Difference between revisions of "Windows Launching Issues"

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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.
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<p><strong>NOTE: Much of the advice given here is no longer necessary with the release of [[GSEA_v4.0.0_Release_Notes|GSEA 4.0.0]] and the Windows installer EXE that it offers.  For now this wiki page will be left here for reference purpose, however, for any users still launching via JNLP or continuing to use v3.0.</strong>
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</p>
  
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Rather than focus on 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.
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<p> 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. </p>
 +
<p> 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. </p>
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Note that these solutions will progress from the <span style="font-weight: bold;">simplest</span> to the <span style="font-weight: bold;">most complex</span>.
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<h2>Launch with 1 GB</h2>
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<p> First, try launching from our [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page using the <span style="font-weight: bold;">1 GB</span> 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. </p>
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<p> <span style="font-weight: bold;">Note:</span> if you are having trouble launching GSEA, we recommend using the above Download page link rather than any previously installed shortcut or JNLP file.&nbsp; <span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 12.8px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 1; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);">It may also be necessary to [https://www.java.com/en/download/help/plugin_cache.xml clear your Java cache] from within the Java Control Panel as well.  Be sure to select the option to delete "Installed Applications and Applets" to fully clear the cache.</span></p>
  
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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.
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<h2>Download the JAR file</h2>
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<p> We make the GSEA Desktop JAR file available from the [http://www.broadinstitute.org/gsea/downloads.jsp 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 [http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Other_Ways_to our User Guide].&nbsp; If the memory issues continue, you may need to launch GSEA from the command line and explicitly tell Java to allocate more memory.&nbsp; See [http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Running_GSEA_from this section of our User Guide] for more details.<br />
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</p>
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<p> 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. </p>
  
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Note that these will progress from the <span style="font-weight: bold;">simplest</span> to the <span style="font-weight: bold;">most complex</span>.
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<h2>Install 64-bit Java</h2>
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<p> 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. </p>
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==Launch with 1 GB==
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<p> 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| Notes on browsers]] for more details if you are interested. </p>
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First, try launching from our [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page using the <span style="font-weight: bold;">1 GB</span>.  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.
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<p> 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 <span style="font-weight: bold;">very careful</span> here; if you are uncomfortable uninstalling programs then you might want to consult your IT staff or a more technically-inclined colleague for help. </p>
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<p> The Oracle website provides [https://java.com/en/download/help/uninstall_java.xml a help page on uninstalling Java from Windows]; go through those steps to remove any 32-bit versions of Java from your system. </p>
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<span style="font-weight: bold;">Note:</span> if you are having trouble launching GSEA, we recommend that you use the above Download page link rather than using any previously installed shortcut.
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<p> The offline 64-bit Java installer is available from Oracle at [https://java.com/en/download/manual.jsp this page].  Download the file from there and follow their instructions.  <span style="font-weight: bold;">Do not use Oracle's 'Download Java' page</span>; 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.  </p>
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<p> 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|More Technical Details]] section for further information. </p>
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==Download the JAR file==
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<h2>More Technical Details</h2>
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We make the GSEA Desktop available from the [http://www.broadinstitute.org/gsea/downloads.jsp 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 [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ#Do_I_have_to_be_connected_to_the_internet_to_run_GSEA_software.3F This FAQ entry].
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<p> This somewhat-dated [https://blogs.oracle.com/java-platform-group/entry/choosing_64_and_or_32 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. </p>
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<p> 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. </p>
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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.
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<h3>Notes on browsers</h3>
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<a name="Notes_on_browsers"></a>
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==Install and configure 64-bit Java==
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<ul>
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    <li><span style="font-weight: bold;">Internet Explorer:</span> 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 [http://winaero.com/blog/how-to-enable-64-bit-internet-explorer-processes/ change Windows to use 64-bit IE], in which case the 'Download Java' page will instead provide 64-bit Java. </li>
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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.
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    <li><span style="font-weight: bold;">Google Chrome:</span> [https://java.com/en/download/faq/chrome.xml Google has removed support from Chrome] for one of the underlying technologies that enables Java (among other things) in the browser. <br />
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    </li>
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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.
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    <li><span style="font-weight: bold;">Mozilla Firefox:</span> At the time of this writing, [https://www.mozilla.org/en-US/firefox/38.0.5/system-requirements/ the only supported builds of Firefox are 32-bit]. </li>
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</ul>
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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 <span style="font-weight: bold;">both</span> steps.  If you're not sure you will need to check.  Be <span style="font-weight: bold;">very careful</span> here; if you are uncomfortable uninstalling programs then you may wish to consult your IT staff or a more technically-inclined colleague for help.
 
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===Remove 32-bit Java===
 
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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.
 
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[http://stackoverflow.com/a/8825785 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 [https://java.com/en/download/help/uninstall_java.xml a help page on uninstalling Java from Windows].  Follow these steps up to the point where you have a list of programs, but <span style="font-weight: bold;">stop before actually uninstalling anything</span>. 
 
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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.
 
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===Offline 64-bit Java installer===
 
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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 [https://java.com/en/download/manual.jsp this page].  Download the file from there and follow their instructions.
 
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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.
 
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==More Technical Details==
 
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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.
 
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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.
 
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===Notes on browsers===
 

Latest revision as of 01:57, 22 August 2019

NOTE: Much of the advice given here is no longer necessary with the release of GSEA 4.0.0 and the Windows installer EXE that it offers. For now this wiki page will be left here for reference purpose, however, for any users still launching via JNLP or continuing to use v3.0.

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 clear your Java cache from within the Java Control Panel as well. Be sure to select the option to delete "Installed Applications and Applets" to fully clear the cache.

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 our User Guide.  If the memory issues continue, you may need to launch GSEA from the command line and explicitly tell Java to allocate more memory.  See this section of our User Guide for more details.

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

<a name="Notes_on_browsers"></a>

Retrieved from "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Windows_Launching_Issues&oldid=4330"