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Java problem when upgrading pixelmed

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  Java problem when upgrading pixelmed Andreas Tille <andreas@an3as.eu> - 2015-10-06 22:30 +0200
    Re: Java problem when upgrading pixelmed Emmanuel Bourg <ebourg@apache.org> - 2015-10-06 22:40 +0200
      Re: Java problem when upgrading pixelmed Andreas Tille <andreas@an3as.eu> - 2015-10-08 13:10 +0200
        Re: Java problem when upgrading pixelmed Emmanuel Bourg <ebourg@apache.org> - 2015-10-08 13:30 +0200
          Re: Java problem when upgrading pixelmed Bas Couwenberg <sebastic@xs4all.nl> - 2015-10-08 13:50 +0200
            Re: Java problem when upgrading pixelmed Andreas Tille <andreas@an3as.eu> - 2015-10-08 17:30 +0200
              Re: Java problem when upgrading pixelmed Wookey <wookey@wookware.org> - 2015-10-09 17:10 +0200
                Re: Java problem when upgrading pixelmed Sebastiaan Couwenberg <sebastic@xs4all.nl> - 2015-10-09 19:40 +0200
                  Re: Java problem when upgrading pixelmed Emmanuel Bourg <ebourg@apache.org> - 2015-10-09 21:30 +0200
            Re: Java problem when upgrading pixelmed Emmanuel Bourg <ebourg@apache.org> - 2015-10-09 00:10 +0200
              Re: Java problem when upgrading pixelmed Sebastiaan Couwenberg <sebastic@xs4all.nl> - 2015-10-09 01:00 +0200
            Re: Java problem when upgrading pixelmed Emmanuel Bourg <ebourg@apache.org> - 2015-10-09 01:00 +0200
              Re: Java problem when upgrading pixelmed Sebastiaan Couwenberg <sebastic@xs4all.nl> - 2015-10-09 01:10 +0200
          Re: Java problem when upgrading pixelmed Andreas Tille <andreas@an3as.eu> - 2016-01-13 15:50 +0100
            Re: Java problem when upgrading pixelmed Emmanuel Bourg <ebourg@apache.org> - 2016-01-13 16:20 +0100
              Re: Java problem when upgrading pixelmed Andreas Tille <andreas@an3as.eu> - 2016-01-14 23:30 +0100
                Re: Java problem when upgrading pixelmed Emmanuel Bourg <ebourg@apache.org> - 2016-01-15 12:20 +0100
                  Bug#800762: Java problem when upgrading pixelmed Andreas Tille <tille@debian.org> - 2016-01-15 14:00 +0100
                    Bug#800762: Packaging javax.json (Was: Bug#800762: Java problem when upgrading pixelmed) Andreas Tille <tille@debian.org> - 2016-04-26 16:10 +0200
                      Bug#800762: Packaging javax.json (Was: Bug#800762: Java problem when upgrading pixelmed) Emmanuel Bourg <ebourg@apache.org> - 2016-04-26 16:30 +0200
                        Re: Packaging javax.json (Was: Bug#800762: Java problem when  upgrading pixelmed) Andreas Tille <andreas@an3as.eu> - 2016-04-26 21:00 +0200
                          Re: Packaging javax.json (Was: Bug#800762: Java problem when  upgrading pixelmed) Markus Koschany <apo@debian.org> - 2016-04-26 22:40 +0200
                            Re: Packaging javax.json (Was: Bug#800762: Java problem when  upgrading pixelmed) Andreas Tille <tille@debian.org> - 2016-04-27 00:40 +0200

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#8429 — Java problem when upgrading pixelmed

