Follow-up Comment #4, bug #61407 (project groff):
I believe the transparent node message occurs when pdf.tmac calls .asciify in
order to "clean" the text to use in the bookmark text, and it includes nodes
which can't be converted back text. Last time I looked this message could not
be suppressed with a -W number.
However, Keith's clever sanitise.tmac, which he has recently included in
Groff, takes a different approach, it "cleans" the text in pure roff code
rather than asciifying after groff has converted the input to nodes. I need to
investigate whether .sanitise could be used as a replacement for .asciify.
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