[Debian-med-packaging] Bug#968739: [benjamin.redelings at gmail.com: Bug#968739: igv will not run]

[Andreas Tille]

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BTW, I do not think that we should stick to that now outdated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.

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