[Debian-med-packaging] Bug#895765: IGV

Andreas Tille andreas at an3as.eu
Wed Oct 17 13:57:42 BST 2018


On Wed, Oct 17, 2018 at 02:09:10PM +0200, Olivier Sallou wrote:
> >> in progress (not uploaded) igv packaging *should* be ok, but needs testing
> > That's a problem for Bio-Linux 9 / Ubuntu 18.04 LTS, because the default
> > is now Java 10 and the only other Java in the standard repo's is Java 8.
> 
> well, in my package env for new igv, I use Java 10, so will nto be a pb

I can confirm that the package now builds also on my side

Unfortunately if I start the package I get the following output:

$ 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].
2018-10-17 14:37:58 INFO  DirectoryManager:179 - IGV Directory: /home/andreas/igv
2018-10-17 14:37:59 INFO  Main:155 - Startup  IGV Version user not_set
2018-10-17 14:37:59 INFO  Main:156 - Java 10.0.2
2018-10-17 14:37:59 INFO  DirectoryManager:84 - Fetching user directory...
2018-10-17 14:37:59 INFO  Main:157 - Default User Directory: /home/andreas
2018-10-17 14:38:00 INFO  Main:158 - OS: Linux


2018-10-17 14:38:00 INFO  Main:208 - Unknown version: user
2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
java.lang.VerifyError: class org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
        at java.base/java.lang.ClassLoader.defineClass1(Native Method)
        at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1009)
        at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
        at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:801)
        at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:699)
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:622)
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:580)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
        at org.broad.igv.ui.Main.open(Main.java:282)
        at org.broad.igv.ui.Main$1.run(Main.java:109)
        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.access$600(EventQueue.java:97)
        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:87)
        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)
2018-10-17 14:38:01 INFO  ShutdownThread:46 - Shutting down


I'm running an up to date testing system.  Here is what reportbug
generates:

-- System Information:
Debian Release: buster/sid
  APT prefers testing
  APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'), (5, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.18.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8), LANGUAGE=de_DE.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

-- no debconf information


Ups, that's a bit less.  Hmmmm. no idea why that's only so few
information.  Here is a bit more:

$ java --version
openjdk 10.0.2 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Debian-1)
OpenJDK 64-Bit Server VM (build 10.0.2+13-Debian-1, mixed mode)

junit4 - 4.12-7
libbatik-java - 1.10-1
libbcprov-java - 1.60-1
libcofoja-java - 1.3-3
libcommons-io-java - 2.6-2
libcommons-logging-java - 1.2-2
libcommons-math-java - 2.2-7
libcommons-net-java - 3.6-1
libconcurrent-java - 1.3.4-4
libgoogle-gson-java - 2.8.2-1
libguava-java - 19.0-1
libhtsjdk-java - 2.16.1+dfsg-1
libhttpclient-java - 4.5.6-1
libhttpcore-java - 4.4.10-1
libjama-java - 1.0.3-1
libjargs-java - 1.0.0-4
libjaxp1.3-java - 1.3.05-5
libjcommon-java - 1.0.23-1
libjfreechart-java - 1.0.19-2
libjgrapht0.8-java - 0.8.3-5
libjhdf5-java - 2.11.0+dfsg-2+b1
libjide-oss-java - 3.7.4+dfsg-1
libjlibeps-java - 0.1.ds3-2
liblog4j1.2-java - 1.2.17-8
libswing-layout-java - 1.0.4-4
libxml-commons-external-java - 1.4.01-3


Any idea what might go wrong here?

Kind regards

     Andreas.

--
http://fam-tille.de



More information about the Debian-med-packaging mailing list