Bug#906371: [Debian-med-packaging] Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
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
Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
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? > > 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. -- http://fam-tille.de
Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
On Tue, Aug 21, 2018 at 08:46:17AM +0200, Andreas Tille wrote: > Hi, > > On Mon, Aug 20, 2018 at 12:39:21AM +0200, Emmanuel Bourg wrote: > > > do you have any hint how to deal with this issue? > > > > The actual error is: > > > > [javac] > > /build/1st/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/1st/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/1st/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/1st/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; > > [javac] ^ > > > > There is an issue with a dependency (alter-sequence-alignment maybe?), > > the Java version isn't to blame here. > > 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? 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] ^ Kind regards Andreas. [1] https://salsa.debian.org/med-team/jmodeltest/commit/4e5707bbe45cb80d3dc96a3800477affaef73680 -- http://fam-tille.de
Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
Hi, On Mon, Aug 20, 2018 at 12:39:21AM +0200, Emmanuel Bourg wrote: > > do you have any hint how to deal with this issue? > > The actual error is: > > [javac] > /build/1st/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/1st/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/1st/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/1st/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; > [javac] ^ > > There is an issue with a dependency (alter-sequence-alignment maybe?), > the Java version isn't to blame here. 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. :-( Any hint? Kind regards Andreas. [1] -- http://fam-tille.de
