Report forwarded
to debian-bugs-dist@lists.debian.org, sanvila@debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#917655; Package src:biojava4-live.
(Sat, 29 Dec 2018 21:42:06 GMT) (full text, mbox, link).
Acknowledgement sent
to Santiago Vila <sanvila@debian.org>:
New Bug report received and forwarded. Copy sent to sanvila@debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Sat, 29 Dec 2018 21:42:06 GMT) (full text, mbox, link).
Subject: biojava4-live: FTBFS (cannot find symbol JAXBContext)
Date: Sat, 29 Dec 2018 21:39:09 +0000
Package: src:biojava4-live
Version: 4.2.11+dfsg-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in buster but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-indep
dh build-indep --with javahelper
dh_update_autotools_config -i
dh_autoreconf -i
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/biojava4-live-4.2.11+dfsg'
dh_auto_configure
sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml
sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml
sed -e 's/BJLIB/biojava4-core/g' debian/build.xml > biojava-core/build.xml
sed -e 's/BJLIB/biojava4-alignment/g' debian/build.xml > biojava-alignment/build.xml
sed -e 's/BJLIB/biojava4-genome/g' debian/build.xml > biojava-genome/build.xml
sed -e 's/BJLIB/biojava4-modfinder/g' debian/build.xml > biojava-modfinder/build.xml
sed -e 's/BJLIB/biojava4-phylo/g' debian/build.xml > biojava-phylo/build.xml
[... snipped ...]
[javac] location: class PeptidePropertiesImpl
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:147: error: cannot find symbol
[javac] JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
[javac] ^
[javac] symbol: class JAXBContext
[javac] location: class PeptidePropertiesImpl
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:147: error: cannot find symbol
[javac] JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
[javac] ^
[javac] symbol: variable JAXBContext
[javac] location: class PeptidePropertiesImpl
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:148: error: cannot find symbol
[javac] Unmarshaller u2 = jc2.createUnmarshaller();
[javac] ^
[javac] symbol: class Unmarshaller
[javac] location: class PeptidePropertiesImpl
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:34: error: method does not override or implement a method from a supertype
[javac] @Override
[javac] ^
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: error: cannot find symbol
[javac] if (ve.getSeverity() == ValidationEvent.FATAL_ERROR || ve.getSeverity() == ValidationEvent.ERROR){
[javac] ^
[javac] symbol: variable ValidationEvent
[javac] location: class MyValidationEventHandler
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: error: cannot find symbol
[javac] if (ve.getSeverity() == ValidationEvent.FATAL_ERROR || ve.getSeverity() == ValidationEvent.ERROR){
[javac] ^
[javac] symbol: variable ValidationEvent
[javac] location: class MyValidationEventHandler
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:37: error: cannot find symbol
[javac] ValidationEventLocator locator = ve.getLocator();
[javac] ^
[javac] symbol: class ValidationEventLocator
[javac] location: class MyValidationEventHandler
[javac] /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java:36: error: method does not override or implement a method from a supertype
[javac] @Override
[javac] ^
[javac] 83 errors
BUILD FAILED
/<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/build.xml:93: Compile failed; see the compiler error output for details.
Total time: 9 seconds
make[1]: *** [debian/rules:39: override_dh_auto_build] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/biojava4-live-4.2.11+dfsg'
make: *** [debian/rules:12: build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit status 2
--------------------------------------------------------------------------------
The build was made in my autobuilder with "dpkg-buildpackage -A"
but it also fails here:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/biojava4-live.html
where you can get a full build log if you need it.
If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.
Thanks.
Added tag(s) buster and sid.
Request was from Adrian Bunk <bunk@debian.org>
to control@bugs.debian.org.
(Tue, 01 Jan 2019 22:36:03 GMT) (full text, mbox, link).
Merged 917655917667
Request was from Adrian Bunk <bunk@debian.org>
to control@bugs.debian.org.
(Tue, 01 Jan 2019 22:36:04 GMT) (full text, mbox, link).
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#917655; Package src:biojava4-live.
(Fri, 11 Jan 2019 22:09:05 GMT) (full text, mbox, link).
Acknowledgement sent
to Andreas Tille <tille@debian.org>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Fri, 11 Jan 2019 22:09:05 GMT) (full text, mbox, link).
Added tag(s) help and upstream.
Request was from Andreas Tille <tille@debian.org>
to 917655-submit@bugs.debian.org.
(Fri, 11 Jan 2019 22:09:06 GMT) (full text, mbox, link).
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#917655; Package src:biojava4-live.
(Sat, 12 Jan 2019 06:00:05 GMT) (full text, mbox, link).
