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Upgrading freehep to latest upstream (needed by cdk and probably others)

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  Upgrading freehep to latest upstream (needed by cdk and probably  others) Andreas Tille <andreas@an3as.eu> - 2020-04-15 15:00 +0200
    Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) Andreas Tille <tille@debian.org> - 2020-04-21 07:00 +0200
    Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) Andreas Tille <tille@debian.org> - 2020-04-28 11:00 +0200
    Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) Andreas Tille <tille@debian.org> - 2020-07-01 11:40 +0200
    Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) Emmanuel Bourg <ebourg@apache.org> - 2020-07-02 01:40 +0200
      Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) Andreas Tille <tille@debian.org> - 2020-07-15 15:00 +0200
        Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) Andreas Tille <andreas@an3as.eu> - 2020-07-23 17:00 +0200
          Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) Andreas Tille <tille@debian.org> - 2020-07-26 10:40 +0200
            Re: Upgrading freehep to latest upstream (needed by cdk and probably  others) tony mancill <tmancill@debian.org> - 2020-07-27 07:40 +0200
              Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to  latest upstream (needed by cdk and probably others)] tony mancill <tmancill@debian.org> - 2020-07-27 16:00 +0200
                Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to  latest upstream (needed by cdk and probably others)] tony mancill <tmancill@debian.org> - 2020-07-29 05:50 +0200
                  Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to  latest upstream (needed by cdk and probably others)] Andreas Tille <andreas@an3as.eu> - 2020-07-29 09:30 +0200

#11571 — Upgrading freehep to latest upstream (needed by cdk and probably others)

Hi,

I was digging through CDK to get the R interface running (see my other
mails here on this list).  I just found another clue that cdk-depict is
missing.  When inspecting cdk source I've found:

  libcdk-java.poms:# depict requires freehep-graphicsio-* 2.4 (Debian has older)

This made me wonder about the status of the freehep-* packages that did
not had a new upload since the move from Alioth.  It seems the new version
of freehep can be found at

    https://github.com/freehep

and the structure of the classes has changed a bit (like
freehep-graphicsio is now freehep-vectorgraphics).  I wonder whether
we should follow upstream freehep to support recent software.

Kind regards

       Andreas.

-- 
http://fam-tille.de

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#11576

Hi Andrius,

On Sat, Apr 18, 2020 at 10:18:04AM +0300, merkys@debian.org wrote:
> Some time ago I had attempted packaging new freehep-vectorgraphics, with
> considerable success. However, I dropped the ball and did not upload it.
> I have pushed my packaging to salsa [1].

Thanks a lot for the promising hint.
 
> There is one issue, though. Old freehep-* JARs are split into multitude
> of source and binary packages, while my packaging uses single source
> package (I find it more convenient than splitting and linking) and
> currently puts all the JARs in one binary package. One of the following
> options has to be chosen:
> 
> 1. Have only one binary package. This would have to replace all old
> binary packages with Conflicts+Replaces.
> 
> 2. Split JARs to resemble old binary packages. AFAIK, this would require
> epoch (1:) for the new binary packages, as they would come from
> different source package.
> 
> I would probably go with the option 2.

I admit I have no strong opinion on this as long as we will get a
feature complete cjk package.  Since you also are maintaining cjk would
you volunteer to care for this?  This would be really appreciated as
a contribution to our covid-19 effort.

Kind regards

      Andreas.
 
> [1] https://salsa.debian.org/java-team/freehep-vectorgraphics

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#11584

Hi Andrius,

thanks a lot for your work on this - also thanks to Giovanni for your
comments.

I'd be really happy to get FreeHEP updated.

Kind regards

      Andreas.

On Fri, Apr 24, 2020 at 08:03:20AM +0300, merkys@debian.org wrote:
> Hello,
> 
> On 2020-04-21 10:40, Giovanni Mascellani wrote:
> > So I have no problems in removing GeoGebra to allow FreeHEP to be
> > updated (maybe it turns out that GeoGebra also works with FreeHEP's new
> > version, but I believe it is unlikely), but then at the same time I give
> > up as FreeHEP maintainer, because I would have no interest any more in
> > it. I don't know what other rev deps of current FreeHEP need, though.
> 
> GeoGebra fails to build with FreeHEP v2.4 due to missing
> EMFPlusGraphics2D class. After patching it out, I ran into other
> incompatibilities – GeoGebra seems to require patching FreeHEP source,
> and that is not nice.
> 
> Apart from GeoGebra, scilab and sweethome3d are the only source packages
> depending on FreeHEP. I have not yet tested building them with FreeHEP
> v2.4, but will do that. If that succeeds, maybe GeoGebra could be indeed
> removed to make way for new FreeHEP.
> 
> Best wishes,
> Andrius
> 
> 
> 

-- 
http://fam-tille.de

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#11740

Hi Andrius,

On Wed, Jul 01, 2020 at 11:09:54AM +0300, merkys@debian.org wrote:
> >   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=964070
> 
> Thanks a lot for the information. I have uploaded freehep-vectorgraphics
> to experimental, waiting for it to clear NEW.

