[Debian-med-packaging] Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails)

[Étienne Mollier]

Hi Nilesh,

Nilesh Patra, on 2024-12-07:
> 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?

Thanks for taking the time to diagnose the error, I have pulled
your changes for pbseqlib, rebuilt it, then built blasr against
the fresh pbseqlib.  I still hit a core dump though.  The back
trace looks like:

	#0  __pthread_kill_implementation (threadid=<optimized out>, 
	    signo=signo at entry=6, no_tid=no_tid at entry=0) at ./nptl/pthread_kill.c:44
	#1  0x00007ffff71e4cef in __pthread_kill_internal (threadid=<optimized out>, 
	    signo=6) at ./nptl/pthread_kill.c:78
	#2  0x00007ffff7190c42 in __GI_raise (sig=sig at entry=6)
	    at ../sysdeps/posix/raise.c:26
	#3  0x00007ffff71794f0 in __GI_abort () at ./stdlib/abort.c:79
	#4  0x00007ffff7530f9e in std::__glibcxx_assert_fail(char const*, int, char const*, char const*) () from /lib/x86_64-linux-gnu/libstdc++.so.6
	#5  0x00005555555bacd0 in std::vector<ChainedMatchPos, std::allocator<ChainedMatchPos> >::operator[] (this=<optimized out>, __n=<optimized out>)
	    at /usr/include/c++/14/bits/stl_vector.h:1128
	#6  std::vector<ChainedMatchPos, std::allocator<ChainedMatchPos> >::operator[]
	    (this=<optimized out>, __n=<optimized out>)
	    at /usr/include/c++/14/bits/stl_vector.h:1128
	#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=..., 
	    readRC=..., genome=..., sarray=..., bwt=..., seqBoundary=..., ct=..., 
	    seqdb=..., params=..., metrics=..., alignmentPtrs=..., mappingBuffers=..., 
	    mapData=<optimized out>, semaphores=...)
	    at ../iblasr/BlasrAlignImpl.hpp:149
	#9  0x0000555555591364 in MapReadsNonCCS (
	    mapData=mapData at entry=0x555555691f38, mappingBuffers=..., smrtRead=..., 
	    smrtReadRC=..., subreads=std::vector of length 0, capacity 0, params=..., 
	    associatedRandInt=@0x7fffffffa73c: 813429720, allReadAlignments=..., 
	    threadOut=...) at ../Blasr.cpp:347
	#10 0x0000555555595119 in MapReads (mapData=mapData at entry=0x555555691f38)
	    at ../Blasr.cpp:763
	#11 0x000055555556c77f in main (argc=<optimized out>, argv=<optimized out>)
	    at ../Blasr.cpp:1376

There does not seem to have been much changes.  Maybe the error
is somewhere else?  I hope I ran the test properly, it was a bit
intricate.

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/1, please excuse my verbosity
   `-
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