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Re: picard-tools updated, and ready?

On 05/04/2018 02:30 PM, Andreas Tille wrote:
> Hi Olivier,
> On Fri, May 04, 2018 at 09:22:11AM +0200, Olivier Sallou wrote:
>> I have updated git repo for picard-tools.
>> Dependencies are in java team (gkl, gatk-native-bindings, barclay) but
>> not uploaded yet. Instead I uploaded them to experimental for the
>> moment, waiting for full validation with picard-tools.
> Cool!  From the naming it smells like a good precondition for GATK4
> which should be also packaged (rather sooner than later if I understood
> correctly).
>> I disabled unit tests due to a testng issue (I created a bug for this),
>> but I patched testng locally and could run all picard-tools unit tests.
> Sounds promising.  Again, thanks a lot.
>> I think however that it would be nice to get other people validation for
>> picard-tools, if you could test build/run. Task was indeed not easy and
>> I'd like to be sure it works in other environments.
> I admit my hope to get more testers from this list is limited.  (I
> explicitly added Vincent who is also in Uploaders but as far as I
> remember is not reading this list very regularly.)  Thus I'd be in
> favour of uploading at least those preconditions to unstable.  Since no
> package in unstable depends from these we can not really break anything.
> In general I also think that uploading to unstable even for picard-tools
> is fine (may be after testng bug is fixed) and use normal Debian QA
> tools as well as rdepends as "testers" in addition to potential readers
> here.  We are in the middle of a release cycle and there is sufficient
> time to fix issues now.
>> I faced issues with Java 9 but more with Java 10 which is now default
>> (in fact may work only with Java 10+).
> Ahhh, will we see another Java migration before buster will be frozen?
>> I tested it with htsjdk from experimental.
> I guess there is no other chance since it depends from the version
> there, right?

I can't upload to unstable as one of the deps (gkl) depends on htsjdk ,
and need a *recent* one (the one in experimental works, the one in sid
So to upload those picard-tools deps, we first need to put htsjdk in sid

>> When I have green flag, I can upload new dependencies to unstable before
>> uploading picard-tools.
> So green flag from my side without testing anything since I do not even
> have a better idea how to test ... 
> Kind regards
>      Andreas.

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

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