geWorkbench

geWorkbench 2.3.0

• 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.

• Building from source on Apple Mac - 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 J3D 1.5, or delete the PCA component from the components directory. (#2495)

Any current release

• 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.
• 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.

Previous Releases

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

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.