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Re: picard-tools progress status

On 05/02/2018 11:04 AM, Andreas Tille wrote:
> Hi Olivier,
> thanks a lot for your work on this and the status update.
> On Wed, May 02, 2018 at 09:39:44AM +0200, Olivier Sallou wrote:
>> after quick and dirty packaging of picard new dependencies (done
>> locally, can't be uploaded in this state), I could build picard-tools.
> Feel free to be more verbose in case you might need some help with those
> preconditions.
that's ok for dependencies, it just need some work for cleanup, set
copyright etc....
just wanted to get a quick "package" to validate picard-tools. I don't
want to do too much work on dependencies if it does not work with picard.
Once picard is ok, I will do the job to do real packaging on those.
>> However, there are many failing tests (168 at this time), though ~2800
>> tests are fine.
>> Some failures I can"t explain (freezing, thread errors , with no
>> detailled log) and others where picard seems to fail with htsjdk (the
>> one from experimental, with nio errors).
>> I am not really confident that I will be able to debug all those errors,
>> which may be related to debian env (patching, gradle etc...) or from
>> packaged dependencies.
>> For htsjdk test errors, it seems they are all related with 2 recurrent
>> errors among failed tests
>> ...
> May be we can ask on debian-java about some gradle (or similar) related
> issues.  But before we surely need those predependencies to keep the
> worklow of helpful people low.
I created an issue upstream for one of the issue (freezing of tests).
for the other ones, it may be related to the dependencies I packaged,
but difficult to know (wrong version ? missing something?).
The issue is there is a stacktrace but no real log helping to understand
what is wrong. Will need much more time to try to fix this.
> Kind regards
>        Andreas. 

Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu

gpg key id: 4096R/326D8438  (keyring.debian.org)
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