[Debian-med-packaging] Upgrading picard-tools

[Vincent Danjean]

Le 04/04/2016 16:22, Andreas Tille a écrit :
> Hi Vincent,
> 
> I checked the situation with htsjdk and noticed that the latest upstream
> version is not in / pushed to pristine-tar.

Can you double check? gitk show me that all my branches are pushed.
In particular, pristine-tar has the 2.1.1+dfsg.1 tarball.

Depending on your git configuration, "git pull" does not necessarily
update all your local branches. I've been trapped myself several times.
You may need to update/merge your local branches.

>  Could you please update
> the repository and may be explain what might be the show-stopper for
> upgrading this package?

  There was an error with the mh_installjar invocation. I did not
investigate more for now.

  Regards,
    Vincent

> Kind regards
> 
>       Andreas.
> 
> On Mon, Mar 14, 2016 at 11:25:35PM +0100, Vincent Danjean wrote:
>>   Hi,
>>
>> Le 13/03/2016 12:27, Andreas Tille a écrit :
>>> There is a remaining build error which should be probably easy to fix
>>> by --source 1.7 (Java 1.5 does not know <> diamond operator according
>>> to the error message I've got).
>>
>>   In fact, 1.8 is required (due to lambda expressions according to
>> the next error message)
>>   And htsjdk must be (at least) at the same version
>> => I added (build)dependencies on libhtsjdk-java (>= 2.1.1),
>>    should we also add libhtsjdk-java (<< 2.1.2)
>>                    or libhtsjdk-java (<< 2.2)
>>                    or ... ?
>>
>>   I also copied the few lines from htsjdk to run the tests without
>> the jacoco tools.
>>   All tests pass (in C locale, not in my French locale => an upstream
>> bug with floating point number representation)
>>
>>> I'll keep my hands now away from it and wait for further messages.
>>
>>   Now, I've a error with the "mh_installjar" invocation in debian/rules.
>> But I will stop here for today...
>>
>>   Regards,
>>     Vincent
>>
>>>
>>> Kind regards
>>>
>>>      Andreas.
>>>
>>
>>
>