Windows Launching Issues

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Recent updates by Oracle, Microsoft and browser vendors have affected some of our Windows users, preventing them from launching the GSEA Desktop. After some research, we have some possible solutions that should help if you're having trouble. Note that these apply as of the writing of this page (June 22, 2015) but that further updates may affect them in the future. We will try to update the page should new issues come up.

Rather than deal with the how and why of those updates and their low-level details, this page will focus on possible fixes. We will touch on some of the details towards the end for those users that need them. The short summary is that the issues are likely related to the use of 32-bit instead of 64-bit Java.

For completeness, it should be noted here that we are still evaluating Java 8 versus Java 7 at this time and do not yet officially support Java 8. We realize that many users may choose - or be forced - to upgrade to Java 8, however, so we are working towards supporting it as well. This page applies to both versions, though more than likely you'll receive Java 8 if you are using any automatic download features.

Note that these solutions will progress from the simplest to the most complex.


Launch with 1 GB

First, try launching from our Downloads page using the 1 GB option. That particular setting should be fine for use with small datasets and also is no issue with 32-bit Java. If you are having trouble launching GSEA, try this fix first, even if you have a large dataset. This will let you confirm that the issue is with 32-bit Java and not something else.

Note: if you are having trouble launching GSEA, we recommend that you use the above Download page link rather than using any previously installed shortcut.

Download the JAR file

We make the GSEA Desktop available from the Downloads page primarily for users that have data connectivity issues, but it should also allow you to avoid this issue. More details are available in This FAQ entry.

You should be aware that there are a couple of downsides to this approach. First, you will not automatically get updates when you launch GSEA so you will need to periodically check for these on your own. Second, 64-bit Java is still required if you are working with large datasets and need to run with more memory. If this is your situation then see the next section.

Install 64-bit Java

If you have 32-bit Windows, this option is not available. Use one of the options above instead. Likewise, if you have small datasets then don't worry about this option.

For 64-bit Windows users, it's possible to install 64-bit Java to allow analysis of larger datasets. While you may be thinking that you already have 64-bit Java, there is a good chance that you do not, due to recent browser changes: Mozilla Firefox, Google Chrome, and Internet Explorer are all affected, though in different ways. See [#Notes on browsers], below, for more details.

We recommend that you first remove 32-bit Java and then install 64-bit Java using an offline installer. This should resolve the issues for most users with the least amount of hassle. Be very careful here; if you are uncomfortable uninstalling programs then you may wish to consult your IT staff or a more technically-inclined colleague for help.

The Oracle website provides a help page on uninstalling Java from Windows; go through those steps to remove any 32-bit versions of Java from your system.

The offline 64-bit Java installer is available from Oracle at this page. Download the file from there and follow their instructions. Do not use Oracle's 'Download Java' page; it will generally install 32-bit Java, which is how you got to this position in the first place. An offline Java installer will download the entire Java package up-front before installation, so you can be sure to have the correct installer.

Note that Oracle makes it possible to have both 32-bit and 64-bit Java installed on your computer at the same time and in fact will default to 32-bit Java for many cases, so installing 64-bit Java is not enough to switch over. Most users will not need both; those that do should consult the [#More Technical Details] section below for further information.

More Technical Details

This somewhat-dated blog posting from an Oracle Java Product Manager says that it's possible to install both 32-bit and 64-bit Java and to configure Windows to prefer the 64-bit version for most cases. It doesn't provide or reference any instructions to do that, however, so it's up to the individual user to figure it out. In our tests on Windows 7, we were unable to configure Java Web Start to use 64-bit Java unless 32-bit Java had been removed and so we give the recommendations above.

Perhaps the situation has changed since that posting and this configuration is no longer possible. If you need both versions of Java and are able to achieve the required set-up, please contact us with those steps so that we can update this page. As most users will not need both, we'll continue to recommend using 64-bit Java without 32-bit present in any case.

Notes on browsers

  • Internet Explorer: Windows (64-bit) ships with both 64-bit and 32-bit versions of IE and defaults to the latter, which is why the Oracle 'Download Java' page installs 32-bit Java. It's possible to change Windows to use 64-bit IE, in which case the 'Download Java' page will instead provide 64-bit Java.
  • Google Chrome: Google has announced plans to remove one of the underlying technologies that enables Java (among other things) in the browser. While it's still present for now, it is disabled by default. Until it is finally removed it is still possible to re-enable it; this GenePattern blog post shows how.
  • Mozilla Firefox: At the time of this writing, the only supported builds of Firefox are 32-bit.
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