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This is an upstream issue which has to do with dune not being able to access other packages installed in the current switch, meaning that it can't access or cross-reference the docs of any dependencies (not even stdlib): ocaml/odoc#794
The workaround I found (discussed here) was to not use dune build @doc but rather odig. On the first time, do:
opam install odig
# install the package into the current opam switchcd whatwhat
dune build
dune build @install
dune install
# generate and view documentation
odig doc whatwhat
For example:
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