Linux GTK+ and GEF don't always work well together, depending on the versions used. If some elements are not appearing, disable anti-aliasing in the Apollo preferences (Window->Preferences->Apollo).
The following has been taken from the Eclipse Project Release Notes 3.2.1.
Here are some common problems that can cause Eclipse not to start:
Eclipse 3.2 requires at least a 1.4.2 VM. Perhaps an older version of the VM is being found in your path. To explicitly specify which VM to run with, use the Eclipse -vm command-line argument.
Eclipse must be installed to a clean directory and not installed over top of a previous installation. If you have done this then please re-install to a new directory. If your workspace is in a child directory of your old installation directory, then see the instructions on "Upgrading Workspace from a Previous Release".
Java sometimes has difficulty detecting whether a file system is writable. In particular, the method java.io.File.canWrite() appears to return true in unexpected cases (e.g., using Windows drive sharing where the share is a read-only Samba drive). The Eclipse runtime generally needs a writable configuration area and as a result of this problem, may erroneously detect the current configuration location as writable. The net result is that Eclipse will fail to start and depending on the circumstances, may fail to write a log file with any details. To work around this, we suggest users experiencing this problem set their configuration area explicitly using the -configuration command line argument.
If you have installed new plug-ins and they aren't showing up when you run, then perhaps you unzipped them into your "plugins" directory and your configuration might need to be refreshed. This can be accomplished by starting Eclipse with the -clean command line argument.
Eclipse will fail to detect the proper content type for XML files that have a UTF-8 byte order mark if Crimson is the XML parser (as it is on Sun 1.4 JREs, but not on Sun 1.5 JREs). This problem will prevent actions normally available when files of the affected content types are selected from being presented to the user. The workaround is to ensure the default XML parser supports UTF-8 BOMs (such as Xerces does).
If you have an old config.ini file and
use it with a new Eclipse build, you may not get the correct
product branding. This is because the id of the standard Eclipse
product changed. Users in shared install scenarios may end up in
this situation as previous builds of Eclipse automatically
generated config.ini files in some cases. The
work around is either to delete the local
config.ini or update the
eclipse.product line to read
eclipse.product=org.eclipse.platform.ide.
Eclipse will fail to launch if installed in a directory whose path contains certain invalid characters, including :%#<>"!. The workaround is to install Eclipse in a directory whose path does not contain invalid characters.
When launching an Eclipse Application from within the
Eclipse IDE it is possible to select the set of plug-ins that are
included in the Eclipse Application. Removing the
org.eclipse.update.configurator plug-in from
the set of plug-ins to an existing configuration can cause the
configuration to become invalid. This can result in extra plug-ins
installed in the target application that are not resolved. To work
around this, after the
org.eclipse.update.configurator plug-in has
been removed, the target configuration area should be cleared
before launching.
The Help browser's Print, Synchronize, and Bookmark buttons do not work for pages that are not actually installed with the product. However, you can always use the print command in the browser's context menu to print the page you're reading.
If your LAN settings are not properly configured for local host access, your Help browser might open to a blank page or display an HTTP error instead of a help page, or you may experience long delays when loading help documents. Your system administrator can configure your LAN settings so that help documents can be accessed from the local help server.
In the Control Panel, open Internet
Options, select the
Connections tab and choose LAN
Settings.
If your host was configured to use DHCP for IP
assignment, make sure that the "Automatically detect
settings" check box is cleared.
If you use a proxy server, ensure that the
"Bypass proxy server for local addresses"
is selected.
In "Advanced" settings for proxies,
add "127.0.0.1;localhost" to the
"Exceptions" if these addresses are not
listed.
If you are using an automatic configuration script for
proxy settings, and are not sure that the script is correct,
clear the "Use automatic configuration
script" check box.
If the above steps do not fix your problem, try changing the
port and host properties on the Help > Help
Server preference page. In general, setting
host to localhost or
127.0.0.1 should work. Also, especially when
running a firewall, you may want to specify port 80 or some other
firewall-friendly value.
