This page includes the known issues for GenePattern running in different browsers, GenePattern running on local servers, and GenePattern module-related issues as of Nov 24, 2014 in GenePattern version 3.9.0.
Chrome and Java 7 do not work together on the Mac OS and therefore cannot run visualizers and cannot upload large files (>2 GB) to the Uploads tab (check with javatester). Workaround: Don't use Chrome if you have Java 7 on your Mac, or download Chrome 39, which is 64 bit and is supported by Java 7.
In Internet Explorer, the Job Status page does not automatically refresh. Workaround: Refresh the page manually.
In Internet Explorer 10 (IE10) the upload button on the job submit page does not work. This is due to a bug in IE10 which Microsoft is aware of. Workaround: update to IE11 (note that IE10 is no longer supported for GenePattern)
Local GenePattern Servers
Running a Local GenePattern Server on Mac OS
For many of our users on OS X Mavericks (10.9) and Yosemite (10.10) the installer will not be allowed to run, due to Mavericks' security features. We are aware of this issue and are looking to resolve it as soon as we can. In the mean time, please read our blog for information on how best to install GenePattern on Marvericks or Yosemite. Note that this does not have an impact on connecting to a remote server from Mavericks or Yosemite. That experience should remain as it is on any other platform. Please see our blog for more information.
There is a known issue with installing on OS X Lion (10.7) or on OS X Mountain Lion (10.8). If you get an "Installation: Successfulnull" error or an error that looks like this:
1. Move Folder: Destination: /Library/Frameworks/R.framework/Versions
WARNING - There was a problem copying /Library/Frameworks/R.framework/Versions/2.5
you may need to install R2.5 separately. Download R2.5 from CRAN and follow the instruction in this section of the Administrators Guide.
There are known issues with installing on OS X Mountain Lion (10.8):
if you select the option to install icons in the dock during install, the icons will not appear in the dock. They will appear when the server is running. Workaround: You can place them in the dock manually.
Running a Local GenePattern Server on Windows
On Windows 7: The StartGenePatternServer and StopGenePatternServer applications must be run as an administrator. To start or stop the GenePattern server, right-click on StartGenePatternServer.exe or StopGenePatternServer.exe and select Run as administrator.
There are known issues regarding some updates to Java 6 and Java 7 that can cause problems for GenePattern users, specifically in using visualizer modules and the file uploader (the Java applet used to upload files larger than 2GB). For more information, see the GenePattern blog.
There is a known issue in GenePattern 3.6 that deleting an attached input file from a pipeline crashes the browser.
There is a known issue regarding pipelines created in GenePattern 3.3.3 that have data files included and that have been imported to a new server at version 3.5.0 or higher of GenePattern. If you are having problems with such a pipeline:
1. On the new server, select your pipeline and click edit to open it in the Pipeline Designer.
2. Click Save. You don't need to make any other changes to your pipeline.
There is a known issue regarding an update to the Java 6 platform which can cause problems for GenePattern users, specifically in using visualizer modules and the file uploader. For more information, see this GenePattern blog entry.
Some GenePattern modules do not work when the input filename contains a space character. Workaround: Rename the input file without a space character.
The MultiplotPreprocess, CoxRegression, LogisticRegression modules will not run on a local GenePattern server on Mac OS X 10.6, 10.7, or 10.8 or Windows 7 or 8 because R 2.0.1 will not install on these OSX versions.