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I get a "Skipped ... exit status 3 message" when scanning and indexing PDF documents, why?

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Error code 3 is relates to PDF document permissions — you don't have permission to electronically read the document.

 

PDF files can have various restrictions placed on them, for example not being able to copy and paste contents. To check PDF document permissions open the document with Adobe Acrobat Reader, execute File->Document Properties menu command and click on the Security tab in the Document Properties dialog (Acrobat 7.0).