Yikes. Next question, is this (in your opinion) worth escalating to
r-devel ?
I can definitely implement something where I require() rstan up
front, (which should be harmless if it's really not available but will
fix issues that brms is having?) ... that might resolve the symptoms
cleanly in the absence of a definitive diagnosis ...
https://github.com/bbolker/broom.mixed/commit/4096d00cf8cb6dd6798079859dfce56ea870b636
... now all I have to do is get a testing framework up and running so
I can see if it helps ...
On 2024-09-25 4:22 p.m., Ivan Krylov wrote:
В Wed, 25 Sep 2024 12:28:25 -0400
Ben Bolker <bbol...@gmail.com> пишет:
What is your current estimate of the probability that this is
something that I've done wrong vs. exposing something wonky elsewhere
(i.e. at the level of testthat, brms, rstan, Rcpp, R-devel, ...) ?
I didn't have a good answer (the most recently updated package should
be the one to suspect, right?), but stopping the investigation now
would be akin to closing a murder mystery in the middle of the last
chapter. Here's what I've been able to find out:
When running library(testthat); debugonce(Rcpp::loadModule);
source('tests/testthat/test-alltibbles.R'), by the time we reach
Rcpp:::loadModule, the reference classes don't come out right. A simple
new('C++OverloadedMethods') returns an object that doesn't have a $show
or $info method. A similar problem happens for 'envRefClass', from
which 'C++OverloadedMethods' inherits: printing it will fail due to a
missing $show() method.
The problem is not in the class definition or object contents. I don't
see differences between serialised class definitions. Reloading a
serialized object from a "broken" R session into a fresh R session makes
it work normally.
The first difference I was able to notice was in how the $ operator
works for the reference semantics objects. In both cases,
.Primitive('$') -> do_subset3 eventually calls DispatchOrEval(). In a
healthy R session, the test [*] for IS_S4_OBJECT(x) &&
R_has_methods(op) succeeds. In a "broken" R session it fails because
R_has_methods(op) is FALSE.
That's because allowPrimitiveMethods had been set to FALSE.
Judging by the traceback, brms::variables(object) ->
variables.brmsfit(object) -> dimnames(x$fit) needs to resolve the S4
'dimnames' method for class 'stanfit'. At this point
methods:::.findInheritedMethods temporarily disables S4 methods for
primitives. The comment says it's done "to avoid infinite recursion,
and somewhat for speed". Unfortunately, later the 'rstan' namespace
needs to be loaded, and 'rstan' calls Rcpp functions that use reference
classes, which break without S4 dispatch for `$`.
As far as endings go, this one is rather like Murder on the Orient
Express. Even understanding what happened doesn't point towards the
"right" fix. Josiah's suggestion should have helped by loading the
namespace at a safer time.
--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
> E-mail is sent at my convenience; I don't expect replies outside of
working hours.
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