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Author Topic: Can't load data into JExpress 2012  (Read 6046 times)
ebent
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« on: January 19, 2016, 07:44:06 PM »

Hi, I am running JExpress on Windows 8 and have had no problem using it last year after re-installing it, but now I find that when I try to open saved projects or import tabluar data for a new project, nothing happens. For example, I see a menu for choosing a file to open, click on the file I want, the menu vanishes, and nothing happens. For tabular data, I go through the wizard and once I'm done selecting my data, I click "OK" and then the tabluar data input window vanishes and nothing happens.

Is my license expired, or something like that?

Thanks

Liz
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annekristin
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« Reply #1 on: January 20, 2016, 08:59:06 AM »

The date for your license validity should be printed to the License information, which you can find under the "About, help and Windows" tab. I don't think this is the problem though.

Could you please take a look at the log file? You can find the log file on the "About, help and Windows" tab and the "View log". This contains a java stack trace which may tell us what's wrong.

Anne-Kristin
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ebent
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« Reply #2 on: February 02, 2016, 07:06:43 PM »

Here is the entirety of what is in the log file: I tried opening a file and this is what came out (below) - it looks like a configuration issue? -Liz



J-Express version: J-Express 2012 Build 119.  March 12. 2012

System properties
java.runtime.name   - Java(TM) SE Runtime Environment
sun.boot.library.path   - C:\Program Files\Java\jre1.8.0_31\bin
java.vm.version   - 25.31-b07
java.vm.vendor   - Oracle Corporation
java.vendor.url   - http://java.oracle.com/
path.separator   - ;
java.vm.name   - Java HotSpot(TM) 64-Bit Server VM
file.encoding.pkg   - sun.io
user.country   - US
user.script   -
sun.java.launcher   - SUN_STANDARD
sun.os.patch.level   -
java.vm.specification.name   - Java Virtual Machine Specification
user.dir   - C:\Users\Liz\Documents\J-express
java.runtime.version   - 1.8.0_31-b13
java.awt.graphicsenv   - sun.awt.Win32GraphicsEnvironment
java.endorsed.dirs   - C:\Program Files\Java\jre1.8.0_31\lib\endorsed
os.arch   - amd64
java.io.tmpdir   - C:\Users\Liz\AppData\Local\Temp\
line.separator   -

java.vm.specification.vendor   - Oracle Corporation
user.variant   -
os.name   - Windows 8.1
sun.jnu.encoding   - Cp1252
java.library.path   - C:\Program Files\Java\jre1.8.0_31\bin;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x86;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x64;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\PROGRA~2\TABLEC~1.01;C:\Program Files (x86)\Common Files\Adobe\AGL;C:\Program Files\Calibre2\;C:\Program Files\SASHome\Secure;C:\Program Files\SASHome\x86\Secure;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\SASHome\Secure\ccme4;C:\Program Files\SASHome\x86\Secure\ccme4;C:\Program Files\NCBI\blast-2.2.29+\bin;.
sun.awt.enableExtraMouseButtons   - true
java.specification.name   - Java Platform API Specification
java.class.version   - 52.0
sun.management.compiler   - HotSpot 64-Bit Tiered Compilers
os.version   - 6.3
user.home   - C:\Users\Liz
user.timezone   - America/New_York
java.awt.printerjob   - sun.awt.windows.WPrinterJob
file.encoding   - Cp1252
java.specification.version   - 1.8
java.class.path   - C:\Users\Liz\Documents\J-express\;C:\Users\Liz\Documents\J-express\lib\edtftpj.jar;C:\Users\Liz\Documents\J-express\lib\freehep-export-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphics2d-2.1.1.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphics2d-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-emf-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-pdf-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-ps-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-svg-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-swf-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-io-2.0.3.jar;C:\Users\Liz\Documents\J-express\lib\freehep-swing-2.0.3.jar;C:\Users\Liz\Documents\J-express\lib\freehep-swing-2.0.4-SNAPSHOT.jar;C:\Users\Liz\Documents\J-express\lib\freehep-util-2.0.3.jar;C:\Users\Liz\Documents\J-express\lib\freehep-xml-2.1.1.jar;C:\Users\Liz\Documents\J-express\lib\freehep-xml-2.1.3-SNAPSHOT.jar;C:\Users\Liz\Documents\J-express\lib\Help.jar;C:\Users\Liz\Documents\J-express\lib\iText.jar;C:\Users\Liz\Documents\J-express\lib\jai_codec.jar;C:\Users\Liz\Documents\J-express\lib\jai_core.jar;C:\Users\Liz\Documents\J-express\lib\jas-plotter-2.2.jar;C:\Users\Liz\Documents\J-express\lib\jcalendar-1.3.2.jar;C:\Users\Liz\Documents\J-express\lib\jcommon-1.0.16.jar;C:\Users\Liz\Documents\J-express\lib\jdom-1.0.jar;C:\Users\Liz\Documents\J-express\lib\jdom.jar;C:\Users\Liz\Documents\J-express\lib\jexpress.jar;C:\Users\Liz\Documents\J-express\lib\jexpressServer.jar;C:\Users\Liz\Documents\J-express\lib\jfreechart-1.0.13.jar;C:\Users\Liz\Documents\J-express\lib\jh.jar;C:\Users\Liz\Documents\J-express\lib\jmathplot.jar;C:\Users\Liz\Documents\J-express\lib\js.jar;C:\Users\Liz\Documents\J-express\lib\jsci-core.jar;C:\Users\Liz\Documents\J-express\lib\jsci.jar;C:\Users\Liz\Documents\J-express\lib\junit.jar;C:\Users\Liz\Documents\J-express\lib\jylib.jar;C:\Users\Liz\Documents\J-express\lib\jython.jar;C:\Users\Liz\Documents\J-express\lib\MAGEHandler.jar;C:\Users\Liz\Documents\J-express\lib\MAGEMLimport.jar;C:\Users\Liz\Documents\J-express\lib\MAGEstk-2004-06-29-v1.1-compatible.jar;C:\Users\Liz\Documents\J-express\lib\mlibwrapper_jai.jar;C:\Users\Liz\Documents\J-express\lib\openide-lookup-1.9-patched-1.0.jar;C:\Users\Liz\Documents\J-express\lib\servlet.jar;C:\Users\Liz\Documents\J-express\lib\swing-layout.jar;C:\Users\Liz\Documents\J-express\;plugins\stat.jar
user.name   - Liz
java.vm.specification.version   - 1.8
sun.java.command   - jexpress.jexpress
java.home   - C:\Program Files\Java\jre1.8.0_31
sun.arch.data.model   - 64
user.language   - en
java.specification.vendor   - Oracle Corporation
awt.toolkit   - sun.awt.windows.WToolkit
java.vm.info   - mixed mode
java.version   - 1.8.0_31
java.ext.dirs   - C:\Program Files\Java\jre1.8.0_31\lib\ext;C:\WINDOWS\Sun\Java\lib\ext
sun.boot.class.path   - C:\Program Files\Java\jre1.8.0_31\lib\resources.jar;C:\Program Files\Java\jre1.8.0_31\lib\rt.jar;C:\Program Files\Java\jre1.8.0_31\lib\sunrsasign.jar;C:\Program Files\Java\jre1.8.0_31\lib\jsse.jar;C:\Program Files\Java\jre1.8.0_31\lib\jce.jar;C:\Program Files\Java\jre1.8.0_31\lib\charsets.jar;C:\Program Files\Java\jre1.8.0_31\lib\jfr.jar;C:\Program Files\Java\jre1.8.0_31\classes
java.vendor   - Oracle Corporation
file.separator   - \
java.vendor.url.bug   - http://bugreport.sun.com/bugreport/
sun.io.unicode.encoding   - UnicodeLittle
sun.cpu.endian   - little
sun.desktop   - windows
sun.cpu.isalist   - amd64

