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

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Control: retitle -1 blasr: autopkgtest failure: core dump
Control: tags -1 + help

Hi,

Lucas Nussbaum, on 2024-03-20:
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
> 
> Relevant part (hopefully):
> > /usr/bin/ld: libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o: in function `main':
> > ./obj-x86_64-linux-gnu/../extrautils/StoreQualityByContextFromCmpH5.cpp:40:
> > 	multiple definition of `main';
> > 	toAfg.p/utils_ToAfg.cpp.o:./obj-x86_64-linux-gnu/../utils/ToAfg.cpp:30:
> > 	first defined here
> > collect2: error: ld returned 1 exit status

This is interesting, I unravelled this bug out of the blue and
tried to reproduce it, but the build went through.  I suspect
that whatever was broken in blasr build-dependency went fixed,
such that the build now goes through.

That being said, I am not closing this bug, because blasr
autopkgtest reveals an issue in the program.  The autopkgtest
run looks like:

	autopkgtest [21:19:17]: test run-unit-test: [-----------------------
	[INFO] 2024-11-20T20:19:18 [blasr] started.
	/usr/include/c++/14/bits/stl_vector.h:1130:
		std::vector<_Tp, _Alloc>::reference
		std::vector<_Tp, _Alloc>::operator[](size_type)
		[
			with _Tp = ChainedMatchPos;
			_Alloc = std::allocator<ChainedMatchPos>;
			reference = ChainedMatchPos&;
			size_type = long unsigned int
		]: Assertion '__n < this->size()' failed.
	/tmp/autopkgtest.WdOt0L/build.sPS/src/debian/tests/run-unit-test:
		line 16: 216319 Aborted                 (core dumped)
		blasr query.fasta ref.fa --sam --out alignment.sam
	autopkgtest [21:19:18]: test run-unit-test: -----------------------]

The backtrace obtained out of the debugger looks like:

	#0  __pthread_kill_implementation (threadid=<optimized out>, 
	    signo=signo@entry=6, no_tid=no_tid@entry=0) at ./nptl/pthread_kill.c:44
	#1  0x00007ffff71e4ebf in __pthread_kill_internal (threadid=<optimized out>, 
	    signo=6) at ./nptl/pthread_kill.c:78
	#2  0x00007ffff7190c82 in __GI_raise (sig=sig@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@entry=0x555555691f38, mappingBuffers=..., smrtRead=..., 
	    smrtReadRC=..., subreads=warning: Type size unknown, assuming 1. Try casting to a known type, or void *.
	warning: Type size unknown, assuming 1. Try casting to a known type, or void *.
	std::vector of length 0, capacity 0, params=..., 
	    associatedRandInt=@0x7fffffffa74c: 1658411691, allReadAlignments=..., 
	    threadOut=...) at ../Blasr.cpp:347
	#10 0x0000555555595119 in MapReads (mapData=mapData@entry=0x555555691f38)
	    at ../Blasr.cpp:763
	#11 0x000055555556c77f in main (argc=<optimized out>, argv=<optimized out>)
	    at ../Blasr.cpp:1376

This file:
/usr/include/pbseq/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp
happens to be part of the libblasr-dev, so it seems the issue
might be self contained in the package.  Trying to liaise
upstream for help with resolving this issue, I realized that the
declared Homepage returns http not found error, and the url
referenced in the watch file shows an archive repository that
has not seen any changes for the past 11 years.  I'm afraid
blasr is becoming a lost cause.

Anyway, in hope this inspires someone,
-- 
  .''`.  Étienne Mollier <emollier@debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/4, please excuse my verbosity
   `-    on air: Peter Gabriel - Here Comes The Flood

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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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