Hi,

I tried to upgrade pixelmed[1] to the latest version (20150917 as per
trunk in SVN) but the build failed with

export JAVAVERSIONTARGETJARFILE=/usr/lib/jvm/default-java/jre/lib/rt.jar; javac -O -target 1.7 -source 1.7 -bootclasspath ${JAVAVERSIONTARGETJARFILE} -encoding "UTF8" -Xlint:           deprecation -XDignore.symbol.file \
        -classpath ../../..:/usr/share/java/commons-compress.jar:/usr/share/java/commons-codec.jar:/usr/share/java/vecmath.jar:/usr/share/java/jai_imageio.jar:/usr/share/java/          pixelmed_codec.jar \
        -sourcepath ../../.. ImageEditUtilities.java
ImageEditUtilities.java:119: error: package com.pixelmed.codec.jpeg does not exist
                                                com.pixelmed.codec.jpeg.Parse.parse(fbis,fbos,shapes);
                                                                       ^
1 error
Makefile:66: recipe for target 'ImageEditUtilities.class' failed

Any help how to solve this would be appreciated.  I tried to address
this by debian/patches/imageio.patch

--- a/com/pixelmed/display/ImageEditUtilities.java
+++ b/com/pixelmed/display/ImageEditUtilities.java
@@ -26,6 +26,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import javax.imageio.*;

 import java.util.Iterator;
 import java.util.Vector;


but this does not have any effect.

Kind regards

     Andreas.

[1] svn://anonscm.debian.org/debian-med/trunk/packages/pixelmed/trunk/

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#8430

Le 06/10/2015 22:28, Andreas Tille a écrit :

> export JAVAVERSIONTARGETJARFILE=/usr/lib/jvm/default-java/jre/lib/rt.jar; javac -O -target 1.7 -source 1.7 -bootclasspath ${JAVAVERSIONTARGETJARFILE} -encoding "UTF8" -Xlint:           deprecation -XDignore.symbol.file \
>         -classpath ../../..:/usr/share/java/commons-compress.jar:/usr/share/java/commons-codec.jar:/usr/share/java/vecmath.jar:/usr/share/java/jai_imageio.jar:/usr/share/java/          pixelmed_codec.jar \
>         -sourcepath ../../.. ImageEditUtilities.java
> ImageEditUtilities.java:119: error: package com.pixelmed.codec.jpeg does not exist
>                                                 com.pixelmed.codec.jpeg.Parse.parse(fbis,fbos,shapes);
>                                                                        ^

Hi Andreas,

I bet you are missing pixelmed_codec.jar which is likely to contain the
com.pixelmed.codec.jpeg package according to its name:

http://www.dclunie.com/pixelmed/software/codec/20141206_current/

Emmanuel Bourg

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#8437

On Tue, Oct 06, 2015 at 10:36:56PM +0200, Emmanuel Bourg wrote:
> Le 06/10/2015 22:28, Andreas Tille a écrit :
> 
> > export JAVAVERSIONTARGETJARFILE=/usr/lib/jvm/default-java/jre/lib/rt.jar; javac -O -target 1.7 -source 1.7 -bootclasspath ${JAVAVERSIONTARGETJARFILE} -encoding "UTF8" -Xlint:           deprecation -XDignore.symbol.file \
> >         -classpath ../../..:/usr/share/java/commons-compress.jar:/usr/share/java/commons-codec.jar:/usr/share/java/vecmath.jar:/usr/share/java/jai_imageio.jar:/usr/share/java/          pixelmed_codec.jar \
> >         -sourcepath ../../.. ImageEditUtilities.java
> > ImageEditUtilities.java:119: error: package com.pixelmed.codec.jpeg does not exist
> >                                                 com.pixelmed.codec.jpeg.Parse.parse(fbis,fbos,shapes);
> 
> I bet you are missing pixelmed_codec.jar which is likely to contain the
> com.pixelmed.codec.jpeg package according to its name:
> 
> http://www.dclunie.com/pixelmed/software/codec/20141206_current/

I think you've won your bet ;-) and I injected some packaging for
pixelmed-codec[1].  Unfortunately I'm not yet through all dependencies
since the build ends with:

...
SetCharacteristicsFromSummary.java:240: error: cannot find symbol
                JsonReader jsonReader = Json.createReader(new FileReader(jsonfile));
                ^
  symbol:   class JsonReader
  location: class SetCharacteristicsFromSummary
SetCharacteristicsFromSummary.java:240: error: cannot find symbol
                JsonReader jsonReader = Json.createReader(new FileReader(jsonfile));
                                        ^
  symbol:   variable Json
  location: class SetCharacteristicsFromSummary
SetCharacteristicsFromSummary.java:241: error: cannot find symbol
                JsonObject obj = jsonReader.readObject();
                ^
  symbol:   class JsonObject
  location: class SetCharacteristicsFromSummary
SetCharacteristicsFromSummary.java:244: error: cannot find symbol
                        JsonObject functionalGroupEntries = (JsonObject)(obj.get(functionalGroupName));
                        ^
  symbol:   class JsonObject
  location: class SetCharacteristicsFromSummary
SetCharacteristicsFromSummary.java:244: error: cannot find symbol
                        JsonObject functionalGroupEntries = (JsonObject)(obj.get(functionalGroupName));
                                                             ^
  symbol:   class JsonObject
  location: class SetCharacteristicsFromSummary
37 errors
Makefile:43: recipe for target 'SetCharacteristicsFromSummary.class' failed
make[3]: *** [SetCharacteristicsFromSummary.class] Error 1
make[3]: Leaving directory '/home/andreas/debian-maintain/repack/pixelmed/pixelmed-20150917/com/pixelmed/apps'


The makefiles are refering to

   lib/additional/javax.json-api-1.0.jar

and it seems none of the json java classes are fitting this.

I remember times when the jar contents were listed in:

   http://ftp-master.debian.org/users/twerner/jar-content.txt.gz

But this does not seem to be updated any more.

Any further hints are welcome

     Andreas.

[1] svn://anonscm.debian.org/debian-med/trunk/packages/pixelmed-codec/trunk/

-- 
http://fam-tille.de

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#8438

Le 08/10/2015 13:03, Andreas Tille a écrit :

> I think you've won your bet ;-)

*cheers*

> The makefiles are refering to
> 
>    lib/additional/javax.json-api-1.0.jar
> 
> and it seems none of the json java classes are fitting this.
> 
> I remember times when the jar contents were listed in:
> 
>    http://ftp-master.debian.org/users/twerner/jar-content.txt.gz
> 
> But this does not seem to be updated any more.

It looks like you need the new standard Java API for JSON processing
(JSR 353) [1], we haven't packaged it yet, but josm has a local copy (if
you search for 'package javax.json' on http://source.debian.net you can
quickly find the package containing the classes your are looking for).

Emmanuel Bourg

[1] https://jsonp.java.net

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#8439

On 2015-10-08 13:28, Emmanuel Bourg wrote:
> It looks like you need the new standard Java API for JSON processing
> (JSR 353) [1], we haven't packaged it yet, but josm has a local copy 
> (if
> you search for 'package javax.json' on http://source.debian.net you can
> quickly find the package containing the classes your are looking for).

Please don't rely on josm for the javax.json classes.

Due to the difficulties getting JCS [0] and its dependencies [1] 
packaged, I've not been able to update to any of the newer JOSM upstream 
releases making the josm package increasingly irrelevant. And if I 
remain unable to get JCS packaged, I'll have josm removed from the 
archive before the freeze.

[0] https://bugs.debian.org/783538
[1] https://bugs.debian.org/792690

Kind Regards,

Bas

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#8441

Hi,

On Thu, Oct 08, 2015 at 01:40:58PM +0200, Bas Couwenberg wrote:
> On 2015-10-08 13:28, Emmanuel Bourg wrote:
> >It looks like you need the new standard Java API for JSON processing
> >(JSR 353) [1], we haven't packaged it yet, but josm has a local copy (if
> >you search for 'package javax.json' on http://source.debian.net you can
> >quickly find the package containing the classes your are looking for).
> 
> Please don't rely on josm for the javax.json classes.