Thanks for this.  I've added it to the COVID-19 relevant list of packages
in new[1]

Kind regards

      Andreas.


[1] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/NEW-Requests 

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#11743

Hi all,

Le 01/07/2020 à 09:46, Giovanni Mascellani a écrit :

>> I have successfully tested rebuilding of FreeHEP reverse dependencies
>> [1]. All but GeoGebra builds fine with FreeHEP 2.4. So if you are really
>> OK with having GeoGebra removed, could you please file the removal request?
>>
>> [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956845
> 
> Sorry, I completely lost track of this thread. Here is the RM bug:
> 
>   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=964070

Sorry for the late reply I'm noticing this thread only now. Even if the
geogebra package is outdated it's still fairly popular. Would it be
possible to package an older version of FreeHEP so we can preserve geogebra?

Emmanuel Bourg

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#11767

On Fri, Jul 10, 2020 at 04:06:03PM +0300, merkys@debian.org wrote:
> On 2020-07-10 15:59, Giovanni Mascellani wrote:
> > Great, then I revoke the intention of RMing geogebra and close the
> > corresponding bug. As soon as freehep-vectographics is available, I will
> > bump patches and dependencies on geogebra and everything should be find.
> 
> Sure, I will ping you once freehep-vectographics clears the NEW queue.

It has cleared new now and I commited some changes ready for a
source-only upload but since I did not followed the full discussion
I'm hesitating with dput.  Feel free to upload what I commited
according to your preference.

Kind regards

      Andreas.

-- 
http://fam-tille.de

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#11787

Hi Andrius,

On Thu, Jul 23, 2020 at 04:42:20PM +0300, merkys@debian.org wrote:
> Hello,
> 
> On 2020-07-22 22:00, Giovanni Mascellani wrote:
> > Thanks, I just pushed geogebra.
> 
> Thanks!

Would you mind to update cdk package (which was the original issue
I stumbled upon freehep)?

Kind regards

       Andreas. 

-- 
http://fam-tille.de

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#11798

Hi Andrius,

On Fri, Jul 24, 2020 at 08:11:29AM +0300, merkys@debian.org wrote:
> On 2020-07-23 17:55, Andreas Tille wrote:
> > Would you mind to update cdk package (which was the original issue
> > I stumbled upon freehep)?
> 
> I have updated cdk yesterday. The cdk-depict module is built now.

Thanks a lot.  Unfortunately I have remaining issues with r-cran-rcdk.
If I try to build it I get:


Executing test function test.mcs2  ... Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  :.
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
Timing stopped at: 0.022 0 0.007
 done successfully.
 

It actually seems that org/openscience/cdk/smsd/Isomorphism is not
part of the currently packaged CDK.  Any idea how to solve this?

Kind regards

       Andreas.

-- 
http://fam-tille.de

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#11803

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Hi Andreas,

On Sun, Jul 26, 2020 at 10:34:07AM +0200, Andreas Tille wrote:
> Hi Andrius,
> 
> On Fri, Jul 24, 2020 at 08:11:29AM +0300, merkys@debian.org wrote:
> > On 2020-07-23 17:55, Andreas Tille wrote:
> > > Would you mind to update cdk package (which was the original issue
> > > I stumbled upon freehep)?
> > 
> > I have updated cdk yesterday. The cdk-depict module is built now.
> 
> Thanks a lot.  Unfortunately I have remaining issues with r-cran-rcdk.
> If I try to build it I get:
> 
> 
> Executing test function test.mcs2  ... Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  :.
>   java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
> Timing stopped at: 0.022 0 0.007
>  done successfully.
>  
> 
> It actually seems that org/openscience/cdk/smsd/Isomorphism is not
> part of the currently packaged CDK.  Any idea how to solve this?

I am just starting to take a look a this, but I think we need to spend
some more time with CDK.  That class is found in the "legacy" directory
of the sources:

➜  cdk-2.3.134.g1bb9a64587 find . -name Isomorphism.java
./legacy/src/main/java/org/openscience/cdk/smsd/Isomorphism.java

But the legacy pom is ignored:

  https://salsa.debian.org/java-team/cdk/-/blob/master/debian/libcdk-java.poms#L91

I'll look into the discrepancy with libjgrapht0.6-java, which doesn't
include maven metadata.

