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

Bernd Rinn brinn at ethz.ch
Tue Sep 25 20:27:06 BST 2018


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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