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

Pierre Gruet pgtdebian at free.fr
Fri Aug 21 08:54:24 BST 2020


Hi Andreas,

Le 21/08/2020 à 07:38, Andreas Tille a écrit :
> 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 BTW, I do not think that we should stick to that now outdated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.

I will have a look at it!
Having this package leave non-free would indeed be great.

Best,
Pierre

> 
> 
> ----- 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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