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

[Carl Schwarz]

Yes, the resubmission and re-building has fixed the problem with buildmer/
Matrix.
Carl

On Tue, Oct 18, 2022 at 12:17 PM Duncan Murdoch <murdoch.duncan using gmail.com>
wrote:

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

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