MarvinSpace starup error in MAC

Hi,

I just started to use Marvin software in Mac OS X 10.8.3, but when i open Marvinspace, it reminds me an error has occured during startup. 

previous post indicates probably it could be solved by degarde Jre, but this probaby leads to other probelm of other software.

many thanks,

 

Jia

 

mesage:

 

ERROR: 

Error opening MarvinSpace

 

STACK TRACE:

java.lang.NoSuchMethodError: javax.media.opengl.GLDrawableFactory.initSingleton()V

at javax.media.opengl.GLProfile.initProfilesForDefaultDevices(GLProfile.java:1385)

at javax.media.opengl.GLProfile.access$000(GLProfile.java:74)

at javax.media.opengl.GLProfile$1.run(GLProfile.java:142)

at java.security.AccessController.doPrivileged(Native Method)

at javax.media.opengl.GLProfile.initSingleton(GLProfile.java:131)

at javax.media.opengl.GLProfile.initSingleton(GLProfile.java:160)

at javax.media.opengl.GLProfile.getDefaultDevice(GLProfile.java:1675)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:244)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:214)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:205)

at chemaxon.marvin.space.GraphicScene.<init>(GraphicScene.java:221)

at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:119)

at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:98)

at chemaxon.marvin.space.gui.MSpaceFrameViewer.getMSpaceFrame(MSpaceFrameViewer.java:68)

at chemaxon.marvin.space.gui.MSpaceFrameViewer.getMSpaceViewer(MSpaceFrameViewer.java:59)

at chemaxon.marvin.space.gui.MSpaceViewerBase.get(MSpaceViewerBase.java:117)

at chemaxon.marvin.space.gui.MSpaceFrameViewer.get(MSpaceFrameViewer.java:51)

at chemaxon.marvin.space.gui.MSpaceViewerBase.callback(MSpaceViewerBase.java:100)

at chemaxon.marvin.common.swing.MolPanel.getMSpaceViewer(MolPanel.java:5832)

at chemaxon.marvin.sketch.swing.SketchPanel.openMSpace(SketchPanel.java:3501)

at chemaxon.marvin.sketch.swing.SketchPanel.doOpenMSpace(SketchPanel.java:2797)

at chemaxon.marvin.sketch.swing.actions.OpenMarvinSpaceAction.actionPerformed(OpenMarvinSpaceAction.java:26)

at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)

at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)

at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)

at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)

at javax.swing.AbstractButton.doClick(AbstractButton.java:389)

at com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)

at java.awt.MenuItem.processActionEvent(MenuItem.java:650)

at java.awt.MenuItem.processEvent(MenuItem.java:609)

at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343)

at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331)

at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:713)

at java.awt.EventQueue.access$400(EventQueue.java:82)

at java.awt.EventQueue$2.run(EventQueue.java:669)

at java.awt.EventQueue$2.run(EventQueue.java:667)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)

at java.awt.EventQueue$3.run(EventQueue.java:683)

at java.awt.EventQueue$3.run(EventQueue.java:681)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:680)

at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)

at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

 

Hi,

Which version of MarvinSpace are you trying to use?

There was a similar problem with some earlier versions (5.10, or 5.11, maybe 5.12 I don't remember exactly), but with different OS. Maybe it is the same issue.

It has been fixed a while ago, so the most recent version (6.0) should work OK.

Regards,

Andras

akovacs wrote:

Hi, Which version of MarvinSpace are you trying to use? There was a similar problem with some earlier versions (5.10, or 5.11, maybe 5.12 I don't remember exactly), but with different OS. Maybe it is the same issue. It has been fixed a while ago, so the most recent version (6.0) should work OK. Regards, Andras

Hi Andras,

 

thank you very much for your reply. 

Actually, I'm using the lastest version (6.0.4) in Mac OS X 10.8.3.

 

Best regards,

 

Jia

I tried some of the examples at chemaxon.com/marvin/examples/applets/space/index.html

I was using Safari with JRE 7 1.7.0_25 x64 on OS X 10.8

It worked for me.

Please clear the Java temporary cache files and the browser cache files, and try again.

Maybe, it helps. You may also try different browsers. You can also try running the desktop version of MarvinSpace, and check if it produces the same error.

It is also possible that Aplle broke backward comatibility (again), somewhere between 10.8 and 10.8.3.

