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

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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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Thread

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

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