Bug#1005503: [Help] Re: Bug#1005503: cdkr: FTBFS: [javac] /<>/rcdkjar/src/org/guha/rcdk/util/Misc.java:14: error: package org.openscience.cdk.inchi does not exist

[Andreas Tille]

Hi Andrius,

Am Mon, Feb 14, 2022 at 08:25:58AM +0200 schrieb Andrius Merkys:
> 
> Thanks for pinging me here. This issue is indeed Debian-specific, so the
> upstreams should not be bothered by it.

OK.
 
> In the upload of cdk 1:2.7.1-1 I have disabled InChI support once again
> due to cdk requirement of DFSG-incompatible version of InChI reference
> library. Thus cdkr is not able to find the related cdk classes no more.
> 
> The only viable solution in cdkr is disabling InChI support too, most
> likely by patching out the related classes. I will give it a look either
> before or during Debian Med Sprint.

Thanks a lot

  Andreas. 

PS: Onkar Shinde  removed from CC since e-mail
is bouncing.

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Bug#1005503: [Help] Re: Bug#1005503: cdkr: FTBFS: [javac] /<>/rcdkjar/src/org/guha/rcdk/util/Misc.java:14: error: package org.openscience.cdk.inchi does not exist

[Andrius Merkys]

Control: tags -1 - help
Control: owner -1 !

Hi Andreas,

On 2022-02-13 20:14, Andreas Tille wrote:
> I noticed that a new version (2.7.1) of cdk was uploaded which is
> possibly responsible for the issue reported below.  Before I'll contact
> cdkr authors I want to make sure that its not a Debian packaging issue
> which is causing the problem below.

Thanks for pinging me here. This issue is indeed Debian-specific, so the
upstreams should not be bothered by it.

In the upload of cdk 1:2.7.1-1 I have disabled InChI support once again
due to cdk requirement of DFSG-incompatible version of InChI reference
library. Thus cdkr is not able to find the related cdk classes no more.

The only viable solution in cdkr is disabling InChI support too, most
likely by patching out the related classes. I will give it a look either
before or during Debian Med Sprint.

Best,
Andrius

Bug#1005503: [Help] Re: Bug#1005503: cdkr: FTBFS: [javac] /<>/rcdkjar/src/org/guha/rcdk/util/Misc.java:14: error: package org.openscience.cdk.inchi does not exist

[Andreas Tille]

Control: tags -1 help

Hi CDK uploaders,

I noticed that a new version (2.7.1) of cdk was uploaded which is
possibly responsible for the issue reported below.  Before I'll contact
cdkr authors I want to make sure that its not a Debian packaging issue
which is causing the problem below.

Kind regards

 Andreas.

Am Sun, Feb 13, 2022 at 08:00:22AM +0100 schrieb Lucas Nussbaum:
> Source: cdkr
> Version: 3.6.0+dfsg-1
> Severity: serious
> Justification: FTBFS
> Tags: bookworm sid ftbfs
> User: lu...@debian.org
> Usertags: ftbfs-20220212 ftbfs-bookworm
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
> 
> 
> Relevant part (hopefully):
> > make[1]: Entering directory '/<>'
> > ant -buildfile rcdkjar/build.xml
> > Buildfile: /<>/rcdkjar/build.xml
> > 
> > compile:
> > [mkdir] Created dir: /<>/rcdkjar/classes
> > [javac] Compiling 18 source files to /<>/rcdkjar/classes
> > [javac] warning: [options] bootstrap class path not set in conjunction 
> > with -source 8
> > [javac] /<>/rcdkjar/src/org/guha/rcdk/util/Misc.java:14: 
> > error: package org.openscience.cdk.inchi does not exist
> > [javac] import org.openscience.cdk.inchi.InChIGenerator;
> > [javac] ^
> > [javac] /<>/rcdkjar/src/org/guha/rcdk/util/Misc.java:15: 
> > error: package org.openscience.cdk.inchi does not exist
> > [javac] import org.openscience.cdk.inchi.InChIGeneratorFactory;
> > [javac] ^
> > [javac] Note: Some input files use or override a deprecated API.
> > [javac] Note: Recompile with -Xlint:deprecation for details.
> > [javac] 2 errors
> > [javac] 1 warning
> > 
> > BUILD FAILED
> > /<>/rcdkjar/build.xml:26: Compile failed; see the compiler 
> > error output for details.
> > 
> > Total time: 1 second
> > make[1]: *** [debian/rules:11: override_dh_auto_build] Error 1
> 
> 
> The full build log is available from:
> http://qa-logs.debian.net/2022/02/12/cdkr_3.6.0+dfsg-1_unstable.log
> 
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
> 
> If you reassign this bug to another package, please marking it as 
> 'affects'-ing
> this package. See https://www.debian.org/Bugs/server-control#affects
> 
> If you fail to reproduce this, please provide a build log and diff it with 
> mine
> so that we can identify if something relevant changed in the meantime.
> 
> ___
> R-pkg-team mailing list
> r-pkg-t...@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team
> 

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