A colleague recently submitted a paper to JSS and was advised to
address the following warning which occurs when their package
(https://CRAN.R-project.org/package=pcoxtime) is loaded:
Warning message:
In .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition
not updated
After much digging I *think* I've concluded that this comes from the
following import chain:
pcoxtime -> riskRegression -> rms -> quantreg -> MatrixModels
that is, loading any of these packages throws the warning.
MatrixModels Imports: *only* {stats, methods, Matrix} and loading these
by themselves is warning-less.
I assume there is some mismatch/incompatibility between MatrixModels
(which was last updated 2021-03-01) and Matrix (2021-05-24), which has
this NEWS item in the most release 1.3-3
<https://cran.r-project.org/web/packages/Matrix/news.html>:
* removed the nowhere used (and unexported but still active) class union
"Mnumeric" which actually trickled into many base classes properties.
Notably would it break validity of factor with a proposed change in
validity checking, as factors were also "Mnumeric" but did not fulfill
its validity method. Similarly removed (disabled) unused class union
"numericVector".
It seems that REINSTALLING the package from source solves the
problem, which is nice, but I don't fully understand why; I guess ????
there are class structures that are evaluated at install time and stored
in the package environment ...
Any more explanations would be welcome.
cheers
Ben
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