEj+0x89b)[0x7fb56a3de39b]
/root/build/src/.libs/libsina.so.0(_ZN4sina11kmer_search4findERKNS_14annotated_cseqERSt6vectorINS_6search11result_itemESaIS6_EEj+0x17)[0x7fb56a3dea47]
/root/build/src/.libs/libsina.so.0(_ZN4sina9famfinder4impl5matchERSt6vectorINS_6search11result_itemESaIS4_EERKNS_14annotated_cseqE+0x429)[0x7fb56a352469]
/root/build/src/.libs/libsina.so.0(_ZN4sina9famfinder4implclENS_4trayE+0xac0)[0x7fb56a358e20]
/root/build/src/.libs/libsina.so.0(_ZN4sina9famfinderclERKNS_4trayE+0x54)[0x7fb56a3595a4]
/root/build/src/.libs/lt-sina(+0x48a8b)[0x559994757a8b]
/root/build/src/.libs/lt-sina(+0x88135)[0x559994797135]
/root/build/src/.libs/lt-sina(+0x8829a)[0x55999479729a]
/root/miniconda/lib/libtbb.so.2(+0x294a9)[0x7fb56a7304a9]
/root/miniconda/lib/libtbb.so.2(+0x22af8)[0x7fb56a729af8]
/root/miniconda/lib/libtbb.so.2(+0x21384)[0x7fb56a728384]
/root/miniconda/lib/libtbb.so.2(+0x1d1e4)[0x7fb56a7241e4]
/root/miniconda/lib/libtbb.so.2(+0x1d45a)[0x7fb56a72445a]
/lib64/libpthread.so.0(+0x7aa1)[0x7fb5695bcaa1]
/lib64/libc.so.6(clone+0x6d)[0x7fb5698bac4d]
[...]
FAIL: tests/accuracy.test 9 - realign msc 0.7
epruesse commented 4 years ago

Hasn't turned up in a year - assuming it got fixed.