geWorkbench

Any current release

• Installer - 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.

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)

geWorkbench 2.2.2

• (#2830) - a parsing problem in tblastx results due to changes in the HTML returned by NCBI is fixed in 2.3.0. The number from column "N" was appearing after the score in the e-value column.
• (#2729) - all versions prior to release 2.3.0 were limited in the number of arrays that could be downloaded in caArray, usually less than 100, due to a problem with memory management. With release 2.3.0, there are now no issues with downloading large numbers of arrays. Downloads of more than 500 arrays have been tested without problem in release 2.3.0.
• (#2925) - In 2.2.2 and previous versions, if two experiments had the same name in caArray, data from only one could be downloaded. Fixed in 2.3.0.

geWorkbench 2.2.1

• Gene Ontology Analysis - if a workspace containing a microarray dataset and its annotation information is saved and then restored, the gene ontology analysis will not work properly and should not be used.
• Gene Ontology Viewer - In some cases when browsing the GO tree, when you select a particular term and view its associated genes, the list contains the "no gene name" entry (---). If this list is in turn copied to a marker set, the "---" will cause all matching markers, that is, those with no gene names, to be included in the new set.
  • Workaround - use the "Multiple Entrez ID filter" to remove all markers that have no gene name associated with them.
• Installation - Windows 7 and Vista users are advised during installation to install to the "C:\geworkbench_2.2.1" directory. However, only users with administrator privileges can install to the c:\ root directory. Instead, users with regular user permissions should install to their own home directory, C:\Users\username\geworkbench_2.2.1, where username is your own login name.

Previous Releases

For issues with previous releases, please see the page 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.