geWorkbench

Revision as of 18:25, 7 February 2011

Installer - Norton Internet Security "Sonar" 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.

SkyBase component could not retrieve data - RESOLVED - changes in December 2010 to the SkyBase backend database temporarily disabled the ability of geWorkbench to query it. This issue has been resolved with changes to the backend database in January 2011.
Linux installation error - A problem was seen when trying to install geWorkbench on Ubuntu Linux in a desktop configuration using the installer with included JRE. The same installer does work on another Linux variant. We are investigating. You may be able to use the Linux installer with no JRE instead - just make sure you have a current Java JRE installed on your system. See the geWorkbench installation instructions.
t-test - the t-test incorrect reports permutation settings into the Dataset History when the t-distribution is used (no permutations involved). This is just a reporting issue. Fixed in development version.
Color Mosaic - The search by gene name or accession number (probeset id) is not working. Problems are seen both when viewing a t-test result and when viewing the main microarray dataset node. The problem has been fixed in the development version.

Alignment Results (BLAST Results Viewer) - Due to recent changes in the NCBI BLAST website (August, 2010), geWorkbench could not retrieve hit sequences to add them to the project. This affected two buttons: "Add Selected Sequences to Project" and "Only Add Aligned Parts". Fixed in release 2.1.0
Dataset History: the settings used by the following normalizers are not recorded in the Dataset History component: Mean Variance Normalizer, Missing Values Normalizer, Quantile Normalizer, Threshold Normalizer. Fixed in 2.1.0.
CNKB - not all listed interaction databases are open for querying. See the page CNKB Data for a summary of available databases and interaction types. Fixed in 2.1.0.

Grid Services - No geWorkbench grid services are currently available outside of the Columbia firewall. Fixed in release 2.0.1.
genSpace - Logging was not working. Fixed in release 2.0.2.

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

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.

@@ Line 7: / Line 7: @@
 * '''Linux installation error''' - A problem was seen when trying to install geWorkbench on Ubuntu Linux in a desktop configuration using the installer with included JRE.  The same installer does work on another Linux variant.  We are investigating.  You may be able to use the Linux installer with no JRE instead - just make sure you have a current Java JRE installed on your system.  See the geWorkbench installation instructions.
 * '''t-test''' - the t-test incorrect reports permutation settings into the Dataset History when the t-distribution is used (no permutations involved).  This is just a reporting issue.  Fixed in development version.
+* '''Color Mosaic''' - The search by gene name or accession number (probeset id) is not working.  Problems are seen both when viewing a t-test result and when viewing the main microarray dataset node.  The problem has been fixed in the development version.
 ==geWorkbench 2.0.2==