Follow-up Comment #3, bug #61407 (project groff): "...can't transparently output node at top level" and "...can't translate character code nnn to special character 'c'in transparent throughput" (point 2) are spurious insofar as they have no impact on pdf output, nor the generation of pdf outlines. The warnings are emitted by troff when the gropdf driver is being used. So far, no one has come up with a solution to getting rid of them. I suspect it isn't possible except by suppressing stderr, which is no solution at all.
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