[Debian-med-packaging] Bug#968739: [benjamin.redelings at gmail.com: Bug#968739: igv will not run]
Andreas Tille
tille at debian.org
Fri Aug 21 10:05:25 BST 2020
Hi again,
I injected the latest upstream version into Git. It does not include so
many binary jar's any more but I think its trying to download these
instead. I gave up for the moment since I have no idea about gradle.
Kind regards
Andreas.
On Fri, Aug 21, 2020 at 07:38:21AM +0200, Andreas Tille wrote:
> Hi Pierre,
>
> do you have some spare cycles for this issue?
>
> BTW, I do not think that we should stick to that now outdated
> version but while fixing the issue package latest upstream.
>
> On a more general note: Igv is another Java package that is in
> non-free only due to the included binary JARs. If we could that
> sorted out it probably could go into main which would be a real
> advantage.
>
> Kind regards
>
> Andreas.
>
>
> ----- Forwarded message from Benjamin Redelings <benjamin.redelings at gmail.com> -----
>
> Date: Thu, 20 Aug 2020 14:01:13 -0400
> From: Benjamin Redelings <benjamin.redelings at gmail.com>
> To: Debian Bug Tracking System <submit at bugs.debian.org>
> Subject: Bug#968739: igv will not run
> X-Debian-PR-Message: report 968739
> X-Debian-PR-Package: igv
> X-Debian-PR-Keywords:
> X-Debian-PR-Source: igv
>
> 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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> ----- End forwarded message -----
>
> --
> http://fam-tille.de
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