Windows Launching Issues

Recent updates by Oracle, Microsoft and browser vendors have affected a number of our Windows users, preventing them from being able to launch the GSEA Desktop in certain modes. After some research, we have some possible fixes and workarounds 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, let's jump ahead to go through some possible fixes. While that may sound strange, the fixes and workarounds that we have found are somewhat general and for the most part do not target specific updates. Thus you can choose the one that best applies to your situation rather than worrying about the specific lower-level technical issues. We will touch on some of those details towards the end for those users that need it. 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 our users may choose - or be forced - to upgrade to Java 8, however, so we are working towards its support 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 will progress from the simplest to the most complex.

Launch with 1 GB

First, try launching from our Downloads page using the 1 GB. The 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 a different problem.

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 allow you to work around this issue as well. 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. Secondly, 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 and configure 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 no need to run against larger datasets then don't worry about this option.

For 64-bit Windows users, it's possible to install and configure Windows to use 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 [#Remove 32-bit Java] and use an [#Offline Java Installer]. This should resolve the issues for most users with the least amount of hassle. Note that users who already have 32-bit Java will need to do both steps. If you're not sure you will need to check. 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.

Remove 32-bit Java

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.

This page presents some ways of checking whether you have 32-bit Java installed. Another way is to check through the "Uninstall Programs" feature of the Control Panel in Windows. The Oracle website provides a help page on uninstalling Java from Windows. Follow these steps up to the point where you have a list of programs, but stop before actually uninstalling anything.

You may have multiple versions of Java installed. Look for the inclusion of "64-bit" in the name to identify those version; the 32-bit versions might have no similar label.

Offline 64-bit Java installer

An offline Java installer will download the entire Java package up-front before installation, so you can be sure to have the correct installer. At the time of this writing, the offline 64-bit Java installer is available from this page. Download the file from there and follow their instructions.

In some cases, it's also possible to reconfigure your browser to run as 64-bit, at which point you should be able to use the auto-detect feature of the Java download page. Most users probably don't care about these are technical details and can skip this. See the [#More Technical Details] section below for further information.

More Technical Details

Due to these recent browser changes, you either have to use an offline Java installer or reconfigure your browser. The first is the easiest option; see below.

Even if you do have 64-bit Java, it is also quite possible that Windows is configured to prefer 32-bit Java regardless. You can either uninstall 32-bit Java or reconfigure Windows to prefer 64-bit. The first is by far the easier option; see [#Uninstalling 32-bit Java] below. In fact, while information from Oracle says that it's possible to reverse this preference, in our tests we found that only complete removal of 32-bit Java would resolve the launching issues. See the [#More Technical Details] section below if you want to pursue this.