Plotting symbols fails in PDF

The problem is that your default font does not have "‰" (which I would speak as "per mil") as the glyph that is produced with \u0028. You need to change to a font that does have that glyph:

?pdfFonts

This is what I get with my setup where there is no problem (at least as I understand ti.)

> str(pdfFonts("sans"))
List of 1
 $ sans:List of 3
  ..$ family  : chr "Helvetica"
  ..$ metrics : chr [1:5] "Helvetica.afm" "Helvetica-Bold.afm" "Helvetica-Oblique.afm" "Helvetica-BoldOblique.afm" ...
  ..$ encoding: chr "default"
  ..- attr(*, "class")= chr "Type1Font"

You probably have to change the encoding. On my mac this gets me the ‰ sign:

pdf('test.pdf',encoding="MacRoman")
plot.new()
text(0,labels="\u2030")
dev.off()

Look in the ‘enc’ directory of package grDevices for available encodings and try them out.