I see the same thing. This sounds like a problem in the handling of
methods that has been discussed somewhat recently:
https://stat.ethz.ch/pipermail/r-devel/2022-September/081971.html
The problem is that when the binary is built, some code from other
packages is kept as part of it. When that other package is updated, you
need a new source install of your own package (or a rebuild at CRAN to
replace the binary) to cache the new code.
This can also be done explicitly by package startup code; I think this
thread
https://stat.ethz.ch/pipermail/r-package-devel/2022q3/008481.html
turned out to be a case where rstan was caching something, and an update
to ggplot2 didn't work with the cached data. Given the error message,
your issue sounds more like the first one.
I don't recall if there was a resolution. Maybe you can ask the CRAN
maintainers to rebuild buildmer.
Duncan Murdoch
On 18/10/2022 2:51 p.m., Carl Schwarz wrote:
I've run into a problem where if you install the lme4, Matrix, and buildmer
packages using the binaries from CRAN on a Mac, I get an error message
about a missing method, but if I install the same packages from SOURCE, the
code runs fine.
I would have thought that installing from source or using the binary
should look the same.
Any suggestions on how to proceed to resolve this issue?
The maintainer of buildmer is also puzzled.
You can follow the issue in more detail at:
https://github.com/cvoeten/buildmer/issues/20
This is way above my paygrade...
Carl Schwarz
------------------------------------------------------
Tried this on an intel-Mac and arm-Mac with the same result.
Works fine on Windows machines under both scenarios.
Here is a test example
library(buildmer)
library(lme4)
nrow <- 100
test <- data.frame(x01=runif(nrow),
y=runif(nrow)<.1, block=as.factor(floor((1:nrow)/50)))
head(test)
fit.model <- lme4::glmer(y~x01 + (1|block), data=test,
family=binomial(link="logit"))
fit.model # this works
class(fit.model)
summary(fit.model)
# gives the following error message
Error in diag(from, names = FALSE) : object 'dgeMatrix_getDiag' not found
A pdf document showing output is attached (shows the sessionInfo etc).
When you install the buildmer and Matrix packages from SOURCE, it runs fine.
I've tried all combinations of installing binary/source and only if both
packages (Matrix and buidmer) are installed from source, does the code run.
Same issue on an intel-Mac.
Same issue when running under the R directly rather than Rstudio on a Mac.
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