FigTree 1.4.2 crash when trying to open a file

[GoogleCodeExporter]

What steps will reproduce the problem?
1. When I try to open a tree file the program close


What is the expected output? What do you see instead?

See the tree, but the program close


What version of the product are you using? On what operating system?

FigTree v1.4.2 under Ubuntu 14.04


Please provide any additional information below.

Error in terminal:

The program 'java' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadMatch (invalid parameter attributes)'.
  (Details: serial 2358 error_code 8 request_code 42 minor_code 0)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)

Original issue reported on code.google.com by [email protected] on 5 Oct 2014 at 2:21

[GoogleCodeExporter]

I'm facing the same problem. Did you fix it?

Original comment by [email protected] on 10 Jan 2015 at 4:16

[lczech]

I am also facing this issue. It does not only happen when opening files, but also when saving. It's not always reproducible, more like with a 1/3 probability.

[lczech]

Not sure if this is the reason for the crash, but I just got

java: ../../src/XlibInt.c:245: _XPrivSyncFunction: Assertion `dpy->synchandler == _XPrivSyncFunction' failed.

before a crash. Might help debugging.

[gaballench]

Same issue on a Linux 4.2.0-41-generic #48-Ubuntu SMP x86_64 x86_64 x86_64 GNU/Linux but with freezing instead of crashing while opening either with the graphical interface or Ctrl+o.

Java version is:

openjdk version "1.8.0_91" OpenJDK Runtime Environment (build 1.8.0_91-8u91-b14-0ubuntu4~15.10.1-b14) OpenJDK 64-Bit Server VM (build 25.91-b14, mixed mode)

Tried to debug with:

cd FigTree_v1.4.2/lib java -agentlib:jdwp=transport=dt_socket,address=8000,server=y,suspend=y -jar figtree.jar jdb -connect com.sun.jdi.SocketAttach:port=8000

Afterwards it freezes again with the following message in terminal:

** (java:1508): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-VUtkmrA9jm: Connection refused

Hope this helps. This issue appears under ubuntu but not under arch linux, where I installed Figtree last week and ran without problem.

[rambaut]

Is there a different Java VM version on the two machines?

Andrew

On 14 Jul 2016, at 23:25, Gustavo A. Ballen [email protected] wrote:

Same issue on a Linux 4.2.0-41-generic #48 https://github.com/rambaut/figtree/issues/48-Ubuntu SMP x86_64 x86_64 x86_64 GNU/Linux but with freezing instead of crashing while opening either with the graphical interface or Ctrl+o. Tried to debug with:

cd FigTree_v1.4.2/lib

java -agentlib:jdwp=transport=dt_socket,address=8000,server=y,suspend=y -jar figtree.jar

jdb -connect com.sun.jdi.SocketAttach:port=8000

Figtree then starts after using the command 'run' on jdb; then it allows the file without problem. Afterwards it does not require debugging in order to open files. Can not reproduce after this point.

This issue appears under ubuntu but not under arch linux, where I installed Figtree last week and ran without problem.

Hope this helps.

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[gaballench]

@rambaut they are actually different. On arch:

java version "1.7.0_101" OpenJDK Runtime Environment (IcedTea 2.6.6) (Arch Linux build 7.u101_2.6.6-1-x86_64) OpenJDK 64-Bit Server VM (build 24.95-b01, mixed mode)

Would this be causing the weird behavior? After trying several times on ubuntu it crashed around 1/3 of the times. Figtree is working perfectly on arch.

UPDATE: I installed oracle java7 in the ubuntu machine and set it to defaul. Afterwards no freezing occurs when opening Figtree. Maybe some commentary on java for linux might help to resolve this issue for linux users.

Thanks in advance,

Gustavo