[R-pkg-devel] Error when install binary from CRAN but not if install from source - Macintoh, lme4, Matrix, buildmer

[Duncan Murdoch]

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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