Source: kallisto Version: 0.48.0+dfsg-3 Severity: serious Tags: ftbfs Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: [email protected]
Following up with analysis after the test failure was mentioned by Andreas in Matrix "Debian Tiny Tasks". I do not have time to attack it and not familiar with the code-base but this analysis should help. Referring to the failed build log: https://salsa.debian.org/med-team/kallisto/-/jobs/8480324#L2345 "corrupted size vs. prev_size" :- The direct cause is out-of-bounds writes into malloc control structure fields. E.g: given `A = calloc(1, 16); B = calloc(1,16)` and A contiguous with B. If `struct *S = A` and `sizeof(A) == sizeof(*S)` then S[0] is valid but S[1] is out-of-bounds and a write may trample on the control structure preamble of B. >From what I can deduce it occurs in >`ext/bifrost/src/CompactDBG.tcc::CompactDBG::construct()` template after line >3323 and before line 3331. Most likely the reference to `size()` in line 3329. if (opt.verbose) cout << "CompactedDBG::construct(): After join tips using mercy k-mers: " << size() << " unitigs" << endl; https://salsa.debian.org/med-team/kallisto/-/blob/72ff60faebbab43eba75e55fe393d88de42116a5/ext/bifrost/src/CompactedDBG.tcc#L3323 Disabling `opt.verbose` would be an easy way to (dis)prove that.