Is there any work ongoing for a separate javax.json package?

> Due to the difficulties getting JCS [0] and its dependencies [1] packaged,
> I've not been able to update to any of the newer JOSM upstream releases
> making the josm package increasingly irrelevant. And if I remain unable to
> get JCS packaged, I'll have josm removed from the archive before the freeze.

Uhmmm, it would be a shame if we would loose JOSM. :-(

Kind regards

      Andreas.

> [0] https://bugs.debian.org/783538
> [1] https://bugs.debian.org/792690

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#8446

[Multipart message — attachments visible in raw view] — view raw

+++ Andreas Tille [2015-10-08 17:22 +0200]:
> Uhmmm, it would be a shame if we would loose JOSM. :-(

A shame? - It would be a disaster! (Unless there is a replacement with
that offline functionality that I don't know about?)

Wookey
-- 
Principal hats:  Linaro, Debian, Wookware, ARM
http://wookware.org/

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#8449

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

On 09-10-15 17:06, Wookey wrote:
> +++ Andreas Tille [2015-10-08 17:22 +0200]:
>> Uhmmm, it would be a shame if we would loose JOSM. :-(
> 
> A shame? - It would be a disaster! (Unless there is a replacement
> with that offline functionality that I don't know about?)

So many people caring about JOSM in Debian, so few people contributing
to its packaging...

Many thanks to Emmanuel Bourgs efforts motivating me to work on josm
packaging again. There may be hope for this package in Debian after all.

Kind Regards,

Bas

- -- 
 GPG Key ID: 4096R/6750F10AE88D4AF1
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#8450

Le 09/10/2015 19:38, Sebastiaan Couwenberg a écrit :

> So many people caring about JOSM in Debian, so few people contributing
> to its packaging...
> 
> Many thanks to Emmanuel Bourgs efforts motivating me to work on josm
> packaging again. There may be hope for this package in Debian after all.

"You will find that help will always be given at Hog^H^H^Hdebian-java to
those who ask for it."

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#8442

Le 08/10/2015 13:40, Bas Couwenberg a écrit :

> Due to the difficulties getting JCS [0] and its dependencies [1]
> packaged, I've not been able to update to any of the newer JOSM upstream
> releases making the josm package increasingly irrelevant. And if I
> remain unable to get JCS packaged, I'll have josm removed from the
> archive before the freeze.

Hi Sebastian,

I packaged geronimo-jcache-1.0-spec and it's now in the NEW queue. I
started completing your commons-jcs package to fix the remaining issues,
I'll let you know when it's ready.

Emmanuel Bourg

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#8443

Hi Emmanuel,

On 09-10-15 00:05, Emmanuel Bourg wrote:
> Le 08/10/2015 13:40, Bas Couwenberg a écrit :
> 
>> Due to the difficulties getting JCS [0] and its dependencies [1]
>> packaged, I've not been able to update to any of the newer JOSM upstream
>> releases making the josm package increasingly irrelevant. And if I
>> remain unable to get JCS packaged, I'll have josm removed from the
>> archive before the freeze.
> 
> I packaged geronimo-jcache-1.0-spec and it's now in the NEW queue. I
> started completing your commons-jcs package to fix the remaining issues,
> I'll let you know when it's ready.

Thanks for your work on this, it's much appreciated!

I didn't expect that fixing jcache would be as easy as adding
<extensions>true</extensions> to the pom.xml.

Kind Regards,

Bas

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 GPG Key ID: 4096R/6750F10AE88D4AF1
Fingerprint: 8182 DE41 7056 408D 6146  50D1 6750 F10A E88D 4AF1

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#8444

Le 08/10/2015 13:40, Bas Couwenberg a écrit :

> Due to the difficulties getting JCS [0] and its dependencies [1]
> packaged, I've not been able to update to any of the newer JOSM upstream
> releases making the josm package increasingly irrelevant. And if I
> remain unable to get JCS packaged, I'll have josm removed from the
> archive before the freeze.

