Your message dated Thu, 30 Aug 2018 12:18:56 +0000 with message-id <[email protected]> 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 907559: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=907559 Debian Bug Tracking System Contact [email protected] 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.
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Andreas Tille <[email protected]> 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 Checksums-Sha1: 0d50c9a9b9c4adfcc7cdb2c6b62c1c2238cc48c6 2063 cgview_0.0.20100111-4.dsc 57eb7881e7d4320e8cf372f2162aacf9636c24af 7816 cgview_0.0.20100111-4.debian.tar.xz Checksums-Sha256: 5c6a64522b6984bee1d648e143d4be8debfd929de3ba7f6c88c01c2ea71b5fd7 2063 cgview_0.0.20100111-4.dsc efa75aca02ea2e99256157fc40158e522cecf2bbfe4fc015005a4a1fc8b69821 7816 cgview_0.0.20100111-4.debian.tar.xz Files: ae3e1fb7adefbfdae3248d9acb5f772f 2063 science optional cgview_0.0.20100111-4.dsc fbb55147c6002af921bb8364be86d94e 7816 science optional cgview_0.0.20100111-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluH3JcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH0Uw/6A//zMc+H/EhOtLR/BMA1wJsoOJB9oBZW 0JqCFcNY1FtS3O3E4+Rmwx3sGq8E+g9oNbaCjlPPnc8VQduoOfbTncvJxeCPjW9P lYRktlQsotElbAD+jUQP28JIb8GIV1M0ityWfY6L5xHz9oEjlWhmo4vp0XKuEe6b Fun07xKFr0eOW3bNGR3+HSXADYtjKIt+aL8O9eWd7wjU1yCKYe+krZVHZuicVfEn STWpw+cKd4ldMLPWFZTgLwGHzWh135NXRHBRxyTjomCmx83KfDb1yO9qpMZzjVxD A57rOtPZ89CXLvTso/wGNQRljjMYL+xWCgk01MEWWW4Dm7UWIJOhe2SUgZ9Mwv6o NiT26+/HF8ZfZ4Rm4Md2ltPIqewfss4S3m5uoQgDINablf3ZF7KUWireemV4fjO/ jt59Kb2LIhojJNWc7cyjlU+y1qOb63BNcHUkc3rxgMlaeV8ce74ayMB4RHHjmIXc DvIEhz+tcZa05Vze48RO15ODUGZXdO0PIG8nejbxTDaCxx0L23xi2UU+1d85FfqE OnN4S/7sBQwZy9Ox6gXV23qoUcXJPkQgN0dxzUgVKJGhXOVErMabyxThlx/hXf0W 1JrPBDBTgOGwuhGQ07UOW8FPlOTKfT3ZHQ3c9M3vutvrNySow0RPBKx3vrLMilsT K16P/liEAf4= =d08I -----END PGP SIGNATURE-----
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