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[ JDK VERSION : other ] Under default Apple JDK, the "Netbeans > Preferences..." can be accessed in the screen-top Menubar (or shortcut CMD-,). But this is not the case for OpenJDK/X11/OSX. Under OpenJDK, there is no screen-top Menubar, and the menubar is located under the window decorations, which starts with "File | Edit | ....". So there is not "Netbeans" menu, and therefore no way to access the "Preferences..." menu item.
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NetBeans.org Migration: changing resolution from LATER to WONTFIX