Kmer-File-Format / kff-tools

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Segfault on bucketing #8

Closed yoann-dufresne closed 3 years ago

yoann-dufresne commented 3 years ago

==289536== Memcheck, a memory error detector ==289536== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==289536== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==289536== Command: ./kff-tools bucket -i data/small.kff -o data/small_buckets.kff -m 3 ==289536== ==289536== Invalid read of size 1 ==289536== at 0x4842BD5: memmove (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so) ==289536== by 0x1143A3: memcpy (string_fortified.h:34) ==289536== by 0x1143A3: subsequence(unsigned char const, unsigned int, unsigned char, unsigned int, unsigned int) (sequences.cpp:61) ==289536== by 0x15A3FB: Bucket::exec() (bucket.cpp:116) ==289536== by 0x112BEF: main (kfftools.cpp:81) ==289536== Address 0x44ddec0d is not stack'd, malloc'd or (recently) free'd ==289536== ==289536== ==289536== Process terminating with default action of signal 11 (SIGSEGV) ==289536== Access not within mapped region at address 0x44DDEC0D ==289536== at 0x4842BD5: memmove (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so) ==289536== by 0x1143A3: memcpy (string_fortified.h:34) ==289536== by 0x1143A3: subsequence(unsigned char const, unsigned int, unsigned char, unsigned int, unsigned int) (sequences.cpp:61) ==289536== by 0x15A3FB: Bucket::exec() (bucket.cpp:116) ==289536== by 0x112BEF: main (kfftools.cpp:81) ==289536== If you believe this happened as a result of a stack ==289536== overflow in your program's main thread (unlikely but ==289536== possible), you can try to increase the size of the ==289536== main thread stack using the --main-stacksize= flag. ==289536== The main thread stack size used in this run was 8388608. ==289536== ==289536== HEAP SUMMARY: ==289536== in use at exit: 27,352 bytes in 147 blocks ==289536== total heap usage: 1,093 allocs, 946 frees, 160,893 bytes allocated ==289536== ==289536== LEAK SUMMARY: ==289536== definitely lost: 5 bytes in 1 blocks ==289536== indirectly lost: 0 bytes in 0 blocks ==289536== possibly lost: 0 bytes in 0 blocks ==289536== still reachable: 27,347 bytes in 146 blocks ==289536== suppressed: 0 bytes in 0 blocks ==289536== Rerun with --leak-check=full to see details of leaked memory ==289536== ==289536== For lists of detected and suppressed errors, rerun with: -s ==289536== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0) ./debug.sh: line 4: 289536 Segmentation fault (core dumped) valgrind ./kff-tools bucket -i data/small.kff -o data/small_buckets.kff -m 3