I am unable to get a summary() of a lme4 model. Whenever I run the summary function of an lme4 object, I get the error:
Error in diag(from, names = FALSE) : object 'unpackedMatrix_diag_get' not found
I am unable to trace the issue, so have written code below that generates the error and included all the packages that are loaded directly into the code. Note. the model won't converge, but I get the same error for converged models.
# packages
library(tidyverse)
library(kableExtra)
library(psych)
library(lavaan)
library(semPlot)
library(qpcR)
library(brms)
library(lme4)
partid <- c("A","B","C","D","A","B","C","D")
count <- c(13, 41, 33, 37, 60, 41, 41, 39)
side <- c("L","L","L","L","R","R","R","R")
dat <- data.frame(partid, count, side)
mod <- lme4::lmer(count~ side + (1 | partid))
summary(mod)
Here is the output from sessionInfo():
R version 4.3.3 (2024-02-29)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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: Europe/London
tzcode source: internal
attached base packages:
stats
graphics
grDevices
utils
datasets
methods
base
other attached packages:
lme4_1.1-35.3
brms_2.21.0
Rcpp_1.0.12
qpcR_1.4-1
Matrix_1.6-5
robustbase_0.99-2
rgl_1.3.1
minpack.lm_1.2-4
MASS_7.3-60.0.1
semPlot_1.1.6
lavaan_0.6-17
psych_2.4.3
kableExtra_1.4.0
lubridate_1.9.3
forcats_1.0.0
stringr_1.5.1
dplyr_1.1.4
purrr_1.0.2
readr_2.1.5
tidyr_1.3.1
tibble_3.2.1
ggplot2_3.5.0
tidyverse_2.0.0
loaded via a namespace (and not attached):
tensorA_0.36.2.1
rstudioapi_0.16.0
jsonlite_1.8.8
magrittr_2.0.3
nloptr_2.0.3
rmarkdown_2.26
vctrs_0.6.5
minqa_1.2.6
base64enc_0.1-3
rstatix_0.7.2
htmltools_0.5.8.1
distributional_0.4.0
broom_1.0.5
Formula_1.2-5
StanHeaders_2.32.6
htmlwidgets_1.6.4
plyr_1.8.9
igraph_2.0.3
lifecycle_1.0.4
pkgconfig_2.0.3
R6_2.5.1
fastmap_1.1.1
OpenMx_2.21.11
digest_0.6.35
fdrtool_1.2.17
colorspace_2.1-0
Hmisc_5.1-2
ggpubr_0.6.0
fansi_1.0.6
timechange_0.3.0
abind_1.4-5
compiler_4.3.3
withr_3.0.0
glasso_1.11
htmlTable_2.4.2
backports_1.4.1
inline_0.3.19
carData_3.0-5
QuickJSR_1.1.3
pkgbuild_1.4.4
ggsignif_0.6.4
corpcor_1.6.10
gtools_3.9.5
loo_2.7.0
tools_4.3.3
pbivnorm_0.6.0
foreign_0.8-86
zip_2.3.1
nnet_7.3-19
glue_1.7.0
quadprog_1.5-8
nlme_3.1-164
lisrelToR_0.3
grid_4.3.3
checkmate_2.3.1
cluster_2.1.6
reshape2_1.4.4
generics_0.1.3
gtable_0.3.4
tzdb_0.4.0
data.table_1.15.4
hms_1.1.3
xml2_1.3.6
car_3.1-2
utf8_1.2.4
sem_3.1-15
pillar_1.9.0
rockchalk_1.8.157
posterior_1.5.0
splines_4.3.3
lattice_0.22-5
kutils_1.73
tidyselect_1.2.1
pbapply_1.7-2
knitr_1.45
gridExtra_2.3
svglite_2.1.3
stats4_4.3.3
xfun_0.43
bridgesampling_1.1-2
qgraph_1.9.8
arm_1.14-4
matrixStats_1.3.0-9001
DEoptimR_1.1-3
rstan_2.32.6
stringi_1.8.3
yaml_2.3.8
boot_1.3-29
evaluate_0.23
codetools_0.2-19
mi_1.1
buildmer_2.11
cli_3.6.2
RcppParallel_5.1.7
rpart_4.1.23
xtable_1.8-4
systemfonts_1.0.6
munsell_0.5.1
coda_0.19-4.1
png_0.1-8
XML_3.99-0.16.1
parallel_4.3.3
rstantools_2.4.0
jpeg_0.1-10
bayesplot_1.11.1
Brobdingnag_1.2-9
viridisLite_0.4.2
mvtnorm_1.2-4
scales_1.3.0
openxlsx_4.2.5.2
rlang_1.1.3
mnormt_2.1.1
I have tried resolving by reinstalling lme4 and Matrix in case they were causing this but no luck.
I believe it's the buildmer package that is out of sync with Matrix. This previously came up on the lme4 issues list and was stated to be a problem with buildmer. There doesn't seem to be anything on the buildmer issues list ...
I ran the following code from a clean R session:
library(lme4)
m1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy)
summary(m1)
library(buildmer)
m2 <- buildmer(Reaction ~ Days + (1|Subject), sleepstudy)
which ended with
Error in diag(from, names = FALSE) : object 'unpackedMatrix_diag_get' not found
Error in tmp@call : no applicable method for@applied to an object of class "try-error"
I then reinstalled buildmer from source, restarted R, and was able to run the example without a problem.
Your example also works for me, after reinstalling buildmer. (I didn't try it before reinstalling and am too lazy to go back and install a mismatched Matrix/buildmer pair to see if I can replicate the error ...)
It's not really clear to me how you got buildmer loaded (I see it in your sessionInfo() output, but it doesn't appear when I load just the packages you specified in your example ...)