Windows Launching Issues

Recent updates by Oracle, Microsoft, and browser vendors have affected some of our Windows users, preventing them from launching the GSEA Desktop. 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 24, 2015) but that further updates may affect them in the future. We will update the page should new issues come up.

Rather than deal with the 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.

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 causes no issues with 32-bit Java while launching with either 2 GB or 4 GB will fail. If you are having trouble launching GSEA, try this first even if you have a large dataset to confirm that the issue is with 32-bit Java and not something else.

Note: if you are having trouble launching GSEA, we recommend using the above Download page link rather than any previously installed shortcut or JNLP file.  It may also be necessary to <a style="color: rgb(17, 85, 204);" target="_blank" href="https://www.java.com/en/download/help/plugin_cache.xml">clear your Java </a><a style="color: rgb(17, 85, 204);" target="_blank" href="https://www.java.com/en/download/help/plugin_cache.xml">cache</a> from within the Java Control Panel as well.

Download the JAR file

We make the GSEA Desktop JAR file 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.

There are a couple of downsides to this approach. First, you will not automatically get updates when launching GSEA so you will need to watch 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 only 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, due to recent browser changes there is a good chance that you do not: Mozilla Firefox, Google Chrome, and Internet Explorer are all affected, though in different ways. See Notes on browsers for more details if you are interested.

To do this, 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 might want 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. 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 if so will usually default to 32-bit. 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 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; thus we recommend its removal.

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.

Notes on browsers

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• 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. For now 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.