R devel - Oct 2023 - After package update, old S4 method is dispatched

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]]

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]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>