[Debian-med-packaging] Fork of args4j (Was: Usage of private interface H5private.h in libsis-jhdf5-java 18.09.0-pre1)

[Bernd Rinn]

Hi Andreas,

Turns out that it is possible to use args4j 2.33 unchanged. I've just
committed the according changes to the git repository.

All the best,
Bernd

On 09/20/2018 04:21 PM, Andreas Tille wrote:
> Hi again,
> 
> for the moment I ignored the issue of using the private interface I
> wrote yesterday and tried to build the Java code.  Unfortunately there
> is another issue which is hopefully not as hard to solve.  In your
> download tarball you are shipping
> 
>     libs/prod/cisd-args4j-9.11.2*.jar
> 
> (fortunately for my purpose also an archive including the sources
> which I might be able to use for the packaging.  For the Debian
> packaging we can not rely on binary JARs and thus I need to remove
> these and need to rebuild from source.  However, I was instead
> considering to use the Debian packaged args4j 2.33[1] which failed
> due to the undefined attribute longName.
> 
> Before I now start to include the cisd-args4j fork of args4j:  Do
> you see any chance to merge your changes into official args4j and
> use the official project?
> 
> Kind regards and thanks for your patience to help me with the
> Debian packaging
> 
>         Andreas.
> 
> [1] https://salsa.debian.org/med-team/libsis-jhdf5-java/blob/use_gradle/debian/patches/use_debian_packaged_args4j.patch
> 
> 
> On Wed, Sep 19, 2018 at 01:00:16PM +0200, Andreas Tille wrote:
>> Hi Bernd,
>>
>> On Wed, Sep 19, 2018 at 09:29:42AM +0200, Bernd Rinn wrote:
>>>
>>> - This fix is in commit 331b8cc (August 21st).
>>
>> This really helped me to upload libsis-base now.  Thanks a lot.
>>
>> Now I tried to build jhdf5 and was running into:
>>
>> ...
>> In file included from h5VLStrHelperImp.c:19:
>> jni/h5jni.h:23:10: fatal error: H5private.h: No such file or directory
>>  #include "H5private.h"
>>           ^~~~~~~~~~~~~
>> compilation terminated.
>> In file included from h5fHelperImp.c:20:
>> jni/h5jni.h:23:10: fatal error: H5private.h: No such file or directory
>>  #include "H5private.h"
>>           ^~~~~~~~~~~~~
>> compilation terminated.
>> In file included from h5lHelperImp.c:19:
>> jni/h5jni.h:23:10: fatal error: H5private.h: No such file or directory
>>  #include "H5private.h"
>>           ^~~~~~~~~~~~~
>> compilation terminated.
>> ...
>>
>> H5private.h is as the name said private to the hdf5 library and its
>> definitions should not be used in stable interfaces.  Did you discussed
>> with the hdf5 developers to move the definitions you need to a public
>> interface?
>>
>> Kind regards
>>
>>       Andreas.
> 

-- 
Dr. Bernd Rinn
Head Scientific IT Services
ETH Zurich IT Services
SIB Swiss Institute of Bioinformatics
Weinbergstr. 11 (WEC D 19), 8092 Zürich, Switzerland, +41 44 632 0608
Mattenstr. 26 (BSB 1.01), 4058 Basel, Switzerland, +41 61 387 3130

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