lmer() fails in R 4.4 prerelease 2024-03-20 r86162

[GabrielHoffman]

I wouldn't usually raise an issue with a prerelease, but Bioconductor is using it for their devel branch. Bioconductor shows that R crashes when checking my variancePartition package: https://master.bioconductor.org/checkResults/3.19/bioc-LATEST/variancePartition/nebbiolo1-buildsrc.html

library(lme4)
fm1 <- lmer(Reaction ~ Days + (1 | Subject), sleepstudy)

# gives a similar error as in link

> sessionInfo()
R Under development (unstable) (2024-03-20 r86162)
Platform: x86_64-apple-darwin23.2.0
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /Users/gabrielhoffman/Downloads/R-devel/lib/libRblas.dylib 
LAPACK: /usr/local/Cellar/r/4.3.2/lib/R/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] lme4_1.1-35.1 Matrix_1.7-0 

loaded via a namespace (and not attached):
 [1] minqa_1.2.6    MASS_7.3-60.2  compiler_4.4.0 tools_4.4.0    Rcpp_1.0.12   
 [6] splines_4.4.0  nlme_3.1-164   grid_4.4.0     nloptr_2.0.3   boot_1.3-30   
[11] lattice_0.22-6

[bbolker]

I'm 99% certain this is caused by the juxtaposition of Matrix version 1.7.0 and a version of lme4 (1.1-35.1) that was built with an earlier version of Matrix. To replicate this, one would:

• install Matrix 1.6-5
• install lme4 (any recent version) from source
• install Matrix 1.7

lme4 should now fail, as should anything built on it.

Getting everything properly updated when the Matrix ABI changes is a giant headache (see here, here, here, here, here, here, here, here ...)

(for the record this is GH issues 756-759, 763-765, 768 ...)

[GabrielHoffman]

I'm aware of the issue with the Matrix package. I'm just concerned that R.4.4 pre-release with lme4 now fails out of the box. I'm not sure why previous versions didn't fail. Is there something we can do to get the right version of Matrix as the default in the next release?

Gabriel

[jaganmn]

Probably Bioconductor has not rebuilt the library tree on each of its check platforms since Matrix 1.7-0 was "added" to R 4.4. Strictly speaking, they need to rebuild only the reverse LinkingTo of Matrix, which is a list of fewer than 20 packages including lme4.

You can contact the maintainer(s) of the check platforms and have them initiate the necessary rebuilds, pointing them to my notice on the R-package-devel mailing list:

https://stat.ethz.ch/pipermail/r-package-devel/2024q1/010463.html

I'd expect them to do a full rebuild eventually, certainly ahead of the release date. But a nudge might help.

[jaganmn]

https://stat.ethz.ch/pipermail/bioc-devel/2024-March/020303.html

[bbolker]

New version of lme4 is on CRAN now, so this should propagate to Bioconductor soon.

Without digging much further, I would try the Bioconductor developers' forum if you want to figure out the right contact point/protocol for asking how long it will take for this to propagate/explicitly requesting a binary rebuild ...