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I am reading into Illustrator a PDF output from R (grid graphics I believe) in which the circles show as boxes with crosses inside them. These pictures illustrate:

In OSX Preview:

enter image description here

In Illustrator:

enter image description here

Any idea why this is happening, and how to work around it?

The following Illustrator message pops up when opening the file, which may be significant.

enter image description here

4

You're missing the AdobePi font, specifically, that glyph. That's exactly what that message states... and the [X] is an indicator of a missing glyph.

Select the [X]s with the text tool, and choose a different font. For example Zapf Dingbats has a Circle glyph.

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