I noticed that JOSM imports directly the sources from the trunk of JCS
using svn externals. JCS is still in a beta state, the API isn't stable,
so if we upload the version 2.0-beta-1 there is no guarantee it will
work with JOSM. In this case I think you should just go ahead and use
the version of JCS bundled with JOSM.

Note that JOSM fetches only the jcs-core module, so you don't need the
jcache stuff and you don't have to wait for geronimo-jcache-1.0-spec to
enter unstable.

Emmanuel Bourg

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#8445

On 09-10-15 00:58, Emmanuel Bourg wrote:
> Le 08/10/2015 13:40, Bas Couwenberg a écrit :
> 
>> Due to the difficulties getting JCS [0] and its dependencies [1]
>> packaged, I've not been able to update to any of the newer JOSM upstream
>> releases making the josm package increasingly irrelevant. And if I
>> remain unable to get JCS packaged, I'll have josm removed from the
>> archive before the freeze.
> 
> I noticed that JOSM imports directly the sources from the trunk of JCS
> using svn externals. JCS is still in a beta state, the API isn't stable,
> so if we upload the version 2.0-beta-1 there is no guarantee it will
> work with JOSM. In this case I think you should just go ahead and use
> the version of JCS bundled with JOSM.
> 
> Note that JOSM fetches only the jcs-core module, so you don't need the
> jcache stuff and you don't have to wait for geronimo-jcache-1.0-spec to
> enter unstable.

Thanks for these hints too.

I've already raised my concerns about the JCS requirement in JOSM which
in my opinion is premature due to the beta stage of JCS 2.0 and its
alpha stage dependency on jcache. But JOSM upstream doesn't care much
about building from source by downstreams.

I'll see what I can do with the embedded dependency, although we need it
for the current upstream releases for both JOSM and JMapViewer. I'd
rather not duplicate JCS for both.

Kind Regards,

Bas

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#8716

Hi Emmanuel,

catching up once libpixelmed-codec-java was accepted in unstable.

On Thu, Oct 08, 2015 at 01:28:44PM +0200, Emmanuel Bourg wrote:
> Le 08/10/2015 13:03, Andreas Tille a écrit :
> 
> > I think you've won your bet ;-)
> 
> *cheers*
> 
> > The makefiles are refering to
> > 
> >    lib/additional/javax.json-api-1.0.jar
> > 
> > and it seems none of the json java classes are fitting this.
> > 
> > I remember times when the jar contents were listed in:
> > 
> >    http://ftp-master.debian.org/users/twerner/jar-content.txt.gz
> > 
> > But this does not seem to be updated any more.
> 
> It looks like you need the new standard Java API for JSON processing
> (JSR 353) [1], we haven't packaged it yet, but josm has a local copy (if
> you search for 'package javax.json' on http://source.debian.net you can
> quickly find the package containing the classes your are looking for).
> 
> Emmanuel Bourg
> 
> [1] https://jsonp.java.net

If I understand correctly I need to package jsonp.java.net to be able to
build the new version of pixelmed and nobody else started with jsonp up
to now, right?

If I understood the mail of Bas correctly I could even help JOSM by
doing so, right?

If you confirm I'd start with packaging.

Kind regards

          Andreas.

-- 
http://fam-tille.de

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#8717

Le 13/01/2016 15:46, Andreas Tille a écrit :

> If I understand correctly I need to package jsonp.java.net to be able to
> build the new version of pixelmed and nobody else started with jsonp up
> to now, right?

Hi Andreas,

Yes that's correct.

