From @|mon@urb@nek @end|ng |rom R-project@org  Mon Oct  2 20:56:26 2023
From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek)
Date: Tue, 3 Oct 2023 07:56:26 +1300
Subject: [Rd] After package update, old S4 method is dispatched
In-Reply-To: <CA+6hu7ekxwdH55eSVs5-PxfCv75khNUURbHjT2rB_jLSrCNgZw@mail.gmail.com>
References: <CA+6hu7ekxwdH55eSVs5-PxfCv75khNUURbHjT2rB_jLSrCNgZw@mail.gmail.com>
Message-ID: <32A80143-4755-4D96-822A-E386840E4438@R-project.org>

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 Net?k <netikja at 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 Net?k
> 
> 	[[alternative HTML version deleted]]
> 
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> 



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