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From: tony mancill <tmancill@debian.org>
Newsgroups: linux.debian.maint.java
Subject: Re: Upgrading freehep to latest upstream (needed by cdk and probably  others)
Date: Mon, 27 Jul 2020 07:40:01 +0200
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Hi Andreas,

On Sun, Jul 26, 2020 at 10:34:07AM +0200, Andreas Tille wrote:
> Hi Andrius,
>=20
> 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)?
> >=20
> > I have updated cdk yesterday. The cdk-depict module is built now.
>=20
> Thanks a lot.  Unfortunately I have remaining issues with r-cran-rcdk.
> If I try to build it I get:
>=20
>=20
> Executing test function test.mcs2  ... Error in .jcall("org.guha.rcdk.uti=
l.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  :.
>   java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
> Timing stopped at: 0.022 0 0.007
>  done successfully.
> =20
>=20
> 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:

=E2=9E=9C  cdk-2.3.134.g1bb9a64587 find . -name Isomorphism.java
=2E/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.p=
oms#L91

I'll look into the discrepancy with libjgrapht0.6-java, which doesn't
include maven metadata.

Cheers,
tony

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