If you see a help launched with a blank page, and no errors
displayed, it can be caused by a conflict between libraries in
org.eclipse.tomcat plug-in and jars
optionally installed in JRE jre/lib/ext
directory. To fix the problem, ensure that the JRE used for
running Eclipse does not contain any J2EE or Apache jars in the
jre/lib/ext directory.
If an OLE document crashes, Eclipse can crash, or the workbench menus can become inconsistent.
Some users who have installed Service Pack 2 on Windows XP have experienced crashes while using editors in Eclipse. The workaround is to place a working version of Windows\System32\USP10.DLL in the Eclipse startup directory or uninstall Service Pack 2.
The Linux-motif build of Eclipse does not launch properly when run on a computer with Xinerama (provides support for dual head monitors) and a UTF-8 locale. The workaround for this problem is to change the locale to a non-UTF-8 value, or to disable Xinerama.
Users of the Bluecurve theme shipped with RedHat Linux 9 may experience problems running Eclipse. These problems may include crashes or reduced performance. We recommend changing to a different theme.
If the application that is supplying the clipboard material is unresponsive, the paste operation hangs Eclipse for several minutes. This situation can be encountered when copying from an Eclipse target workbench, suspending the target workbench at a breakpoint and pasting into the hosting Eclipse workbench.
Typically, in Gnome Linux installs running with 8-bit visuals (i.e. 256 color mode), before the Eclipse application is started there are no free colors. This may mean that Eclipse is unable to allocate the default widget background color, causing it to display a white background. The functionality, however, is otherwise unaffected.
On some versions of Debian, Eclipse key bindings may stop working. In this context the only way to make the key bindings work again is to restart Eclipse.
The problem is that a focus issue exists in GTK+ 2.6.7 and earlier, for which SWT has a workaround. This workaround is incompatible with the GTK+ 2.6.7 fix, so a GTK+ version check is done at runtime to determine whether the workaround should be used or not. However, Debian backported the GTK+ focus fix into their libgtk+2.0 (2.6.4-2) package, so the SWT workaround and GTK+ fix are both incorrectly applied in this context.
To work around this problem, either get the Debian unstable
version of GTK+, compile your own GTK+, or hack SWT's
Shell.gtk_realize(int) and change the version
that it checks.
When features and plug-ins are manually installed on top of an Eclipse-based product install located on a FAT file system that has already been run at least once, the product must be explicitly restarted with -clean. That is,
eclipse.exe -clean
Then, open the Help > Software Updates >
Manage Configuration dialog and toggle on the
"Show disabled features" button in its
toolbar. Select the newly "installed" feature and press on the
"Enable feature" action on the right pane (or
select the action from the feature's context menu).
By default, Eclipse will allocate up to 256 megabytes of Java heap memory. This should be ample for all typical development tasks. However, depending on the JRE that you are running, the number of additional plug-ins you are using, and the number of files you will be working with, you could conceivably have to increase this amount. Eclipse allows you to pass arguments directly to the Java VM using the -vmargs command line argument, which must follow all other Eclipse specific arguments. Thus, to increase the available heap memory, you would typically use:
eclipse -vmargs -Xmx<memory size>
with the <memory size> value set to greater than "256M" (256 megabytes -- the default).
When using a Sun VM, you may also need to increase the size of the permanent generation memory. The default maximum is 64 megabytes, but more may be needed depending on your plug-in configuration and use. The maximum permanent generation size is increased using the -XX:MaxPermSize=<memory size> argument:
eclipse -vmargs -XX:MaxPermSize=<memory size>
This argument may not be available for all VM versions and platforms; consult your VM documentation for more details.
Note that setting memory sizes to be larger than the amount of available physical memory on your machine will cause Java to "thrash" as it copies objects back and forth to virtual memory, which will severely degrade your performance.