geWorkbench

geWorkbench 2.3.0

• Java 7 - geWorkbench 2.3.0 was developed and tested using the Java 6 JDK and JRE. Subsequent testing with Java 7 has shown a number of problems, shown below. For this reason, please only use Java 6 JREs when running geWorkbench 2.3.0 or earlier.
  • CNKB - (#3008) activated markers not transfered from Markers component.
  • Color Mosaic - (#3011) activated array set causes color mosaic display to turn red.
  • Expression profiles - (#2980) activated array set causes expression profile not to be drawn.

• IDEA - (#3001) Some edges appear twice in the results list, differing only in node order: N1-N2 and N2-N1.

• BLAST - (#2825) the maximum number of hits returned is 50, even if more were requested.
• caArray - (#2893) due to a synchronization problem, a large empty white space may occasionally appear in the caArray list of experiments.
• Cytoscape
  • (#2843) if an instance of Cytoscape is running on a machine, and then Cytoscape is also loaded in geWorkbench, you may see a warning "org.cytoscape.coreplugin.cpath2.http.HTTPServer[WARN]: HTTPServer couldn't create socket.".
  • (#2716) Direct LinkOuts from the right-click menu to UniProt may not work. However, they do work when selected from the Cytoscape Data Panel.
• GenePattern connectivity (#2701) - if you successfully connect to a GenePattern server, and later that server is no longer available, you will experience a time-out delay. This was seen when first connecting to a GP server through a firewall via VPN, then trying again without the VPN.
• Grid Services/Dispatcher Service:

As of release 2.3.0, outbound data (from geWorkbench to the grid service) is moved using caTransfer, both from geWorkbench to the Dispatcher, and from the Dispatcher to the grid service. Returning data is transferred for both hops as a base-64 encoded string, which for very large data sets can lead to an out-of-memory error. Full replacement with caTransfer is being investigated.

The error message will read:

Out-of-memory error: Java heap space
It is advisable to restart geWorkbench.
You may also wish to increase the geWorkbench memory size. 

In this case, as the message states, it is advisable to restart geWorkbench. Instructions for increasing the amount of memory available to Java are available in the geWorkbench FAQ. For Java memory requests larger than about 1.5 GB, running geWorkbench using a 64-bit Java Runtime Environment (JRE) will be necessary.

• MINDy - (#2698) if the MINDy Heatmap window is resized, and then scrolled down/up, the heatmap does not redraw correctly. A redraw can be forced by switching between two different modulators. In earlier versions, a "Refresh" button was available to force the redraw.

• Duplicate Markers - microarray datasets should not contain duplicate marker names. If they do, duplicates will be silently removed. In a subsequent release, a warning will be issued.

Any current release

Mac-related issues

Building from source on Apple Mac OS X (tested in Lion 10.7)

There is an issue with the Java 3D library included with Mac OS X. In order to build geWorkbench from source, one must either install certain files from J3D 1.5, or delete the PCA component from the geWorkbench components directory (#2495).

• To configure J3D on the Mac, please see the instructions below.
• To just remove the PCA component, find the geWorkbench installation directory and follow this path: components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule. In the gpmodule directory, delete the folder "pca".

Mouse-button issues (tested in Lion 10.7)

• Right-click contextual menu: On the Mac, control-click can substitute for the PC's "right-click" action, and bring up a contextual menu. However, this is not implemented in geWorkbench on the Mac. The following work-arounds are available:
  • Trackpad: In System Preferences, enable "Secondary click". You can choose 3 options on how this will work, including clicking in the lower-right-hand corner of the trackpad.
  • Magic Mouse: In System Preferences, enable "Secondary click".
• List multi-select: List multi-select does not work in geWorkbench 2.3.0 and earlier on the Mac. However, in geWorkbench 2.4.0 development version, list multi-select can be accomplished with command-click.

PowerPC-based Macintosh computers

Java 6 is not available for the PowerPC platform, regardless of the version of OS X. For this reason, recent versions of geWorkbench which require Java 6 will not run on PowerPC Macintosh computers.

Installer Issues

• We observed on a Windows 7 platform, that if geWorkbench 2.3.0, including the JRE6, is installed directly from a USB memory stick, that (1), the installer is detected as a cell-phone, and (2) some aspect of the install silently fails, and the JRE will not start. The machine was running the current version of Norton Internet Security. Copying the installer to the hard disk and installing from there solved the problem.
• Versions of Norton Internet Security "Sonar" prior to NIS2011 may detect and delete a file generated during the installation process, "Install.exe". This will silently terminate the install. If this occurs, disable the Sonar feature during installation, or disable your antivirus protection during the installation.

Previous Releases

For issues with previous releases, please see the Previous Release Issues page.

Configuring J3D on the Mac for gpmodule PCA

The Java3D version included in geworkbench is 1.5. On the Mac platform, an earlier version (1.3) is installed in /System/Library/Java/Extensions/. Unless this is fixed on the user's Mac,

1. geWorkbench cannot be built from source, as a compile error is generated, and
2. PCA 3D plots cannot be used on the Mac when the Installer version is used.

These problems arise because the j3d libraries in the system java extension directory have higher priority than those in geworkbench.

By copying the appropriate j3d and jogl files into a directory with higher precedence, these problems can be avoided. The following steps have been tested under Mac OS X 10.7 (Lion) but should work for earlier version also.

The safest method is to place the updated files within the user's own directory structure. These changes will then apply only to that user and can be easily undone if needed.

• If the directory ~/Library/Java/Extensions does not exist, create it, where "~" refers to the User's home directory.
  • Note - in OS X 10.7 Lion, the ~/Library folder may be hidden by default. You can make it visible in the Finder by holding down the "option" key while selecting "Go" in the Finder menu.
  • Alternatively, to make the ~/Library folder always visible, execute the following command in a terminal window:

 chflags nohidden ~/Library/
 You can undo this with
 chflags hidden ~/Library

• Copy the following java3d 1.5 libs from the geworkbench installation to the above java extensions directory:
  • geworkbench/lib/j3dcore.jar
  • geworkbench/lib/j3dutils.jar
  • geworkbench/lib/vecmath.jar

• Next, download jogl libs from http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1/jogl-1.1.1-macosx-universal.zip, extract and copy the following files from the extracted lib directory to the extensions directory ~/Library/Java/Extensions:
  • gluegen-rt.jar,
  • jogl.jar,
  • libgluegen-rt.jnilib,
  • libjogl.jnilib,
  • libjogl_awt.jnilib,
  • libjogl_cg.jnilib

If you have system admin privileges on the machine, you can instead update the files for all users in /Library/Java/Extensions, however we do not recommend this.

General

• Filtering a data set may after an analysis has already been run may invalidate objects that arose from the original, unfiltered dataset. Any filtering should be done before any analysis which creates child result nodes, e.g. a t-test, ANOVA etc.

• Promoter panel (issue #1988) - under very particular conditions, where a letter has a score and height of zero, and where an external display is being used on a Macintosh computer, a graphics error can be reported to the console. However, this error does not cause any problems.