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Old 02-12-2011, 05:45 PM
Andreas Tille
 
Default Help wanted in Java library packaging (JEBL2)

Hi,

I uploaded two source packages to

http://people.debian.org/~tille/packages/figtree-help-wanted/

One is the just ITPed (#613080) and the other one is FigTree which is
actually my target package. The originial tarball contained a jebl.jar
which I stripped from the tarball. I assumed that making figtree
Build-Depend from libjebl2-java sufficient to let java find the classes
in JEBL - which is not the case unfortunately. I just get erros like

[javac] Compiling 115 source files to /home/tillea/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/build
[javac] /home/tillea/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/applet/FigTreeApplet.java:3: package jebl.evolution.trees does no
[javac] import jebl.evolution.trees.Tree;
[javac] ^
[javac] /home/tillea/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/applet/FigTreeApplet.java:4: package jebl.evolution.io does not e
[javac] import jebl.evolution.io.NewickImporter;
[javac] ^
...

Any hints?

Kind regards

Andreas.

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Old 02-12-2011, 06:15 PM
Vincent Fourmond
 
Default Help wanted in Java library packaging (JEBL2)

On Sat, Feb 12, 2011 at 7:45 PM, Andreas Tille <andreas@an3as.eu> wrote:
> I uploaded two source packages to
>
> * http://people.debian.org/~tille/packages/figtree-help-wanted/
>
> One is the just ITPed (#613080) and the other one is FigTree which is
> actually my target package. *The originial tarball contained a jebl.jar
> which I stripped from the tarball. *I assumed that making figtree
> Build-Depend from libjebl2-java sufficient to let java find the classes
> in JEBL - which is not the case unfortunately.

No. I don't know what build system you use, but with cdbs/ant, you
need to give the list of jars necessary for building in the DEB_JARS
variable, such as:

DEB_JARS := ant-launcher ant-nodeps
miglayout wstx-lgpl commons-cli cortado

This may be enough. I don't have time to dig further for now.

Cheers,

Vincent


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Old 02-13-2011, 01:19 AM
Scott Howard
 
Default Help wanted in Java library packaging (JEBL2)

On Sat, Feb 12, 2011 at 1:45 PM, Andreas Tille <andreas@an3as.eu> wrote:
> Hi,
>
> I uploaded two source packages to
>
> * http://people.debian.org/~tille/packages/figtree-help-wanted/
>
> One is the just ITPed (#613080) and the other one is FigTree which is
> actually my target package. *The originial tarball contained a jebl.jar
> which I stripped from the tarball. *I assumed that making figtree
> Build-Depend from libjebl2-java sufficient to let java find the classes
> in JEBL - which is not the case unfortunately.

The problem is in build.xml:
<javac source="1.5" target="1.5" srcdir="${src}" destdir="${build}"
classpath="${lib}/jebl.jar:${lib}/jam.jar:${lib}/freehep.jar:${lib}/iText.jar:${lib}/quaqua.jar:${lib}/jwt/servlet-api-2.5-6.0.2.jar:${lib}/jwt/jwt-3.1.7pre1.jar">

while ${lib} is defined as "lib/" in the source tree

the classpath should be changed to:
classpath="/usr/share/java/jebl.jar:/usr/share/java/jam.jar:/usr/share/java/freehep.jar:/usr/share/java/iText.jar:
etc... ">

Also, probably should avoid using specific library versions but use
the debian provided symlinks.

Also, you B-D on libtrove-java in the jebl and jam libraries and the
FigTree package, but the binary packages themselves don't depend on
them (and don't use any symbols from them). You can use the
"java-propose-classpath" to help hint what symbols are used. I'm not
familiar with packages using trove, so you might be using it
correctly.

