Your message dated Wed, 02 Sep 2020 07:03:39 +0000 with message-id <[email protected]> and subject line Bug#968739: fixed in igv 2.6.3+dfsg-1 has caused the Debian Bug report #968739, regarding igv will not run 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.) -- 968739: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=968739 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: igv Version: 2.4.17+dfsg-1 Severity: grave Justification: renders package unusable Dear Maintainer, The IGV package seems not to work. It throws a NoSuchMethodError exception on startup with the following trace: $ igv log4j: reset attribute= "false". log4j: Threshold ="null". log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [org.broad.igv] additivity to [true]. log4j: Level value for org.broad.igv is [INFO]. log4j: org.broad.igv level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n]. log4j: Adding appender named [console] to category [org.broad.igv]. 2020-08-20 13:59:59 INFO DirectoryManager:179 - IGV Directory: /home/bredelings/igv 2020-08-20 13:59:59 INFO Main:155 - Startup IGV Version user not_set 2020-08-20 13:59:59 INFO Main:156 - Java 11.0.8 2020-08-20 13:59:59 INFO DirectoryManager:84 - Fetching user directory... 2020-08-20 13:59:59 INFO Main:157 - Default User Directory: /home/bredelings 2020-08-20 13:59:59 INFO Main:158 - OS: Linux 2020-08-20 13:59:59 INFO Main:208 - Unknown version: user 2020-08-20 14:00:00 ERROR DefaultExceptionHandler:49 - Unhandled exception java.lang.NoSuchMethodError: 'void htsjdk.tribble.util.ParsingUtils.registerHelperClass(java.lang.Class)' at org.broad.igv.util.HttpUtils.<init>(HttpUtils.java:104) at org.broad.igv.util.HttpUtils.getInstance(HttpUtils.java:97) at org.broad.igv.ui.Main.open(Main.java:279) at org.broad.igv.ui.Main$1.run(Main.java:110) at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) 2020-08-20 14:00:01 INFO ShutdownThread:46 - Shutting down -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (2000, 'unstable'), (1999, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.7.0-2-amd64 (SMP w/12 CPU threads) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages igv depends on: ii default-jre 2:1.11-72 ii junit4 4.12-8 ii libbatik-java 1.12-1.1 ii libbcprov-java 1.65-1 ii libcofoja-java 1.3-4 ii libcommons-io-java 2.6-2 ii libcommons-logging-java 1.2-2 ii libcommons-math-java 2.2-7 ii libcommons-net-java 3.6-1 ii libgoogle-gson-java 2.8.6-1 ii libguava-java 29.0-5 ii libhtsjdk-java 2.22.0+dfsg-1 ii libhttpclient-java 4.5.11-1 ii libhttpcore-java 4.4.13-1 ii libjama-java 1.0.3-1 ii libjargs-java 1.0.0-5 ii libjaxb-api-java 2.3.1-1 ii libjaxp1.3-java 1.3.05-5 ii libjcommon-java 1.0.23-1 ii libjfreechart-java 1.0.19-2 ii libjgrapht0.8-java 0.8.3-5 ii libjhdf5-java 2.11.0+dfsg-4 ii libjide-oss-java 3.7.6+dfsg-1 ii liblog4j1.2-java 1.2.17-9 ii liblog4j2-java 2.11.2-1 ii libpicard-java 2.22.8+dfsg-1 ii libswing-layout-java 1.0.4-4 ii libxml-commons-external-java 1.4.01-5 Versions of packages igv recommends: ii libmariadb-java 2.5.3-1 igv suggests no packages. -- no debconf information