If I can access somewhere an OS X 10.8.3 I will test it.

 

Andras

 

akovacs wrote:

I tried some of the examples at chemaxon.com/marvin/examples/applets/space/index.html I was using Safari with JRE 7 1.7.0_25 x64 on OS X 10.8 It worked for me. Please clear the Java temporary cache files and the browser cache files, and try again. Maybe, it helps. You may also try different browsers. You can also try running the desktop version of MarvinSpace, and check if it produces the same error. It is also possible that Aplle broke backward comatibility (again), somewhere between 10.8 and 10.8.3. If I can access somewhere an OS X 10.8.3 I will test it.   Andras

Actually i am using the desktop version. i have emptied the JAVA cache files and browser files, it still doestn't work. when i used web version, ii didn't come out with any interface. i'm using JAVA 1.7.0_25

That's strange...

I upgraded to 10.8.4 (that was the only option for me), and checked the desktop MarvinSpace application and it also works OK for me.

Are you using OS X on a virtual machine?
Do you know the type of the video card/GPU?
Did any of the earlier versions of MarvinSpace were tried/worked on this machine ever?

I don't use it in virtual machine and this is my first time to use this software. the information about graphic in my computer is as follow:

Chipset Model: Intel HD Graphics 4000

  Type: GPU

  Bus: Built-In

  VRAM (Total): 512 MB

  Vendor: Intel (0x8086)

  Device ID: 0x0166

  Revision ID: 0x0009

  Displays:

Color LCD:

  Display Type: LCD

  Resolution: 1280 x 800

  Pixel Depth: 32-Bit Color (ARGB8888)

  Main Display: Yes

  Mirror: Off

  Online: Yes

  Built-In: Yes

Does this softeware relative with JAVA 3D? I moved some java extension from /System/Library/Java/Extensions to other folder due to other software, but then i moved them back.

Hi,

That config seems fine.

As far as I know MarvinSpace/JOGL has nothing to do with Java3D.

Altough, it is not healthy to tinker with the system files.

I found this:

https://www.chemaxon.com/forum/ftopic9381.html

It was about a similar problem, and reinstalling the Java runtime fixed it.

 

thank you foryour suggestion. but unfortunately, it is not working for me. 

i have uninstalled the JAVA, downloaded from Apple JAVa web and then reinstalled it, there is still same error information.

 

regards,

 

Jia

I'm totallly confused now, since i follow one post to degrade Java to 1.6:

java version "1.6.0_51"

Java(TM) SE Runtime Environment (build 1.6.0_51-b11-457-11M4509)

Java HotSpot(TM) 64-Bit Server VM (build 20.51-b01-457, mixed mode)

 

but there is still same problem.

 

regards,

 

Jia

Hi,

Hm, the About MarvinSpace window tells me that I'm using Apple Java 1.6.0_51.

(It has its control panel in System Preferences in the 'Other' section.)

I suggest you should also use that.

Could you please do the following:

- Right click on MarvinSpace icon on the desktop

- Click 'Show Original'

- In the finder window appears go into the bin directory.

- open a Terminal window

- drag the 'mspace' from the finder window to the terminal and add the following to the end of the comand:

 -Djogl.debug.GLJPanel -Djogl.verbose -Djogl.gljpanel.nohw -Djogl.gljpanel.noogl

My command line looks like this:

/Application/ChemAxon/MarvinBeans/bin/mspace -Djogl.debug.GLJPanel -Djogl.verbose -Djogl.gljpanel.nohw -Djogl.gljpanel.noogl

- now run the command and see what happens.

Also, It would be helpful, if you could paste what was written to the terminal

---------------------------------------

for testing purposes you might try adding the line:

grant { permission java.security.AllPermission; };

in the beginning of the file java.policy.

(Mine is located at: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/ )

Regards,

Andras

correction: "It has its control panel in System Preferences in the 'Other' section."

No, that is only for Oracle Java.