Cheers,
Scott


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Old 02-13-2011, 01:29 AM
Scott Howard
 
Default Help wanted in Java library packaging (JEBL2)

On Sat, Feb 12, 2011 at 9:19 PM, Scott Howard <showard314@gmail.com> wrote:
> On Sat, Feb 12, 2011 at 1:45 PM, Andreas Tille <andreas@an3as.eu> wrote:
>> Hi,
>>
>> I uploaded two source packages to
>>
>> * http://people.debian.org/~tille/packages/figtree-help-wanted/
>>
>> One is the just ITPed (#613080) and the other one is FigTree which is
>> actually my target package. *The originial tarball contained a jebl.jar
>> which I stripped from the tarball. *I assumed that making figtree
>> Build-Depend from libjebl2-java sufficient to let java find the classes
>> in JEBL - which is not the case unfortunately.
>
> the classpath should be changed to:
> classpath="/usr/share/java/jebl.jar:/usr/share/java/jam.jar:/usr/share/java/freehep.jar:/usr/share/java/iText.jar:
> *etc... * *">

Alternatively, you can use jh_linkjars to link them to lib/ in the
source directory and then use jh_classpath to change the classpaths to
point to debian locations [1]. You also can install symlinks from
/usr/share/figtree to the debian jars in /usr/share/java, however this
technique won't work with the javaepends substvars and jh_depends.

Cheers,
Scott

[1] http://pkg-java.alioth.debian.org/docs/tutorial.html


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Old 02-13-2011, 09:09 AM
Andreas Tille
 
Default Help wanted in Java library packaging (JEBL2)

Hi Scott,

thanks for the helpful hints which brough me one definitely one step
further.

On Sat, Feb 12, 2011 at 09:29:16PM -0500, Scott Howard wrote:
> > the classpath should be changed to:
> > classpath="/usr/share/java/jebl.jar:/usr/share/java/jam.jar:/usr/share/java/freehep.jar:/usr/share/java/iText.jar:
> > *etc... * *">

I tried this way as you can see on the updated

http://people.debian.org/~tille/packages/figtree-help-wanted/

> Alternatively, you can use jh_linkjars to link them to lib/ in the
> source directory and then use jh_classpath to change the classpaths to
> point to debian locations [1]. You also can install symlinks from
> /usr/share/figtree to the debian jars in /usr/share/java, however this
> technique won't work with the javaepends substvars and jh_depends.

When using

dh --with javahelper

jh_linkjars seems to be called automatically (but I probably need to
provide an input file for this. However if this does not work with
javaepends I'm not in favour of this method anyway.

Now to my remaining problem: If you look at the updated build log
at the given URL I ran into

[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:20: package org.fr
[javac] import org.freehep.graphicsio.ps.PSGraphics2D;
[javac] ^
[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:21: package org.fr
[javac] import org.freehep.graphicsio.pdf.PDFGraphics2D;
[javac] ^
...

even after having the classpath adapted to include

${deblib}/freehep-graphics2d.jar

(deblib:=/usr/share/java). Any further ideas?

Kind regards

Andreas.

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Old 02-13-2011, 01:54 PM
Scott Howard
 
Default Help wanted in Java library packaging (JEBL2)

On Sun, Feb 13, 2011 at 5:09 AM, Andreas Tille <andreas@an3as.eu> wrote:
> When using
>
> * * * *dh --with javahelper
>
> jh_linkjars seems to be called automatically (but I probably need to
> provide an input file for this. *However if this does not work with
> javaepends I'm not in favour of this method anyway.

It looks like you got it working, and in a sane way - that's all that matters!

> Now to my remaining problem: *If you look at the updated build log
> at the given URL I ran into
>
> * *[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:20: package org.fr
> * *[javac] import org.freehep.graphicsio.ps.PSGraphics2D;
> * *[javac] * * * * * * * * * * * * * * * * ^
> * *[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:21: package org.fr
> * *[javac] import org.freehep.graphicsio.pdf.PDFGraphics2D;
> * *[javac] * * * * * * * * * * * * * * * * *^
> * *...
>
> even after having the classpath adapted to include
>
> * ${deblib}/freehep-graphics2d.jar
>
> (deblib:=/usr/share/java). *Any further ideas?

