Have look at the Internal FAQ, if you cannot find your answer here. Write to the OpenMS mailing list, if the problem persists.
Known Issues on Windows
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Starting a (GUI) TOPP executable (like TOPPView or FeatureFinderCentroided) gives "The application was unable to start correctly (0xc0000005). Click OK to close the application"
 When you run the tool in Debug mode and look where it crashes, you might actually find it to be a very weird place - e.g. when creating a perfectly legal String from a QString:QFileInfo fi(file.toQString()); return fi.path() 
'MSSimulator.exe': Loaded 'C:\Windows\winsxs\amd64_microsoft.vc90.debugcrt_1fc8b3b9a1e18e3b_9.0.21022.8_none_4ec74c6b3093419c\msvcp90d.dll', Symbols loaded. 'MSSimulator.exe': Loaded 'C:\Windows\winsxs\amd64_microsoft.vc90.debugcrt_1fc8b3b9a1e18e3b_9.0.21022.8_none_4ec74c6b3093419c\msvcr90d.dll', Symbols loaded. 'MSSimulator.exe': Loaded 'C:\dev\qt-everywhere-opensource-src-4.7.1\bin\QtSqld4.dll', Symbols loaded. 
 Solution: recompile Qt (in this case) using VS10 and link against the new Qt.
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Starting a (GUI) TOPP executable (like TOPPView or FeatureFinderCentroided) gives "Entry point not found"
 This usually happens when your PATH contains multiple versions of DLL's on which TOPP/OpenMS depends. Candidates are all QT (QtGui4.dll, QtCore4.dll, ...) or Xerces-C (xerces-c_3_0) libraries. Usually other external programms (Miktex, Mendeley etc) put their own binary directory (which contains these incompatible DLL's) before the contrib directory in your PATH%.
 Solution: put the contrib directory at the very beginning of your PATH%. The other tools should be unaffected as DLL's are first searched in the path of the executable (where their DLL's should be as well). We do that for OpenMS as well, but only in the binary installer packages, not for the developer version.
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Compiling the contrib or OpenMS, the windows.h header file seems to be missing!
 Your error message might look like this:c:\dev\contrib_build\src\bzip2-1.0.5\bzlib.h(79) : fatal error C1083: Cannot open include file: 'windows.h': No such file or directory 
 Solution: You need to download the Microsoft SDK for Windows 7 (or whatever your OS is). Make sure to select "Header Files" Section during install and make sure that the SDK's include path is in your INCLUDE environment.
Known Issues on Linux
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Contrib fails to compile on Ubuntu 10.04 Your error message might look like: gzip: stdin: invalid compressed data--crc error  
 Solution: To solve this issue update gzip using lucid-proposed (see https://wiki.ubuntu.com/Testing/EnableProposed)