I added the permission in that file, but it is still not working.

the massage from terminal is :

uos-12035:~ jh2u11$ /Applications/ChemAxon/MarvinBeans/bin/mspace.bat  -Djogl.debug.GLJPanel -Djogl.verbose -Djogl.gljpanel.nohw -Djogl.gljpanel.noogl

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 1: @ECHO: command not found

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 2: SETLOCAL: command not found

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 4: REM: command not found

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 5: REM: command not found

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 6: REM: command not found

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 9: GOTO: command not found

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 11: :getJavaPath: command not found

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 13: syntax error near unexpected token `('

/Applications/ChemAxon/MarvinBeans/bin/mspace.bat: line 13: `IF EXIST "%configfile%". ('

 

best regrads,

 

Jia

mspace without '.bat'

akovacs wrote:

mspace without '.bat'

sorry. 

but it finally produced similar error information;

uos-12035:~ jh2u11$ /Applications/ChemAxon/MarvinBeans/bin/mspace  -Djogl.debug.GLJPanel -Djogl.verbose -Djogl.gljpanel.nohw -Djogl.gljpanel.noogl

JOGL specification version 1.1.1

JOGL implementation version 1.1.1

JOGL implementation vendor Sun Microsystems, Inc.

Exception in thread "main" java.lang.NoSuchMethodError: javax.media.opengl.GLDrawableFactory.initSingleton()V

at javax.media.opengl.GLProfile.initProfilesForDefaultDevices(GLProfile.java:1385)

at javax.media.opengl.GLProfile.access$000(GLProfile.java:74)

at javax.media.opengl.GLProfile$1.run(GLProfile.java:142)

at java.security.AccessController.doPrivileged(Native Method)

at javax.media.opengl.GLProfile.initSingleton(GLProfile.java:131)

at javax.media.opengl.GLProfile.initSingleton(GLProfile.java:160)

at javax.media.opengl.GLProfile.getDefaultDevice(GLProfile.java:1675)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:244)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:214)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:205)

at chemaxon.marvin.space.GraphicScene.<init>(GraphicScene.java:221)

at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:119)

at chemaxon.marvin.space.gui.MSpace.<init>(MSpace.java:123)

at chemaxon.marvin.space.gui.MSpace.main(MSpace.java:63)

Okay, I think I got the problem:

" JOGL specification version 1.1.1

JOGL implementation version 1.1.1 "

That's a very old jogl library version. It isn't supposed to work on this system anyways.

Are you sure you are using the latest MarvinSpace(/Marvinsketch, etc)?

If yes, please remove all occurences of jogl*, gluegen* jar-s from the system (java runtime classpaths, or anywhere java can load this version of jogl libraries) and if necessary, reinstall Marvin

Regards,

Andras

i downloaded the latested version (6.0.4). 

when i removed all old  JOGL and another one file in my computer, i reinstalled the software again, but the terminal still give me same information. 

 

JOGL specification version 1.1.1

 

when i tried to use 5.12

 

it gave me:

/Applications/ChemAxon/MarvinBeans/bin/mspace  -Djogl.debug.GLJPanel -Djogl.verbose -Djogl.gljpanel.nohw -Djogl.gljpanel.noogl

Exception in thread "main" java.lang.NoSuchMethodError: javax.media.opengl.GLDrawableFactory.initSingleton()V

at javax.media.opengl.GLProfile.initProfilesForDefaultDevices(GLProfile.java:1385)

at javax.media.opengl.GLProfile.access$000(GLProfile.java:74)

at javax.media.opengl.GLProfile$1.run(GLProfile.java:142)

at java.security.AccessController.doPrivileged(Native Method)

at javax.media.opengl.GLProfile.initSingleton(GLProfile.java:131)

at javax.media.opengl.GLProfile.initSingleton(GLProfile.java:160)

at javax.media.opengl.GLProfile.getDefaultDevice(GLProfile.java:1675)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:244)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:214)

at javax.media.opengl.awt.GLJPanel.<init>(GLJPanel.java:205)

at chemaxon.marvin.space.GraphicScene.<init>(GraphicScene.java:220)

at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:119)

at chemaxon.marvin.space.gui.MSpace.<init>(MSpace.java:130)

at chemaxon.marvin.space.gui.MSpace.main(MSpace.java:70)

 

best regards,

 

Jia

Hi,

you can find all the instances of the files in question by invoking the command:

locate jogl

and,

locate gluegen

in a terminal window.

You should get rid of them (except where MarvinBeans was installed.

A.

thank you very much for your help. after removing the relative files in JAVA extension, it works now.

 

many thanks again,

 

Jia