Public bug reported:
On a system recently upgraded to Bionic, igv fails to launch, producing
the following error:
INFO [2018-10-15 14:48:06,972] [DirectoryManager.java:171] [AWT-EventQueue-0]
IGV Directory: /home/david/igv
INFO [2018-10-15 14:48:06,972] [DirectoryManager.java:171] IGV Directory:
/home/david/igv
INFO [2018-10-15 14:48:06,978] [Main.java:154] [AWT-EventQueue-0] Startup
IGV Version user 01/22/2018 08:52 AM
INFO [2018-10-15 14:48:06,978] [Main.java:155] [AWT-EventQueue-0] Java 10.0.2
INFO [2018-10-15 14:48:06,979] [DirectoryManager.java:76] [AWT-EventQueue-0]
Fetching user directory...
INFO [2018-10-15 14:48:07,022] [Main.java:156] [AWT-EventQueue-0] Default
User Directory: /home/david
INFO [2018-10-15 14:48:07,023] [Main.java:157] [AWT-EventQueue-0] OS: Linux
ERROR [2018-10-15 14:48:07,041] [DefaultExceptionHandler.java:49]
[AWT-EventQueue-0] Unhandled exception
java.lang.NoClassDefFoundError: org/apache/commons/io/output/StringBuilderWriter
at org.broad.igv.util.HttpUtils.isRemoteURL(HttpUtils.java:120)
at
org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:109)
at org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:96)
at
org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:78)
at
org.broad.igv.prefs.PreferencesManager.load(PreferencesManager.java:168)
at
org.broad.igv.prefs.PreferencesManager.loadUserPreferences(PreferencesManager.java:126)
at
org.broad.igv.prefs.PreferencesManager.init(PreferencesManager.java:92)
at
org.broad.igv.prefs.PreferencesManager.getPreferences(PreferencesManager.java:53)
at
org.broad.igv.prefs.PreferencesManager.getPreferences(PreferencesManager.java:109)
at org.broad.igv.ui.Main.updateTooltipSettings(Main.java:175)
at org.broad.igv.ui.Main.initApplication(Main.java:162)
at org.broad.igv.ui.Main.access$000(Main.java:72)
at org.broad.igv.ui.Main$1.run(Main.java:102)
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)
Caused by: java.lang.ClassNotFoundException:
org.apache.commons.io.output.StringBuilderWriter
at
java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
at
java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
... 27 more
INFO [2018-10-15 14:48:08,045] [ShutdownThread.java:47] [Thread-1] Shutting
down
As I understand it, StringBuilderWriter is provided by libcommons-io-
java, which is installed. I have tried deleting the configuration files
written to ~/igv and uninstalling the package and libraries. All to no
avail, so I think this may be a packaging bug?
Some relevant information:
$ java --version
openjdk 10.0.2 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2)
OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2, mixed mode)
$ apt-cache policy igv
igv:
Installed: 2.4.6+dfsg-1
Candidate: 2.4.6+dfsg-1
$ apt-cache policy libcommons-io-java
libcommons-io-java:
Installed: 2.6-2
Candidate: 2.6-2
$ lsb_release -rd
Description: Ubuntu 18.04.1 LTS
Release: 18.04
** Affects: igv (Ubuntu)
Importance: Undecided
Status: New
--
You received this bug notification because you are a member of Ubuntu
Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/1797819
Title:
fails to launch (unable to find libraries)
To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/igv/+bug/1797819/+subscriptions
--
ubuntu-bugs mailing list
[email protected]
https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
