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I have used hyperlinks throughout my thesis, but then after previewing the pdf output and saving it for printing, the links are gone. Any idea why this occurred?

Here's a working example:

\documentclass[11pt]{amsart}
\usepackage{geometry}              
\geometry{letterpaper}                   
\usepackage{epstopdf}
\usepackage[colorlinks]{hyperref}
\usepackage{cleveref}
%
\begin{document}
\href{http://www.google.com}{Google} %
\end{document}  
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    No problem here compiling your minimal example. It shows coloured text 'Google' that links to the proper address when clicked. When you say "..., the links are gone.", are you saying that the word disappears ('Google' in this case) or the embedded hyperlink ('google.com' in this case)? – Werner Jul 18 '11 at 21:04
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    What is the original file type that you save it from - DVI? If this is the case, I would suggest following the latex->dvips->epstopdf sequence or pdflatex rather than saving a DVI as a PDF. – Werner Jul 18 '11 at 21:26
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    What previewer do you use? Preview? Is it on a Mac? What PDF viewer do you use? Adobe Acrobat/Reader? – Werner Jul 18 '11 at 22:01
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    @BrettHarry: Your MWE works for me after compiling it with pdflatex directly to a PDF. Please tell use which compiler and other software you are using. Otherwise it's basically impossible to help you. – Martin Scharrer Jul 18 '11 at 22:49
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    I think this is your problem - (Print) Preview on a Mac does not support hyperlinks. See this post. Here's the suggestion, instead of saving a print preview (from within Preview), rename the original Thesis.pdf to Myname_mysurname.pdf and then recompile Thesis.tex. – Werner Jul 21 '11 at 17:09
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I think this is your problem - (Print) Preview on a Mac does not support hyperlinks. See this post. Here's the suggestion, instead of saving a print preview (from within Preview), rename the original Thesis.pdf to Myname_mysurname.pdf and then recompile Thesis.tex.

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