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

[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.

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.

Cheers
Sascha

[1] https://www.debian.org/doc/packaging-manuals/java-policy/x126.html
[2] https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/issues/37

> On 18 Jul 2016, at 09:59, Sascha Steinbiss <satta at debian.org> wrote:
> 
> Hi Afif,
> 
>> I was trying to backport libssw (thanks for packaging it, by the way),
>> but I ran into a couple of issues.
> 
> Thanks for looking into the backport!
> 
>> One was (and I'm not sure whether this is related to my second problem)
>> that I get the following error when trying to build:
>> 
>> dpkg-source: error: unwanted binary file: debian/tests/run-example.out
>> 
>> dpkg-source: error: detected 1 unwanted binary file (add it in
>> debian/source/include-binaries to allow its inclusion)
>> 
>> This goes away if I create the debian/source/include-binaries file
>> listing debian/tests/run-example.out. But I'm not sure why I had to do
>> this and everyone else has been successful in working with this package
>> without making this change.
> 
> Indeed interesting! Looking at this file in an editor shows that
> apparently upstream's example tool (ssw_text or ssw-align) seems to
> output binary data in the text alignment at the end of one sequence.
> This (bug?) seems to explain why this file is treated as a binary.
> However, that doesn't explain why I do not get the error you encountered
> at all... does anyone else have an idea?
> 
>> My second problem is that the last autopkgtest fails (adt-run test log
>> attached). For the run described by the log, I just added the "-u" flag
>> to diff so I could better understand the output, but the test was still
>> failing before.
> 
> Yes, I can reproduce that in a LXC based testbed for jessie.
> 
> To make the build-lib-java autopkgtest pass, I had to add 'default-jdk'
> to this test's Depends line in d/tests/control.
> 
> As far as the run-example test is concerned -- if the binary data output
> is garbage (memory contents?) then comparing the output to the reference
> may yield different results. I haven't looked at this case in more
> detail but can do so later today. It would probably also help trying to
> fix the bug in the example tool (main.c).
> 
> Cheers
> Sascha
> 
> 
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