It seems that this could be mostly avoided if instead of caching copies
of Matrix methods when buildmer was installed, R would cache promises to
get those methods. Then if the method for some particular signature
changed, on first use buildmer would retrieve the current version.
There would still be a problem if Matrix completely dropped a method or
it migrated to a different package, but I think that's less frequent
than a change to the internal implementation.
Has any thought been given to making this change for R 4.3.0?
Duncan Murdoch
On 19/10/2022 3:39 a.m., Martin Maechler wrote:
Duncan Murdoch
on Tue, 18 Oct 2022 15:17:33 -0400 writes:
> 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
Yes, thank you, Duncan!
The binary version of 'builmer' (or also lme4 ?) must have been created
with an older version of Matrix (which did not have the
dgeMatrix_getDiag C code) and the respective maintainer of the
binary builds (*) must rebuild the binary versions of those
Matrix-reverse-dependant packages,
---
*) in this case the macOS ones (both for Intel and ARM Macs)
Martin Maechler
(maintainer of Matrix)
> 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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