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For long-term archival, the PAC system of CINES requires specific conditions for PDF files. This is required for french Ph.D thesis in particular. The document must pass the online validation at http://facile.cines.fr/.

PDF files produced by pdflatex usually do not pass the validation. The website suggests using latex + dvips + ps2pdf, but this may not be applicable if the document requires pdflatex.

What are the alternatives?

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Use GhostScript (gs) to embed all fonts

Compile your document normally, and then process it with this command:

gs -DSAFER -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dEmbedAllFonts=true -sOutputFile=$NEWFILE.pdf -f $YOURFILE.pdf

(Replace $YOURFILE.pdf with the name of the file produced by pdflatex, and $NEWFILE.pdf by the name of the file you want to obtain)

Use Adobe Acrobat

I did not test this myself, but according to the documentation, Adobe Acrobat Pro can process a PDF file to produce one which should satisfy the CINES criteria.

Warning: Adobe Acrobat Pro is not the same as the free of charge Acrobat Reader (aka acroread). The later can only read PDF file.

Other Solutions

See this discussion for alternatives http://forum.ubuntu-fr.org/viewtopic.php?id=635661

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    You don't need to use gs to get all fonts embedded; pdftex can do that. – Reinstate Monica - M. Schröder May 5 '15 at 10:45
  • I tried playing with pdflatex's configuration to embed fonts, but couldn't manage to produce a document accepted by CINES. It does not mean there is no way, but I'm just sharing the way I found and tested to work. If you have another recipe that works for CINES, feel free to add, I've set my answer as "community wiki" for that (but please do test with CINES: I'm not sure exactly what the criteria are, embedded fonts seems to be only a part of it). – Matthieu Moy May 5 '15 at 11:54
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The mentioned page lists the more useful information, which PDF variant is required. It is essentially , whereas PDF/A-1a is the most preferred one.

However, having doubts that pdflatex is smart enough to add document structure, you might have to rely on PDF/A-1b, or PDF/A-2b. In any case, you will have to provide sufficient Metadata.

A standard way to create PDF/A is using Acrobat Pro (not Standard, not Reader), and there use the Preflight tool with the standard fixup to create PDF/A of the variant you can do.

Other suitable applications would be pdfapilot by Callas Software, or the 3Heights PDF to PDF/A converter by PDF-Tools. You might also ask those vendors whether there are services available (assuming that you have a one-time need).

Edit/Update: Apparently, that system accepts non-archival quality PDF versions, beginning with 1.4. Therefore, a dedicated PDF/A generator would not be needed, but Acrobat Pro would do, and instead of using the PDF/A creation preflight profile, using a PDF 1.4 or higher profile would do; and if you know what you are doing, you could even use the PDF Optimizer, which (in Acrobat X and newer) is accessible via Save as optimized…

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    What is special, in that case, about the PDF generated using Acrobat Pro? Since pdfTeX can produce PDFs using a suitable version of the PDF spec...? – cfr May 5 '15 at 11:30

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