Cheers,
tony

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#11812 — Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to latest upstream (needed by cdk and probably others)]

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Hi Andrius,

On Mon, Jul 27, 2020 at 08:51:49AM +0300, merkys@debian.org wrote:
> Hello,
> 
> On 2020-07-27 08:38, tony mancill wrote:
> >> It actually seems that org/openscience/cdk/smsd/Isomorphism is not
> >> part of the currently packaged CDK.  Any idea how to solve this?
> > I am just starting to take a look a this, but I think we need to spend
> > some more time with CDK.  That class is found in the "legacy" directory
> > of the sources:
> > 
> > ➜  cdk-2.3.134.g1bb9a64587 find . -name Isomorphism.java
> > ./legacy/src/main/java/org/openscience/cdk/smsd/Isomorphism.java
> > 
> > But the legacy pom is ignored:
> > 
> >   https://salsa.debian.org/java-team/cdk/-/blob/master/debian/libcdk-java.poms#L91
> 
> Indeed, cdk-smsd pom is ignored (I made that so). However, if I remove
> the '--ignore' instruction, the built jar is codeless:

Based upon the sources layout, I wouldn't expect the cdk-smsd.pom in the
root project to include that class anyway.

> W: libcdk-java: codeless-jar usr/share/java/cdk-smsd.jar
> 
> What is more, the subtree tool/smsd/ contains only pom.xml, what might
> be the reason of codeless jar. It seems to me that cdk-smsd is legacy
> now, and I would suggest asking the upstream for advice how to port code
> depending on it.

I still plan to take a look at what it would take to compile the
legacy/pom.xml.

Cheers,
tony

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#11814 — Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to latest upstream (needed by cdk and probably others)]

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On Tue, Jul 28, 2020 at 11:56:24AM +0300, merkys@debian.org wrote:
> Hi Tony,
> 
> On 2020-07-27 16:50, tony mancill wrote:
> > On Mon, Jul 27, 2020 at 08:51:49AM +0300, merkys@debian.org wrote:
> >> What is more, the subtree tool/smsd/ contains only pom.xml, what might
> >> be the reason of codeless jar. It seems to me that cdk-smsd is legacy
> >> now, and I would suggest asking the upstream for advice how to port code
> >> depending on it.
> > I still plan to take a look at what it would take to compile the
> > legacy/pom.xml.
> 
> Sure, please do. However, I would not count too much on this pom, as it
> may get removed in the upcoming cdk releases.

Fair enough...  In the long run, it is likely that porting r-cran-rcdk
is a better use of time.  However, I got interested in it and here is
the status so far:

1) I updated jgrapht0.6 to install a pom file and uploaded a new
package to unstable. 

2) I updated the cdk source package to build-dep on the javacc maven
plugin and re-enabled the legacy pom.

3) I used ratt to build packages that build-depend on cdk.  The
new package addresses the issue with r-cran-rcdk, but cinfony fails:

2020/07/28 20:27:10 PASSED: r-cran-rcdklibs
2020/07/28 20:27:10 FAILED: cinfony (see buildlogs/cinfony_1.2-4)

However, the cinfony failure on my system is for:

      unsat-dependency: python-indigo:amd64

And it also fails when built against cdk_2.3.134.g1bb9a64587-1, so I
don't think this is related to my change.

I created a merge request [1] so you can take a look.  I'm happy to
prepare an upload if it looks okay to you.

Cheers,
tony

[1] https://salsa.debian.org/java-team/cdk/-/merge_requests/4

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#11815 — Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to latest upstream (needed by cdk and probably others)]

Hi Tony & Andrius,

On Wed, Jul 29, 2020 at 09:18:52AM +0300, merkys@debian.org wrote:
> > [1] https://salsa.debian.org/java-team/cdk/-/merge_requests/4
> 
> The MR looks good to me.

Thanks a lot for you both working on it.

> I posted a tiny suggestion to depend on
> jgrapht0.6 with a version to prevent well-known FTBFS. Otherwise it's
> good to go. Feel free to upload.

I'd be really happy if you could upload.  I'm currently swamped with
other stuff (mainly at payed work) and would be happy if I simply can
just test with r-cran-rcdk whether it builds or not against the uploaded
package.
 
> Thanks a lot for looking into this!

+1 (again)

Kind regards

      Andreas.

-- 
http://fam-tille.de

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