Acknowledgement sent
to tony mancill <tmancill@debian.org>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Sat, 12 Jan 2019 06:00:05 GMT) (full text, mbox, link).
Cc: Santiago Vila <sanvila@debian.org>, 917655@bugs.debian.org,
917667@bugs.debian.org, Lucas Nussbaum <lucas@debian.org>,
Debian Java List <debian-java@lists.debian.org>
Subject: Re: Bug#917655: biojava4-live: FTBFS (cannot find symbol JAXBContext)
On Fri, Jan 11, 2019 at 10:26:58PM +0100, Andreas Tille wrote:
> Control: tags -1 help upstream
>
> Hi,
>
> I've commited a new minor upstream version to Git but the problem exists
> also in this version. I've asked at debian-java list for help[1]
Hello Andreas,
I took a quick look at this and was able to resolve the build problems
by dropping the references to the java.se.ee. module and adding
jaxb-impl and jaxb-api JARs to the classpath.
It might not be the cleanest way - strictly speaking, you should only
need the jaxb-api JAR during the build and only the jaxb-impl on the
classpath while running tests.
Attached are a set of commits that let the package build for me locally.
Cheers,
tony
Subject: Bug#917655: fixed in biojava4-live 4.2.12+dfsg-1
Date: Mon, 14 Jan 2019 16:20:32 +0000
Source: biojava4-live
Source-Version: 4.2.12+dfsg-1
We believe that the bug you reported is fixed in the latest version of
biojava4-live, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 917655@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated biojava4-live package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 14 Jan 2019 16:05:19 +0100
Source: biojava4-live
Binary: libbiojava4.0-java libbiojava4-java libbiojava4-java-doc
Architecture: source
Version: 4.2.12+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libbiojava4-java - Java API to biological data and applications (default version)
libbiojava4-java-doc - [Biology] Documentation for BioJava
libbiojava4.0-java - Java API to biological data and applications (version 4)
Closes: 917655917667
Changes:
biojava4-live (4.2.12+dfsg-1) unstable; urgency=medium
.
* Team upload.
.
[ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
.
[ Andreas Tille ]
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.3.0
.
[ tony mancill ]
* Add build-dep on libjaxb-api-java and libjaxb-java
* Add jaxb-api and jaxb-impl JARs to classpaths in debian/build.xml
Closes: #917655, #917667
* Drop --add-modules java.se.ee from javadoc task
Checksums-Sha1:
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Checksums-Sha256:
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Files:
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c66ea841163dc423be3713cf937cef2a 12178028 java optional biojava4-live_4.2.12+dfsg.orig.tar.xz
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Reply sent
to Andreas Tille <tille@debian.org>:
You have taken responsibility.
(Mon, 14 Jan 2019 16:21:12 GMT) (full text, mbox, link).
Notification sent
to Lucas Nussbaum <lucas@debian.org>:
Bug acknowledged by developer.
(Mon, 14 Jan 2019 16:21:12 GMT) (full text, mbox, link).
Subject: Bug#917667: fixed in biojava4-live 4.2.12+dfsg-1
Date: Mon, 14 Jan 2019 16:20:32 +0000
Source: biojava4-live
Source-Version: 4.2.12+dfsg-1
We believe that the bug you reported is fixed in the latest version of
biojava4-live, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 917667@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated biojava4-live package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 14 Jan 2019 16:05:19 +0100
Source: biojava4-live
Binary: libbiojava4.0-java libbiojava4-java libbiojava4-java-doc
Architecture: source
Version: 4.2.12+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libbiojava4-java - Java API to biological data and applications (default version)
libbiojava4-java-doc - [Biology] Documentation for BioJava
libbiojava4.0-java - Java API to biological data and applications (version 4)
Closes: 917655917667
Changes:
biojava4-live (4.2.12+dfsg-1) unstable; urgency=medium
.
* Team upload.
.
[ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
.
[ Andreas Tille ]
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.3.0
.
[ tony mancill ]
* Add build-dep on libjaxb-api-java and libjaxb-java
* Add jaxb-api and jaxb-impl JARs to classpaths in debian/build.xml
Closes: #917655, #917667
* Drop --add-modules java.se.ee from javadoc task
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Bug archived.
Request was from Debbugs Internal Request <owner@bugs.debian.org>
to internal_control@bugs.debian.org.
(Thu, 21 Feb 2019 07:30:52 GMT) (full text, mbox, link).
Debbugs is free software and licensed under the terms of the GNU General
Public License version 2. The current version can be obtained
from https://bugs.debian.org/debbugs-source/.