Re: [Debian-med-packaging] Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
- To: 906371@bugs.debian.org, Debian Java List <debian-java@lists.debian.org>, Debian Med Project List <debian-med@lists.debian.org>
- Subject: Re: [Debian-med-packaging] Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
- From: Olivier Sallou <olivier.sallou@irisa.fr>
- Date: Mon, 17 Dec 2018 15:40:30 +0100
- Message-id: <[🔎] 701be5b9-e5d4-344e-f6b1-2cae87880791@irisa.fr>
- In-reply-to: <20181217100748.owuikwkubnmijrsh@an3as.eu>
- References: <E1fqcnb-0008Bl-8D@paradis.debian.org> <20180817125647.55fncemqvkqqcoci@an3as.eu> <d26c127d-3bec-a152-0d7f-8774ef9db302@apache.org> <20180821064616.nketw4xkcgs2kg36@an3as.eu> <20181017083258.nbr5jy66xbozr3le@an3as.eu> <E1fqcnb-0008Bl-8D@paradis.debian.org> <20181217100748.owuikwkubnmijrsh@an3as.eu>
On 12/17/18 11:07 AM, Andreas Tille wrote:
> Hi,
>
> after I tried to follow the initial hint of Emmanuel I admit I was not
> successful to finally build the package:
>
> On Wed, Oct 17, 2018 at 10:32:58AM +0200, Andreas Tille wrote:
>>> Good catch. The latest upstream version of alter-sequence-alignment has
>>> split these to an additional alter-lib.jar and the time of the build
>>> failure of jmodeltest correlates with the upload of
>>> alter-sequence-alignment 1.3.4-1. But now the question is: How to
>>> teach the jmodeltest build system to use alter-lib.jar. I think adding
>>> it to debian/manifest[1] is needed to *run* jmodeltest but it surely
>>> does not help at build time. I have not found any place where the
>>> build system specifies the needed jars. :-(
>> I tried to add alter-lib.jar to build.xml[1]. Unfortunately this does
>> not help to fix the issue
>>
>> [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:28: error: package parser does not exist
>> [javac] import parser.ParseException;
>> [javac] ^
>> [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:29: error: package converter does not exist
>> [javac] import converter.Converter;
>> [javac] ^
>> [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:30: error: package converter does not exist
>> [javac] import converter.DefaultFactory;
>> [javac] ^
>> [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:31: error: package converter does not exist
>> [javac] import converter.Factory;
>>
>> Any hint how to get the classes in alter-lib.jar found?
I fixed the issue and pushed to git my patch d/patches/fix_alter-lib.patch
The lib was used but the package name in alter-lib.jar is different.
ModelTestService is patched to use correct package name
>> Moreover I get lots of
>>
>> [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/exe/Distributor.java:23: warning: [deprecation] Observable in java.util has been deprecated
>> [javac] import java.util.Observable;
>> [javac] ^
> Any more hints?
>
> Kind regards
>
> Andreas.
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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