[Debian-med-packaging] backporting libssw - autopkgtest fails on jessie

[Afif Elghraoui]

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Hi, Sascha,

على الإثنين 18 تـمـوز 2016 ‫14:09، كتب Sascha Steinbiss:
> Hi Afif,
> 
> just to follow up here. I just managed to find a little time to
> look into this.
> 
> I took the liberty of moving the JDK dependencies back into their
> original place; please see my mail to Andreas and the list for my
> reasons. Supported by Lintian’s output, the libssw-java binary
> package shouldn’t depend on a JRE [1] as there is nothing to ‘run’,
> and I would assume the also applies to JDKs (as they also contain a
> JRE). The JDK is indeed only needed in the test case to build a
> test driver against the libssw-java library.
> 

Yes, sorry about that. While I was experimenting, I had issues because
default-jdk-headless isn't available on jessie. That's when I started
getting confused about why java wasn't a dependency of a java library.

I see that, while you were undoing the damage I did, you changed
debian/tests/control in master to be default-jdk when you had
default-jdk-headless before. I think headless is fine for
Unstable/Stretch since it's a valid package there.

> As far as the run-example autopkgtest is concerned, I have
> identified some invalid memory accesses in upstream’s code (and
> also confirmed that in a clean source checkout from upstream’s
> GitHub repo). This apparently leads to binary data in the reference
> output, failing the test. What strikes me most is that, looking at
> your diff, your Jessie test output looks much more correct than the
> reference output that my sid binary produced. It seems like the new
> build tries to avoid indels as much as possible; the CIGAR string
> that I get when asking for SAM output also looks pretty dodgy! Can
> you reproduce this ‘good’ output on sid? I can’t — on sid I always
> get garbled results. There might be some fragility involved that’s
> not obvious to me… I have put in a ticket [2] with upstream, maybe
> they can help.
> 

Very interesting. I haven't run it on Sid, though. I did notice that
the output was very strange. Thanks for reporting the issue upstream.

Thanks and regards
Afif

- -- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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