I created several simple ggplot2 plots and saved them to PDF files using the following commands:
p <- ggplot(plotobject, aes(x=Pos, y=Pval),res=300) ggsav
Use useDingbats=FALSE for the pdf output, then Illustrator will no complain.
useDingbats=FALSE
pdf("example.pdf", useDingbats=FALSE) ggplot(plotobject, aes(x=Pos, y=Pval),res=300) dev.off()