You might need to B-D on libfreehep-graphicsio-java [1,2] and include
${deblib}/freehep-graphicsio.jar in your classpath.

Also, now that you are properly setting the classpaths for your jars,
you can make the figtree's Depends in debian/control be:

Depends: ${shlibsepends}, ${miscepends}, ${javaepends}.

That should add default-jre | sun-java and also try to resolve which
java libraries you are using. Debhelper won't do that automatically
through dh_shlibdeps. See jh_depends manpage.

Cheers,
Scott

[1] http://packages.debian.org/sid/libfreehep-graphicsio-java
[2] http://java.freehep.org/vectorgraphics/apidocs/org/freehep/graphicsio/pdf/PDFGraphics2D.html


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Old 02-13-2011, 03:30 PM
Andreas Tille
 
Default Help wanted in Java library packaging (JEBL2)

On Sun, Feb 13, 2011 at 09:54:58AM -0500, Scott Howard wrote:
> It looks like you got it working, and in a sane way - that's all that matters!
>
> > Now to my remaining problem: *If you look at the updated build log
> > at the given URL I ran into
> >
> > * *[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:20: package org.fr
> > * *[javac] import org.freehep.graphicsio.ps.PSGraphics2D;
> > * *[javac] * * * * * * * * * * * * * * * * ^
> > * *[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:21: package org.fr
> > * *[javac] import org.freehep.graphicsio.pdf.PDFGraphics2D;
> > * *[javac] * * * * * * * * * * * * * * * * *^
> > * *...
> >
> > even after having the classpath adapted to include
> >
> > * ${deblib}/freehep-graphics2d.jar
> >
> > (deblib:=/usr/share/java). *Any further ideas?
>
> You might need to B-D on libfreehep-graphicsio-java [1,2] and include
> ${deblib}/freehep-graphicsio.jar in your classpath.

I did both:

$ grep libfreehep-graphicsio-java debian/control
libfreehep-graphics2d-java, libfreehep-graphicsio-java, libjebl2-java, libjam-java,

$ grep freehep-graphicsio.jar build.xml
classpath="${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/freehep-graphics2d.jar:${deblib}/freehep-graphicsio.jar:${deblib}/freehep-export.jar:${lib}/iText.jar">

as I hoped to show at

http://people.debian.org/~tille/packages/figtree-help-wanted/

However, the problem above remained and I have no idea why.

> Also, now that you are properly setting the classpaths for your jars,
> you can make the figtree's Depends in debian/control be:
>
> Depends: ${shlibsepends}, ${miscepends}, ${javaepends}.
>
> That should add default-jre | sun-java and also try to resolve which
> java libraries you are using.

Fixed in SVN.

Kind regards

Andreas.

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Old 02-13-2011, 04:09 PM
Scott Howard
 
Default Help wanted in Java library packaging (JEBL2)

On Sun, Feb 13, 2011 at 11:30 AM, Andreas Tille <andreas@an3as.eu> wrote:
> On Sun, Feb 13, 2011 at 09:54:58AM -0500, Scott Howard wrote:
>> It looks like you got it working, and in a sane way - that's all that matters!
>>
>> > Now to my remaining problem: *If you look at the updated build log
>> > at the given URL I ran into
>> >
>> > * *[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:20: package org.fr
>> > * *[javac] import org.freehep.graphicsio.ps.PSGraphics2D;
>> > * *[javac] * * * * * * * * * * * * * * * * ^
>> > * *[javac] /home/andreas/debian-maintain/todo/0_debian-med_todo/0phylogeny/figtree/figtree-wo_jam_jebl/figtree-1.3.1/src/figtree/application/FigTreeApplication.java:21: package org.fr
>> > * *[javac] import org.freehep.graphicsio.pdf.PDFGraphics2D;
>> > * *[javac] * * * * * * * * * * * * * * * * *^

