[Debian-med-packaging] Bug#915450: staden-io-lib FTBFS on big endian: test failures

[James Bonfield]

On Tue, Dec 04, 2018 at 07:53:35AM +0100, Andreas Tille wrote:
> unfortunately there is a series of new errors on different architectures.
> Here comes the first one.

Hmm. Some of this at least appears to be a Debian specific thing.

> > === testing ./data/c1#bounds.sam ===
> > ./scram.test: 27: [: ./data/c1#bounds.sam: unexpected operator

The [ .. unexpected operator normally comes about due to bashisms,
like if [ "$a" == "$b" ] then (etc).  However this line doesn't do
that - it is a single equals (I *did* have a bashism there at one
point, but not in 1.14.11).

I've tested the test harness using both bash and dash and I do not get
these errors.  I'm struggling to work out how come it reports this and
then continues regardless.  It looks like the shell just has a warning
and doesn't treat it as a hard error.  I'm confused!

I'm curious to know if you're getting the same issue on x86-64 and
i386, but the more recent automakes sadly hide all test output if it
works even with VERBOSE=1 on, grrr.  (The only reason I stick with
autotools is because cmake is even worse!)

> >  ../progs/scramble  ./data/c1#bounds.sam test.out/c1#bounds.sam
> >  ../progs/scramble  -r ./data/c1.fa ./data/c1#bounds.sam test.out/c1#bounds.full.cram
> >  ../progs/scramble  ./data/c1#bounds.sam > test.out/tmp.sam
> >  ../progs/scramble  test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> >  ../progs/scramble  -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
> >  ../progs/scramble  test.out/c1#bounds.full.bam test.out/tmp.sam
> > Invalid CRC in Deflate stream: 6614764d vs 00006614
> > Failed to open file test.out/c1#bounds.full.bam
> > FAIL scram.test (exit status: 1)

This however appears to be a genuine bug.  I'll try and reproduce it.

I'm guessing I'll need the exact OS rather than the RedHat based AWS
image I launched last time to test non-intel platforms.
Do you have AWS-ified Debian ARM images for people test launch tests
against?

James

-- 
James Bonfield (jkb at sanger.ac.uk)
The Sanger Institute, Hinxton, Cambs, CB10 1SA


-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.