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