>> You might need to B-D on libfreehep-graphicsio-java [1,2] and include
>> ${deblib}/freehep-graphicsio.jar in your classpath.
>
> I did both:
>
> $ grep libfreehep-graphicsio-java debian/control
> *libfreehep-graphics2d-java, libfreehep-graphicsio-java, libjebl2-java, libjam-java,
>
> $ grep freehep-graphicsio.jar build.xml
> * * * * * * * * * * * classpath="${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/freehep-graphics2d.jar:${deblib}/freehep-graphicsio.jar:${deblib}/freehep-export.jar:${lib}/iText.jar">
>
> as I hoped to show at
>
> * http://people.debian.org/~tille/packages/figtree-help-wanted/
>
> However, the problem above remained and I have no idea why.

The joy of java libraries... I think we need even more specific
libraries: libfreehep-graphicsio-pdf-java
libfreehep-graphicsio-ps-java [1,2]. I'm away from machines I can use
to build, but I check the debian git repos for those two packages and
they have the .java files you are looking for [3 4

then add the following to the classpath
${deblib}/freehep-graphicsio-pdf.jar
${deblib}/freehep-graphicsio-ps.jar

Cheers,
Scott

[1] http://packages.debian.org/sid/libfreehep-graphicsio-pdf-java
[2] http://packages.debian.org/sid/libfreehep-graphicsio-ps-java
[3] http://git.debian.org/?p=pkg-java/freehep/freehep-graphicsio-pdf.git;a=blob;f=src/main/java/org/freehep/graphicsio/pdf/PDFGraphics2D.java
[4] http://git.debian.org/?p=pkg-java/freehep/freehep-graphicsio-ps.git;a=blob;f=src/main/java/org/freehep/graphicsio/ps/PSGraphics2D.java


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Old 02-13-2011, 07:33 PM
Andreas Tille
 
Default Help wanted in Java library packaging (JEBL2)

On Sun, Feb 13, 2011 at 12:09:05PM -0500, Scott Howard wrote:
> > as I hoped to show at
> >
> > * http://people.debian.org/~tille/packages/figtree-help-wanted/
> >
> > However, the problem above remained and I have no idea why.
>
> The joy of java libraries... I think we need even more specific
> libraries: libfreehep-graphicsio-pdf-java
> libfreehep-graphicsio-ps-java [1,2]. I'm away from machines I can use
> to build, but I check the debian git repos for those two packages and
> they have the .java files you are looking for [3 4
>
> then add the following to the classpath
> ${deblib}/freehep-graphicsio-pdf.jar
> ${deblib}/freehep-graphicsio-ps.jar

I did so and this has solved 4 out of 10 errors. The remaining ones are
concerning EMF, SVG and SWF (see build log at the URL above). I tried to
fix it in an analogue manner as for PS and PDF ... but failed. I gazed
for hours on the bits of code but failed to find the reason why PS and
PDF now are OK but EMF, SVG and SWF are not working the same way.

Hope this will be the last iteration of this problem and thanks for your
help in any case

Andreas.


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Old 02-13-2011, 09:32 PM
Giovanni Mascellani
 
Default Help wanted in Java library packaging (JEBL2)

Hi Andreas.

On 13/02/2011 21:33, Andreas Tille wrote:
> I did so and this has solved 4 out of 10 errors. The remaining ones are
> concerning EMF, SVG and SWF (see build log at the URL above). I tried to
> fix it in an analogue manner as for PS and PDF ... but failed. I gazed
> for hours on the bits of code but failed to find the reason why PS and
> PDF now are OK but EMF, SVG and SWF are not working the same way.

I would try to debug it, but your package wants to depend against
libjam-java and I don't know where to find it. Searching on your page on
p.d.o didn't help.

> Hope this will be the last iteration of this problem and thanks for your
> help in any case

Unfortunately in Java is more than usual to have tree problems: to fix a
package you have to fix, update or create two other packages, each of
them in turn requiring two new, updated or fixed package, and so on. Oh
joy...

Giovanni.
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