[Debian-med-packaging] Bug#1091721: pbsuite: autopkgtest regression in testing

[Étienne Mollier]

Control: tags -1 + confirmed

Greetings,

For reference, the issue caused by blasr looks like this in
pbsuite's autopkgtest in unstable:

	autopkgtest [15:27:50]: test run-unit-test: [-----------------------
	PIEMapping
	
	Please Cite: English, Adam C., William J. Salerno, Jeffery G.
	             Reid. "PBHoney: identyfying genomic variants via
	             long-read discordance and interrupted mapping."
	             BMC Bioinformatics 2014, 15:180 (June 10, 2014).
	             doi:10.1186/1471-2105-15-180
	
	2025-02-16 14:27:50,543 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam
	2025-02-16 14:27:50,543 [INFO] Running Blasr
	2025-02-16 14:28:21,727 [INFO] [0, b'[INFO] 2025-02-16T14:27:50 [blasr] started.\n[INFO] 2025-02-16T14:28:21 [blasr] ended.\n', None]
	2025-02-16 14:28:21,727 [INFO] Mapping Tails
	2025-02-16 14:28:21,727 [INFO] Extracting tails
	2025-02-16 14:28:21,891 [INFO] Parsed 433 reads
	2025-02-16 14:28:21,891 [INFO] Found 278 tails
	2025-02-16 14:28:21,891 [INFO] 21 reads had double tails
	2025-02-16 14:28:21,891 [INFO] Running Blasr
	2025-02-16 14:28:22,201 [ERROR] blasr mapping failed!
	2025-02-16 14:28:22,201 [ERROR] RETCODE 134
	2025-02-16 14:28:22,201 [ERROR] STDOUT b"[INFO] 2025-02-16T14:28:21 [blasr] started.\n/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.\nAborted\n"
	2025-02-16 14:28:22,202 [ERROR] STDERR None
	2025-02-16 14:28:22,202 [ERROR] Exiting
	[…]

There are further error messages, but they are caused by the
initial Honey command's failure to produce files that are
further on processed.  I don't really have much idea how to
resolve any of the two issues.

For reference,
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from my alarm clock
   `-
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