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--- Begin Message ---Source: igv Source-Version: 2.6.3+dfsg-1 Done: Pierre Gruet <[email protected]> We believe that the bug you reported is fixed in the latest version of igv, 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. Pierre Gruet <[email protected]> (supplier of updated igv 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: Tue, 01 Sep 2020 22:14:41 +0200 Source: igv Binary: igv Architecture: source all Version: 2.6.3+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Pierre Gruet <[email protected]> Description: igv - Integrative Genomics Viewer Closes: 940606 968739 Changes: igv (2.6.3+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Standards-Version: 4.5.0 (Rules-Requires-Root field added) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Use secure URI in Homepage field. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. . [ Pierre Gruet ] * New upstream version Closes: #940606 * Updating build directory to Java 11 * Add runtime dependency to batik * Adapting paths for gradle as we use Debian libs * Adapting the code, written for an old htsjdk version Closes: #968739 * Skipping build-time tests that require an access to network Checksums-Sha1: 8d22c4b125fb4a1ab9ee0aaa00d784e5b9766c47 2637 igv_2.6.3+dfsg-1.dsc a074429832967304678d925f3b5e012ce64a76d1 111944404 igv_2.6.3+dfsg.orig.tar.xz 0a644083f46d865977236547d3d7229842e5c265 13800 igv_2.6.3+dfsg-1.debian.tar.xz 75b95c88c788afb9fc695fb9b507b8431145900a 3382200 igv_2.6.3+dfsg-1_all.deb 6faa4b921ccd4ed1d9231a8db6a84220d310e18f 19432 igv_2.6.3+dfsg-1_amd64.buildinfo Checksums-Sha256: c27813b6845b9dba5da777b02d7438a056b376b80280f9888c81bc6f5e5ad3c7 2637 igv_2.6.3+dfsg-1.dsc 507b4b1331d258630a9719366a6585f3f7b7762c2825e10818888129a60d1709 111944404 igv_2.6.3+dfsg.orig.tar.xz 7ff65040b4d8aac38715a64276721ed9250e5dd35b81a983f66ce98eff2e549e 13800 igv_2.6.3+dfsg-1.debian.tar.xz ad1802d5f04c6f400186f023de5c5a97f20b8ee4db7ba3d823544c78eaaa573b 3382200 igv_2.6.3+dfsg-1_all.deb 486a3d16a5b79581c79494835d355a32dc417332dfa8235413aa470a499fac00 19432 igv_2.6.3+dfsg-1_amd64.buildinfo Files: ce0b8096939a6da87c3b5f57b5281630 2637 non-free/science optional igv_2.6.3+dfsg-1.dsc c310bbca9f02601545aeda609b2d90c4 111944404 non-free/science optional igv_2.6.3+dfsg.orig.tar.xz f3ab2eb693305f7732d83701d0ff8fe6 13800 non-free/science optional igv_2.6.3+dfsg-1.debian.tar.xz 3f5a78efd3374f1538a5508b2524a363 3382200 non-free/science optional igv_2.6.3+dfsg-1_all.deb 488eb6cbc9738ace9d6b49fe78a698b3 19432 non-free/science optional igv_2.6.3+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl9PQCoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFySQ/+J02CXcgH5YOwBpDof+5vHoe7k0bc9zR1 z6xw5bgGp7km8X4sHziqV3IcYVoy1aRaClYXOoIKVVnPpseIqhkJ1qgnHegTN1aA /rldxET4Buebxze3KLNttBOraOjIBrzosOXP/yqzbhdAV5wvuCrHWhU3crpIRLem wt+C8R8hBDoUvRQ+RGMwML4EZ04eCqeoUhg5jixzp+Gcdt2Gg7ljayBf84EOUBsn RLUB6NH5vYDTMHARMkf7AEY2dW8GkAhKmNLhrVfMVKX/RVp64G87x61JyGwKtrHe LL2Pb8T1uj+uvqwXRVRwP+qVo0Gn6xxd8MsQ0a+2PcoUnlNLN8Gz1QqpSLH4ShsP CZleUYjMZSwuYAd6duAzrS8vOqzcgvvCCnFuvpy4nvXe9JJTNffKOmBHR18wcabT LJNghFRxgd12s3b+8Ey8lMc78ItKshQchreCMWdoROhE2mWYUhqSR2MMcGgQRhfu /FAxyhiY8GmZIeMNHFVzXbZa3WPTXk24ArM3HnUHE4myS1n/y0/XbmZ9gNkbxoRL JIP54Nvqy4KHz/DPQFCXFNel9zy7F2pLzKoNYPXi+G/KIqPn4KWqwougPoqI6QQu EFsXo3se/j5JjTPlTPMdGlDXkO5i76DefaZgFRAquw+m8I5ERln1TclzfjrwtTY2 Ef2r7FQ2KXg= =WeUT -----END PGP SIGNATURE-----
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