[Debian-med-packaging] Bug#1129866: bioperl-run: FTBFS: Failed 1/60 test programs. 1/1650 subtests failed.

[Étienne Mollier]

Greetings,

The relevant part of the error does not appear in the excerpt,
but it is available in the full log[1] and looks like:

	Usage: kalign-avx2  -i <seq file> -o <out aln> 
	
	Modes:
	
	   (default)          : Consistency anchors + VSM (best general-purpose)
	   --fast             : VSM only, no consistency (fastest)
	   --precise          : Ensemble(3) + VSM + realign (highest precision)
	
	Options:
	
	   --format           : Output format. [Fasta]
	   --type             : Alignment type (rna, dna, internal). [rna]
	                        Options: protein, divergent (protein) 
	                                 rna, dna, internal (nuc). 
	   --gpo              : Gap open penalty. []
	   --gpe              : Gap extension penalty. []
	   --tgpe             : Terminal gap extension penalty. []
	   --refine           : Refinement mode. [none]
	                        Options: none, all, confident 
	   -n/--nthreads      : Number of threads. [auto: N-1, max 16]
	
	Ensemble options:
	
	   --ensemble         : Number of ensemble runs. [off; 5 if no value given]
	   --ensemble-seed    : RNG seed for ensemble. [42]
	   --min-support      : Explicit consensus threshold. [auto]
	   --save-poar        : Save POAR table to file. [off]
	   --load-poar        : Load POAR table for re-threshold. [off]
	
	Advanced (usually managed by modes):
	
	   --consistency      : Anchor consistency (K anchors). [5]
	   --consistency-weight: Consistency anchor weight. [2.0]
	   --realign          : Alignment-guided tree rebuild iters. [0]
	   --vsm-amax         : VSM amplitude (0 to disable). [auto]
	   --adaptive-budget  : Scale refinement trials by uncertainty. [off]
	   --version (-V/-v)  : Prints version. [NA]
	
	Examples:
	
	Passing sequences via stdin:
	
	   cat input.fa | kalign -i - -f fasta > out.afa
	
	Combining multiple input files:
	
	   kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa
	not ok 5
	Dubious, test returned 25 (wstat 6400, 0x1900)
	Failed 3/7 subtests

I also happen to reproduce it on an avx2-capable equipment.  It
could be that the encoded invocation of kalign in bioperl-run is
going to require an update.  Upstream repository[2] has been
inactive in the past few years, so it seems that we're going to
be on our own here.

[1]: https://people.debian.org/~sanvila/build-logs/202603/bioperl-run_1.7.3-13_amd64-20260305T171652.100Z
[2]: https://github.com/bioperl/bioperl-run/

In hope this helps,
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/2, please excuse my verbosity
   `-    on air: Steve Hackett - Firth of Fifth (Live in Birmin…
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