Your message dated Mon, 14 Jan 2019 16:20:32 +0000
with message-id <e1gj4yw-000cws...@fasolo.debian.org>
and subject line Bug#917667: fixed in biojava4-live 4.2.12+dfsg-1
has caused the Debian Bug report #917667,
regarding biojava4-live: FTBFS (cannot find symbol JAXBContext)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
917667: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=917667
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
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 917...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@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 ftpmas...@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-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@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: 917655 917667
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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--- End Message ---
