Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails)

From	Nilesh Patra <nilesh@riseup.net>
Newsgroups	linux.debian.bugs.rc
Subject	Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails)
Date	2024-12-07 10:40 +0100
Message-ID	<JQZs5-eot2-3@gated-at.bofh.it> (permalink)
References	<Ikbw0-u9x-127@gated-at.bofh.it> <JKZXP-ajXv-3@gated-at.bofh.it> <JKZXP-ajXv-3@gated-at.bofh.it> <Ikbw0-u9x-127@gated-at.bofh.it> <JKZXP-ajXv-3@gated-at.bofh.it>
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On Wed, 20 Nov 2024 21:48:23 +0100 =?utf-8?Q?=C3=89tienne?= Mollier 
<emollier@debian.org> wrote:
> Control: retitle -1 blasr: autopkgtest failure: core dump
> Control: tags -1 + help
> ...
> 	#7  RemoveOverlappingAnchors<std::vector<ChainedMatchPos, std::allocator<ChainedMatchPos> > > (matchList=std::vector of length 34, capacity 64 = {...})
> 	    at /usr/include/pbseq/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp:144
> 	#8  0x00005555555cd01f in MapRead<SMRTSequence, FASTASequence, SuffixArray<unsigned char, std::vector<int, std::allocator<int> >, DefaultCompareStrings<unsigned char>, DNATuple>, TupleCountTable<FASTASequence, DNATuple> > (read=..., 

Thanks for debugging this. The error to me appears to be here:

https://salsa.debian.org/med-team/pbseqlib/-/blob/master/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp?ref_type=heads#L140

and consequently at 
https://salsa.debian.org/med-team/pbseqlib/-/blob/master/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp?ref_type=heads#L144

It is then trying to access matchList[m] and m is matchList.size() in 
the first iteration which is undefined behavior.

It should start from  matchList.size() - 1. I've pushed a fix -- do 
blasr autopkgtest pass now?

If it looks fine, could you sponsor me an upload?

Thanks
Nilesh

Thread

Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails) Étienne Mollier <emollier@debian.org> - 2024-11-20 22:00 +0100
  Processed: Re: Bug#1067374: blasr: FTBFS fixed by itself (but  autopkgtest fails) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2024-11-20 22:00 +0100
  Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails) Nilesh Patra <nilesh@riseup.net> - 2024-12-07 10:40 +0100
    Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails) Étienne Mollier <emollier@debian.org> - 2024-12-07 12:00 +0100
      Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails) Nilesh Patra <nilesh@riseup.net> - 2024-12-07 14:50 +0100
        Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails) Nilesh Patra <nilesh@riseup.net> - 2024-12-08 10:00 +0100

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