PJ 20160503

Making sure all fonts are embedded appears to be not so
easy across platforms.  When I compile the ku thesis document,
I notice the Wingding and symbols are not embedded.

However, this is not a flaw in pdflatex as it currently exists.  It
was a pdflatex flaw in the past. So far as I can tell, all fonts
needed in the pdflatex run are embedded.

Except that when a document includes other documents, using
\includegraphics{} for example, then if those included
documents are lacking in embedded fonts, then pdflatex
does not fix that.

In my example document, before 20160503, the fonts were missing
because they were not embedded in the R plots that are included in the
example chapters. I had to to go back and re-run the R code to make
sure the fonts are embedded in the pdf files for the graphs. After
that, the pdflatex output of the thesis template is fine.

You can check for yourself, Run

$ pdffonts thesis-ku.pdf

If we don't fix the R output files before compiling the thesis itself,
we are in a somewhat dangerous situation.  People suggest using
various magic wands to add fonts, but all of them seem to have major
flaws. They either corrupt the quality of the output or destroy its
internal structure.

I found ways to embed fonts using ghostscript. This converts document
over to ps and then back to pdf.

$ pdf2ps  thesis-ku.pdf test.ps
$ ps2pdf14 -dPDFSettings=/prepress -dEmbedAllFonts=true test.ps
test.pdf

The bad news.
1 It destroys internal hyperlinks.
2 IT DOES NOT embed fonts needed for material in embedded graphs
(things inserted by \includegraphics, such as PDF produced by R).


See: 

http://askubuntu.com/questions/50274/fonts-are-not-embedded-into-a-pdf

In my opinion, this is a bad outcome, should not happen. But
it does.

As a result, it seems necessary to fix the individual PDF
graphics files before compiling the larger thesis document.

This reminds me that at one point I had a post-processing script written
for R Sweave sessions that would embed fonts in all pdf output files. 

The shell script would cycle through all of the R output and embed
fonts. Enjoy!

for i in *.pdf; do
base=`basename $i .pdf`;
basenew="${base}/newtemp.pdf"

##echo "$i base: $base new: $basenew"
  /usr/bin/gs -o $basenew -dNOPAUSE -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite $i

mv -f $basenew $i
done;

 
Same can be achieved inside R. Each time a PDF is created, embed the
fonts with the embedFonts() function. See ?embedFonts