[Rd] After package update, old S4 method is dispatched

[Jan Netík]

Hello R-devel,

I hope that you are all doing well and that this is the right place to
discuss my somewhat mysterious issue with S4.

On our Ubuntu server, we have "mirt" package installed which defines S4
method for "coef" standard generic. We updated the package with the usual
"install.packages", restarted, and observer error calling coef on mirt
object that should not be possible: "Error in which: argument "nfact" is
missing, with no default" (which has no such argument).

After days of investigation, I found that from mirt 1.37 to current 1.40,
the method changed as well as some internal functions used by the method.
The aforementioned error stems from the fact that these internal ordinary
functions were changed properly as we updated the package, but the S4
method dispatched stuck with the 1.37 version. I am by no means an expert
on S4 matter, but I know that these are cached to some extent. I thought
the cache is session-bound and have no idea how the issue can possibly
persist even after a complete reboot of the machine. I can detach and
library() mirt in one R session which solves the issue temporarily, but
emerges right back in any new R session.

Sadly, I cannot provide any reproducible example as I am completely unaware
of the cause and even I cannot reproduce this issue outside of the server.

Any insights on how this issue could have started would be highly
appreciated.

Best regards,
Jan Netík

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