Jan, have you re-installed all packages? If you change (update) any package that uses S4 it may be necessary to re-install all its reverse-dependencies as well since they may include cached values in their namespaces, so the easiest is to make sure you re-install all packages.
Cheers, Simon > On Oct 3, 2023, at 4:18 AM, Jan Netík <neti...@gmail.com> wrote: > > 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
