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Gephi forums •Gephi 0.8.2 initilizes but fails to launch in linux...

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Gephi 0.8.2 initilizes but fails to launch in linux...

https://forum-gephi.org/viewtopic.php?f=3&t=3515

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Gephi 0.8.2 initilizes but fails to launch in linux...

Posted: 21 Jul 2014 05:17
by vidyaraj.r@gmail.com
I use Ubuntu 14.04 OS

Attching the dmesg|tail output here:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[ 17.446842] init: plymouth-upstart-bridge main process ended, respawning
[ 30.539938] alx 0000:03:00.0 eth0: NIC Up: 100 Mbps Full
[ 45.004761] type=1400 audit(1405911967.961:68): apparmor="STATUS" operation="profile_replace" profile="unconfined" name="/usr/lib/cups/backend/cups-pdf" pid=2200 comm="apparmor_parser"
[ 45.004773] type=1400 audit(1405911967.961:69): apparmor="STATUS" operation="profile_replace" profile="unconfined" name="/usr/sbin/cupsd" pid=2200 comm="apparmor_parser"
[ 45.005428] type=1400 audit(1405911967.961:70): apparmor="STATUS" operation="profile_replace" profile="unconfined" name="/usr/sbin/cupsd" pid=2200 comm="apparmor_parser"
[ 53.257304] systemd-hostnamed[2262]: Warning: nss-myhostname is not installed. Changing the local hostname might make it unresolveable. Please install nss-myhostname!
[ 1190.487895] type=1400 audit(1405913113.809:71): apparmor="STATUS" operation="profile_replace" profile="unconfined" name="/usr/lib/cups/backend/cups-pdf" pid=3182 comm="apparmor_parser"
[ 1190.487908] type=1400 audit(1405913113.809:72): apparmor="STATUS" operation="profile_replace" profile="unconfined" name="/usr/sbin/cupsd" pid=3182 comm="apparmor_parser"
[ 1190.488586] type=1400 audit(1405913113.809:73): apparmor="STATUS" operation="profile_replace" profile="unconfined" name="/usr/sbin/cupsd" pid=3182 comm="apparmor_parser"
[ 2595.452320] systemd-hostnamed[4242]: Warning: nss-myhostname is not installed. Changing the local hostname might make it unresolveable. Please install nss-myhostname!

Re: Gephi 0.8.2 initilizes but fails to launch in linux...

Posted: 21 Jul 2014 05:25
by vidyaraj.r@gmail.com
Seems not relevant but tried installing: libnss-myhostname ->but does not help!

Re: Gephi 0.8.2 initilizes but fails to launch in linux...

Posted: 07 Oct 2014 14:39
by artintsystem
Ditto!
The logo comes up with the message "Loading cached objects..." for about 7 seconds and then gephi dies, returns control at the console.
Tried https://gist.github.com/dcht00/432caaf3e6c50a2202b8, but to no avail. Then, unistalled this bit.
After that probed a bit more in gephi/0.8.2/dev/var/log to find:

Code: Select all

java.lang.IllegalStateException: java.lang.IllegalAccessException: Class org.openide.util.WeakListenerImpl$ProxyListener can not access a member of class org.openide.filesystems.$Proxy0 with modifiers "public"
        at org.openide.util.WeakListenerImpl$ProxyListener.<init>(WeakListenerImpl.java:423)
        at org.openide.util.WeakListenerImpl.create(WeakListenerImpl.java:164)
        at org.openide.util.WeakListeners.create(WeakListeners.java:271)
        at org.openide.filesystems.MultiFileObject.<init>(MultiFileObject.java:125)
        at org.openide.filesystems.MultiFileObject.<init>(MultiFileObject.java:142)
        at org.openide.filesystems.MultiFileSystem.getMultiRoot(MultiFileSystem.java:267)
        at org.openide.filesystems.MultiFileSystem.findResource(MultiFileSystem.java:355)
        at org.openide.filesystems.FileUtil.getConfigFile(FileUtil.java:2276)
        at org.openide.filesystems.FileUtil.getConfigRoot(FileUtil.java:2306)
        at org.netbeans.core.startup.Main.getModuleSystem(Main.java:158)
        at org.netbeans.core.startup.Main.start(Main.java:305)
        at org.netbeans.core.startup.TopThreadGroup.run(TopThreadGroup.java:123)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalAccessException: Class org.openide.util.WeakListenerImpl$ProxyListener can not access a member of class org.openide.filesystems.$Proxy0 with modifiers "public"
        at sun.reflect.Reflection.ensureMemberAccess(Reflection.java:101)
        at java.lang.reflect.AccessibleObject.slowCheckMemberAccess(AccessibleObject.java:295)
        at java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:287)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:398)
        at org.openide.util.WeakListenerImpl$ProxyListener.<init>(WeakListenerImpl.java:413)
System info etc:

Code: Select all

>Log Session: Tuesday, October 7, 2014 6:59:01 PM IST
>System Info: 
  Product Version         = Gephi 0.8.2 201210100934
  Operating System        = Linux version 3.13.0-36-generic running on amd64
  Java; VM; Vendor        = 1.8.0_20; Java HotSpot(TM) 64-Bit Server VM 25.20-b23; Oracle Corporation
  Runtime                 = Java(TM) SE Runtime Environment 1.8.0_20-b26
  Java Home               = /usr/lib/jvm/java-8-oracle/jre
  System Locale; Encoding = en_US (gephi); UTF-8
  Home Directory          = /home/usrName
  Current Directory       = /home/usrName/sw/gephi
  User Directory          = /home/usrName/.gephi/0.8.2/dev
  Cache Directory         = /home/usrName/.gephi/0.8.2/dev/var/cache
  Installation            = /home/usrName/sw/gephi/gephi
                            /home/usrName/sw/gephi/platform
                            /home/usrName/sw/gephi/platform
Any help would be appreciated. The sooner the better!
Please let me know if I've:
1. Missed installing some dependency; fyi followed the instructions at http://gephi.github.io/users/install/ for linux, to the letter.
2. Having memory issues. Shouldn't be is my guess!

Thanks for your time!
Cheers,
A.

Re: Gephi 0.8.2 initilizes but fails to launch in linux...

Posted: 22 Oct 2014 17:10
by lotterylaunch
I get the exact same behavior on two computers, one with 14.04 and another with 14.10.

Re: Gephi 0.8.2 initilizes but fails to launch in linux...

Posted: 24 Apr 2015 19:12
by chunkyks
I figured this out. Two things:

1) The documentation on setting JDK_HOME is full of lies
2) Gephi doesn't work for me with jdk 8 on Linux

From here: gephi.github.io/users/install/ [apologies I had to de-linkify that URL because the spam blocker on this forum takes umbrage with github.io]
If you still have the wrong Java package running after following the linux installation procedure described above, then manually set the Java virtual machine. To do so, you have to set the home folder of the desired JVM in the environment variable JAVA_HOME or in the environment variable JDK_HOME.
Actually, the script bin/gephi looks for "jdkhome" [all lowercase, no underscore] rather than "JDK_HOME"

So, I extracted an oracle jdk1.7 into a directory someplace and it successfully launches thus:

Code: Select all

jdkhome=/usr/lib/jvm/jdk1.7.0_67/ ./bin/gephi
You can also edit bin/gephi to permanantise this

Cheers,
Gary
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