IGV crashes after Linux update

[Robert S]

Dear developers,

after Ubuntu advised me to upgrade to version 18.04

Distributor ID:    Ubuntu
Description:    Ubuntu 18.04 LTS
Release:    18.04
Codename:    bionic

I cannot open IGV more. After starting IGV version 2.4.9 see log file

INFO [2018-05-07 13:26:45,701] [Main.java:154]  Startup  IGV Version 2.4.9 03/05/2018 01:38 PM
INFO [2018-05-07 13:26:45,702] [Main.java:155]  Java 1.8.0_112
INFO [2018-05-07 13:26:45,703] [DirectoryManager.java:76]  Fetching user directory...
INFO [2018-05-07 13:26:45,740] [Main.java:156]  Default User Directory: /home/slany
INFO [2018-05-07 13:26:45,740] [Main.java:157]  OS: Linux

the program crashes with following error:

WARN [2018-05-07 13:32:37,324]  [Globals.java:138] [AWT-EventQueue-0]  Development mode is enabled
INFO [2018-05-07 13:32:37,386]  [DirectoryManager.java:171] [AWT-EventQueue-0]  IGV Directory: /home/slany/igv
INFO [2018-05-07 13:32:37,386] [DirectoryManager.java:171]  IGV Directory: /home/slany/igv
INFO [2018-05-07 13:32:37,391]  [Main.java:154] [AWT-EventQueue-0]  Startup  IGV Version 2.4.9 03/05/2018 01:38 PM
INFO [2018-05-07 13:32:37,391]  [Main.java:155] [AWT-EventQueue-0]  Java 1.8.0_112
INFO [2018-05-07 13:32:37,392]  [DirectoryManager.java:76] [AWT-EventQueue-0]  Fetching user directory...
INFO [2018-05-07 13:32:37,424]  [Main.java:156] [AWT-EventQueue-0]  Default User Directory: /home/slany
INFO [2018-05-07 13:32:37,424]  [Main.java:157] [AWT-EventQueue-0]  OS: Linux


**
GLib-GObject:ERROR:gtype.c:4356:g_type_init: assertion failed: (static_quark_type_flags)

Other java programs like GSEA (version 3_0) still work. From the net I could get that this may be a java-related problem.

Any suggestions would be warmely welcome.

Thanks

Robert

[Robert S]

Additional info for above error:

After updating all underlying programs through conda (reinstalling igv) the error log looks as follows:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0000000000000000, pid=19703, tid=0x00007fe8552a0700
#
# JRE version: OpenJDK Runtime Environment (8.0_121-b15) (build 1.8.0_121-b15)
# Java VM: OpenJDK 64-Bit Server VM (25.121-b15 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  0x0000000000000000
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/slany/hs_err_pid19703.log
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.

[Robert S]

Another bit of forensics:

I can run 'igvtools gui" without problems. It opens the window as a standalone just as if called from the main igv program...
only igv itself throws an exception, see also below...

[David Eby]

Hi Robert,

You are probably correct that it's a Java error.  I run IGV 2.4.x (various versions) on Linux Mint (Ubuntu 16.04 variant) on a regular basis with no problem.  Also, I think in general the IGV developers stick with Oracle Java instead of OpenJDK but that shouldn't make a difference (though I guess it's possible).  

One thing to note is your version of OpenJDK 8 is fairly old.  Not exactly ancient but the current is 8u172.  I just gave it a quick try with OpenJDK (8u162) and it started up fine.  Try updating OpenJDK or installing Oracle Java.  Make sure to stick with Java 8 for now; Java 9 & 10 are not yet supported (we're working on it).

FWIW, we don't officially create any Conda releases so we can only support those up to a point.  The only official builds are the ones on the website, so if these errors continue you might want to try those instead.

Regards,

David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

[Robert S]

Hi Eby,

thank you very much for your suggestions with the Java version. That was exactly the point and I found a workaround.
I'll post it here in case somebody else runs into the same problem.

1. Install original java 8 as described in https://thishosting.rocks/install-java-ubuntu/

- sudo apt-get install software-properties-common
- sudo add-apt-repository ppa:webupd8team/java
- sudo apt-get update
- sudo apt-get install oracle-java8-installer

2. check what versions of java are installed and where they are

- update-alternatives --config java

There are 3 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-11-openjdk-amd64/bin/java      1101      auto mode
  1            /usr/lib/jvm/java-11-openjdk-amd64/bin/java      1101      manual mode
  2            /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java   1081      manual mode
* 3            /usr/lib/jvm/java-8-oracle/jre/bin/java          1081      manual mode

3. Don't bother to set one as default as - at least in my case - it wouldn't change anything and I am not such a Ubuntu buff to search out all environmental variables that have to be changed for the new default choice to take effect.

Start IGV directly with the appropriate java by entering in a terminal the correct path. In this case:

- /usr/lib/jvm/java-8-oracle/jre/bin/java  -jar '/home/anaconda3/bin/igv.jar'
  (path where oracle java sits as above)    (path to the igv.jar file, in this case installed by 'conda' and therefore in the anaconda3 folder) 

This did the job. Actually igv runs also with the java-8-openjdk-amd64 version. I've no idea why the simple command 'java" brings up a different older version and where that may be located. See below:

java -version

openjdk version "1.8.0_121"
OpenJDK Runtime Environment (Zulu 8.20.0.5-linux64) (build 1.8.0_121-b15)
OpenJDK 64-Bit Server VM (Zulu 8.20.0.5-linux64) (build 25.121-b15, mixed mode)

But:

echo $JAVA_HOME
/usr/lib/jvm/java-8-oracle

and:

/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java -version
openjdk version "1.8.0_162"
OpenJDK Runtime Environment (build 1.8.0_162-8u162-b12-1-b12)
OpenJDK 64-Bit Server VM (build 25.162-b12, mixed mode)


so if only the build _162 is installed, how can 'java' point to build_121 ??? (mysteries of Ubuntu)

Anyway, I can go on analyzing my data with IGV, hurray!

Best wishes
Robert

[Qi Yu]

Similar problem, and very helpful. Thanks!

Qi Yu

在 2018年5月8日星期二 UTC-4上午8:06:30，Robert S写道：

[decoste...@gmail.com]

Same issue - solution worked for me. Thanks!