emmeans maybe a dependency not a suggested package?

[davidjanke]

Hi afex dev team,

We tried to install the afex package but that failed with the following error:
Error: package or namespace load failed for ‘afex’: .onLoad failed in loadNamespace() for 'afex', details: call: NULL error: '.emm_register' is not an exported object from 'namespace:emmeans'

Installing package lme4 mannually (as it was not installed as a dependency automatically) did not help, but installing emmeans did solve the issue, though it is listed as a suggested package.

Versions currently installed:
R 3.4.4
afex 0.25.1
lme4 1.1.21
emmeans 1.4.2
Running on Ubuntu 18.04.3 LTS

[singmann]

Hmm, that is probably due to an old R version. I cannot replicate with R 3.6.1 as shown below. And I fear there is not a lot of incentive to try to get this to work with such an old R version.

> library("afex")
Loading required package: lme4
Loading required package: Matrix
Registered S3 methods overwritten by 'car':
  method                          from
  influence.merMod                lme4
  cooks.distance.influence.merMod lme4
  dfbeta.influence.merMod         lme4
  dfbetas.influence.merMod        lme4
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'KR', 'S', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- NEWS: library('emmeans') now needs to be called explicitly!
- Get and set global package options with: afex_options()
- Set orthogonal sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************

Attaching package: ‘afex’

The following object is masked from ‘package:lme4’:

    lmer

> library("emmeans")
Error in library("emmeans") : there is no package called ‘emmeans’
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_Switzerland.1252  LC_CTYPE=English_Switzerland.1252   
[3] LC_MONETARY=English_Switzerland.1252 LC_NUMERIC=C                        
[5] LC_TIME=English_Switzerland.1252    

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

other attached packages:
[1] afex_0.25-1   lme4_1.1-21   Matrix_1.2-17

loaded via a namespace (and not attached):
 [1] zip_2.0.4           Rcpp_1.0.2          plyr_1.8.4          compiler_3.6.1      pillar_1.4.2       
 [6] cellranger_1.1.0    nloptr_1.2.1        forcats_0.4.0       tools_3.6.1         boot_1.3-22        
[11] zeallot_0.1.0       gtable_0.3.0        tibble_2.1.3        nlme_3.1-140        lattice_0.20-38    
[16] pkgconfig_2.0.2     rlang_0.4.0         openxlsx_4.1.0.1    rstudioapi_0.10     parallel_3.6.1     
[21] curl_4.0            haven_2.1.1         rio_0.5.16          stringr_1.4.0       dplyr_0.8.3        
[26] vctrs_0.2.0         hms_0.5.1           tidyselect_0.2.5    lmerTest_3.1-0      grid_3.6.1         
[31] glue_1.3.1          data.table_1.12.6   R6_2.4.0            readxl_1.3.1        foreign_0.8-71     
[36] minqa_1.2.4         carData_3.0-2       reshape2_1.4.3      purrr_0.3.2         ggplot2_3.2.1      
[41] car_3.0-4           magrittr_1.5        scales_1.0.0        backports_1.1.4     MASS_7.3-51.4      
[46] splines_3.6.1       assertthat_0.2.1    abind_1.4-5         colorspace_1.4-1    numDeriv_2016.8-1.1
[51] stringi_1.4.3       lazyeval_0.2.2      munsell_0.5.0       crayon_1.3.4    

[davidjanke]

Thanks for checking it out. If I have some time, I'll try to narrow it down if it is an issue with the old R version.

[natsrm]

Hi guys,
Just letting you know I just tried installing afex with R version 3.5.0 and this issue also happened to me. I re-installed with install.packages("afex", dependencies = T) and package emmeans was one of the many installed. If I try to load afex without loading emmeans, it still gives the same error, and if I try to load emmeans I get the following:
library(emmeans)
Error: package or namespace load failed for ‘emmeans’ in get(method, envir = home): lazy-load database 'C:/Users/Natii/Documents/R/win-library/3.5/emmeans/R/emmeans.rdb' is corrupt
In addition: Warning messages:
1: package ‘emmeans’ was built under R version 3.5.3
2: In get(method, envir = home) : internal error -5 in R_decompress1
So I guess the problem is R's version, as emmeans was built under version 3.5.3...

[singmann]

Can you please post the full output of sessionInfo() for the situation in which the error occurs?

[natsrm]

I suppose this is the important part, or do you actually need all of it?
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

[singmann]

the package currently works without emmeans (even though it is recommended for post-hoc analyses)