Your message dated Thu, 30 Aug 2018 12:18:56 +0000
with message-id <e1fvlua-000apy...@fasolo.debian.org>
and subject line Bug#907559: fixed in cgview 0.0.20100111-4
has caused the Debian Bug report #907559,
regarding cgview: Does not start
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.
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--
907559: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=907559
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: cgview
Severity: grave
Justification: renders package unusable
Hi,
cgview in sid/testing does not start while the same code base in stable
works perfectly. It just dies with:
$ cgview
Error: Unable to initialize main class ca.ualberta.stothard.cgview.CgviewIO
Caused by: java.lang.NoClassDefFoundError: org/apache/batik/util/XMLConstants
Olivier Sallou suspected that the issue could be caused by the version of
Batik which is 1.8 in stable and 1.10 in testing/sid. I've checked both
source code and JARs for instance like
$ grep -wl XMLConstants /usr/share/java/batik*
/usr/share/java/batik-all-1.10.jar
/usr/share/java/batik-all.jar
/usr/share/java/batik-constants-1.10.jar
/usr/share/java/batik-constants.jar
/usr/share/java/batik.jar
/usr/share/java/batik-libs.jar
on a machine (testing) where it fails and where cgview works (stable):
$ $ grep -wl XMLConstants /usr/share/java/batik*
/usr/share/java/batik-1.8.jar
/usr/share/java/batik-all-1.8.jar
/usr/share/java/batik-all.jar
/usr/share/java/batik.jar
/usr/share/java/batik-libs-1.8.jar
/usr/share/java/batik-libs.jar
/usr/share/java/batik-util-1.8.jar
/usr/share/java/batik-util.jar
The only interesting difference is that on stable (batik-1.8) the symbol
is inside /usr/share/java/batik-util.jar while it is not any more in
batik 1.10.
The tricky thing is that the string XMLConstants itself is not part of
the cgview source code so simply changing util in something else that
can be found is not possible and may be the bug is simply in one of the
dependencies and not in cgview itself. That's why I take the freedom to
add Debian Java list in CC of this bug report.
Kind regards
Andreas.
-- System Information:
Debian Release: 9.5
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.9.0-6-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8),
LANGUAGE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages cgview depends on:
pn default-jre | java8-runtime <none>
pn jarwrapper <none>
pn libbatik-java <none>
pn libcommons-lang-java <none>
pn libjargs-java <none>
pn libxerces2-java <none>
cgview recommends no packages.
cgview suggests no packages.
--- End Message ---
--- Begin Message ---
Source: cgview
Source-Version: 0.0.20100111-4
We believe that the bug you reported is fixed in the latest version of
cgview, 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 907...@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 cgview 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: Thu, 30 Aug 2018 13:57:12 +0200
Source: cgview
Binary: cgview
Architecture: source
Version: 0.0.20100111-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
cgview - Circular Genome Viewer
Closes: 907559
Changes:
cgview (0.0.20100111-4) unstable; urgency=medium
.
* Add batik-constants.jar to CLASSPATH (Thanks for the hint to
Emmanuel Bourg)
Closes: #907559
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
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