[Debian-med-packaging] Bug#895765: IGV
Olivier Sallou
olivier.sallou at irisa.fr
Thu Oct 18 10:13:31 BST 2018
On 10/17/2018 02:57 PM, Andreas Tille wrote:
> 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
could be an htsjdk version issue versus what expects igv.....
or getting 2 different definitions of
htsjdk.samtools.seekablestream.SeekableStream in classpath
> 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
>
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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