Cannot start IGV

[David Condon]

Hello,

I am running version IGV_2.3.88, and I see the following message when IGV starts:

INFO [2016-11-18 06:45:56,765]  [DirectoryManager.java:169] [main]  IGV Directory: /home/con/igv
INFO [2016-11-18 06:45:56,765] [DirectoryManager.java:169]  IGV Directory: /home/con/igv
INFO [2016-11-18 06:45:56,772]  [Main.java:134] [main]  Startup  IGV Version 2.3.88 (140)11/07/2016 05:47 AM
INFO [2016-11-18 06:45:56,773]  [Main.java:135] [main]  Java 9-internal
INFO [2016-11-18 06:45:56,774]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-11-18 06:45:56,912]  [Main.java:136] [main]  Default User Directory: /home/con
INFO [2016-11-18 06:45:56,912]  [Main.java:137] [main]  OS: Linux
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007ff4f9c9e009, pid=3862, tid=3866
#
# JRE version: OpenJDK Runtime Environment (9.0) (build 9-internal+0-2016-04-14-195246.buildd.src)
# Java VM: OpenJDK 64-Bit Server VM (9-internal+0-2016-04-14-195246.buildd.src, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# C  [libjava.so+0x1d009]  JNU_GetEnv+0x19
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport %p %s %c %P" (or dumping to /home/con/core.3862)
#
# An error report file with more information is saved as:
# /home/con/hs_err_pid3862.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted (core dumped)

I've attached the log file.

why is IGV failing to start? How can I fix this?

[James Robinson]

Hi,

That error is in the Java virtual machine,  outside of IGV code,  there is not much we can do about it.  If possible I suggest you install Oracle java and try that.    Also,  you might submit a bug report as suggested in the error printout.

Doing a web search on   "[libjava.so+0x1d009] JNU_GetEnv+0x19" brings up lots of hits on this bug.

Jim

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