Emmanuel Bourg

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#8721

Hi Emmanuel,

On Wed, Jan 13, 2016 at 04:15:56PM +0100, Emmanuel Bourg wrote:
> > If I understand correctly I need to package jsonp.java.net to be able to
> > build the new version of pixelmed and nobody else started with jsonp up
> > to now, right?
> 
> Yes that's correct.

OK,  I did my first shot at it under

    git://anonscm.debian.org/pkg-java/libjsonp-java.git

The maven stuff is to hard for me at this time of the day.  I'd be super
happy if I wake up tomorrow and realise that this is fixed in Git.
Otherwise I'll ask some more detailed questions.

Kind regards

         Andreas.

-- 
http://fam-tille.de

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#8722

Le 14/01/2016 23:21, Andreas Tille a écrit :

> The maven stuff is to hard for me at this time of the day.  I'd be super
> happy if I wake up tomorrow and realise that this is fixed in Git.

Hocus Pocus :)

I reworked the package to use maven-debian-helper, I agree this one was
tricky. I let you finish the job (ITP, copyright review and upload to NEW).

Emmanuel Bourg

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#8723 — Bug#800762: Java problem when upgrading pixelmed

On Fri, Jan 15, 2016 at 12:16:40PM +0100, Emmanuel Bourg wrote:
> Le 14/01/2016 23:21, Andreas Tille a écrit :
> 
> > The maven stuff is to hard for me at this time of the day.  I'd be super
> > happy if I wake up tomorrow and realise that this is fixed in Git.
> 
> Hocus Pocus :)

I like this kind of magic a lot! :-)
 
> I reworked the package to use maven-debian-helper, I agree this one was
> tricky. I let you finish the job (ITP, copyright review and upload to NEW).

I'll do so as agreed upon.

Thanks a lot for your support

       Andreas.

-- 
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#9064 — Bug#800762: Packaging javax.json (Was: Bug#800762: Java problem when upgrading pixelmed)

Hi Markus,

just for clarification:  Pixelmed was introduced by Mathieu Malaterre
who left the Debian Med team and the burden to maintain several packages
of medical imaging.  I do not use these and do not have any competence
here but I'd be willing to do upgrades and simple maintaining tasks as
long as possible.  I have no free capacity to do large scale packaging
of new dependencies.  So if somebody volunteers to package javax.json
(which might be interesting also for other projects) I might care for
pixelmed.  Otherwise I'll keep the package in its current state or even
remove it from Debian.

Kind regards

        Andreas.

On Mon, Apr 25, 2016 at 09:54:10AM +0200, Markus Koschany wrote:
> Am 25.04.2016 um 08:04 schrieb Olivier Sallou:
> [...]
> > Do you need someone to package javax.json ? (that would need to go to Java team)
> > 
> > I can help if needed, though not really at ease with Maven part in Debian.
> > 
> 
> Hi,
> 
> I don't need javax.json at the moment but Andreas would like to upgrade
> Pixelmed and javax.json is a new dependency.
> 
> Packaging javax.json would be fairly simple and you could use for
> instance https://packages.qa.debian.org/j/jboss-jdeparser2.html as a
> template package.
> 
> Project website:
> 
> https://jsonp.java.net/
> 
> Sources:
> 
> https://repo1.maven.org/maven2/org/glassfish/javax.json/1.0.4/
> 
> Regards,
> 
> Markus
> 




> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging


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#9066 — Bug#800762: Packaging javax.json (Was: Bug#800762: Java problem when upgrading pixelmed)

Le 26/04/2016 16:06, Andreas Tille a écrit :

> I have no free capacity to do large scale packaging
> of new dependencies.  So if somebody volunteers to package javax.json
> (which might be interesting also for other projects) I might care for
> pixelmed.  Otherwise I'll keep the package in its current state or even
> remove it from Debian.

As a reminder, you did package jsonp :)

    git://anonscm.debian.org/pkg-java/libjsonp-java.git

The package builds fine, it just needs an ITP and a proper copyright review.

Emmanuel Bourg

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