After updating lme4 (1.1-12), I'm getting this error when I invoke varComp package.
library(varComp)
Error : object ‘sigma’ is not exported by 'namespace:lme4'
Error: package or namespace load failed for ‘varComp’
Here is my sessionInfo()
sessionInfo()
R version 3.3.0 beta (2016-03-30 r70404)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lme4_1.1-12 Matrix_1.2-4 devtools_1.11.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.4 Formula_1.2-1 roxygen2_5.0.1.9000 magrittr_1.5 cluster_2.0.3
[6] MASS_7.3-45 mutoss_0.1-10 splines_3.3.0 BiocGenerics_0.12.1 mnormt_1.5-4
[11] xtable_1.8-2 colorspace_1.2-6 lattice_0.20-33 R6_2.1.2 quadprog_1.5-5
[16] parallel_3.3.0 broom_0.4.0 latticeExtra_0.6-28 coda_0.18-1 TH.data_1.0-7
[21] withr_1.0.1 MatrixModels_0.4-1 assertthat_0.1 digest_0.6.9 multtest_2.22.0
[26] acepack_1.3-3.3 StroupGLMM_0.1.0 phia_0.2-1 scales_0.4.0 lsmeans_2.23
[31] Hmisc_3.17-3 lmerTest_2.0-30 stats4_3.3.0 survey_3.30-3 munsell_0.4.3
[36] multcomp_1.4-4 minqa_1.2.4 plyr_1.8.3 dplyr_0.4.3.9000 stringr_1.0.0
[41] car_2.1-2 tools_3.3.0 grid_3.3.0 nnet_7.3-12 pbkrtest_0.4-6
[46] nlme_3.1-127 Biobase_2.26.0 gtable_0.2.0 mgcv_1.8-12 quantreg_5.21
[51] psych_1.5.8 plotrix_3.6-1 DBI_0.3.1 survival_2.39-2 gridExtra_2.2.1
[56] ggplot2_2.1.0 tidyr_0.4.1 nloptr_1.0.4 reshape2_1.4.1 RColorBrewer_1.1-2
[61] codetools_0.2-14 rpart_4.1-10 aod_1.3 memoise_1.0.0 sandwich_2.3-4
[66] stringi_1.0-1 estimability_1.1-1 CompQuadForm_1.4.1 mvtnorm_1.0-5 SparseM_1.7
[71] foreign_0.8-66 zoo_1.7-12
The varComp package depends on RLRsim. RLRsim uses the S3 generic sigma, which was moved from lme4 to stats in R 3.3.0. If you use a Windows binary for RLRsim built under R < 3.3.0, then RLRsim will look for sigma in lme4 instead on in stats:
> install.packages("https://cran.r-project.org/bin/windows/contrib/3.2/RLRsim_3.1-2.zip", repos=NULL)
...
package ‘RLRsim’ successfully unpacked and MD5 sums checked
> library(varComp)
Error : object ‘sigma’ is not exported by 'namespace:lme4'
Error: package or namespace load failed for ‘varComp’
If you reinstall RLRsim you should get a recent build and varComp will load:
> install.packages("RLRsim")
...
package ‘RLRsim’ successfully unpacked and MD5 sums checked
...
> library(varComp)
>