File SystemJ-Express file system -- File locations
Settings file does not exist..
Used Paths:
User path: C:\Users\Liz\Documents\J-express
User data path: C:\Users\Liz\Documents\J-express\data
Annotation path: C:\Users\Liz\Documents\J-express\resources\Annotation
Sequence path: C:\Users\Liz\Documents\J-express\resources\SEQUENCE
GO path: C:\Users\Liz\Documents\J-express\resources\GO
PLUGIN path: C:\Users\Liz\Documents\J-express\resources\PLUGINS
Libraries path: C:\Users\Liz\Documents\J-express\lib
Pathways path: C:\Users\Liz\Documents\J-express\resources\PW
Settings file: C:\Users\Liz\Documents\J-express\jexpress.cfg
Spotpix path: C:\Users\Liz\Documents\J-express\resources\EXPERIMENTS
VM memory use min (MB): 256
VM memory use max (MB): 512
File system out done
Looking for license file in C:\Users\Liz\Documents\J-express
Looking for settings at C:\Users\Liz\Documents\J-express\jexpress.cfg
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
   at jexpress.cluster.addRecentFile(cluster.java:1222)
   at expresscomponents.filehandler.loadProjectNEW(filehandler.java:1096)
   at jexpress.cluster.actionPerformed(cluster.java:2673)
   at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
   at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$500(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)

No infosNew Project
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ebent
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« Reply #3 on: February 24, 2016, 09:38:52 PM »

Hi- I've realized that I don't have an exec.properties file- I downloaded the one Kjell linked to and made the alteration to the file (directory path) to the install directory, and now the program doesn't open at all. If I remove the exec.properties file (by renaming it), J-Express opens but does not load data.

I've tried reinstalling J-Express by manually removing folders and re-installing, and it doesn't seem to have helped.

Liz

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ebent
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« Reply #4 on: February 24, 2016, 10:14:09 PM »

I seem to have solved it by following the advice of someone else on this forum: I uninstalled Java, deleted all files associated with J-Express, then reinstalled Java and then reinstalled J-Express. I didn't even need to add in the exec.properties file- it seems to have installed just fine. Whew!

Update: And then I turned my computer off and on again, and the program no longer will open. I tried putting in and altering the exec.properties file and am back to the problem I had before- when the file is preasent, the program doesn't open, no matter what memory settings I put in (and yes, I also altered the file paths to be correct). When the file is removed, the program opens but won't load data.

 Huh
« Last Edit: February 25, 2016, 05:35:59 PM by ebent » Logged
aye163
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« Reply #5 on: April 22, 2016, 06:50:37 PM »

Hello
Colleagues,

I seem to have a very similar problem of running JExpress on Ubuntu Linux. Once launched the software freezes on the step of project loading or it is loaded and the first working steps are executed. This may not be java version dependent, since it started since about 2 weeks ago after running fine for many years. The problem is replicated on various machines with the different Ubuntu version and java versions installed. I used to run the software on Java 7 before.

Thank you for you help,

Alex.
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aye163
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« Reply #6 on: May 07, 2016, 10:35:39 PM »

Here is the solution that works for those who run JExpress under Linux, but may also work on Windows and Mac. The following editing should be done:

comment out the line "assistive_technologies=org.GNOME.Accessibility.AtkWrapper" in /etc/java-7-openjdk/accessibility.properties.

or "assistive_technologies=org.GNOME.Accessibility.AtkWrapper" in /etc/java-8-openjdk/accessibility.properties.

After this no crushing is observed.

I hope this helps to solve problem for others.

Sincerely,

Alex.
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