[R-meta] Same command works on one machine but not another

Benoît Bediou Beno|t@Bed|ou @end|ng |rom un|ge@ch
Mon Jun 7 07:56:05 CEST 2021

Hi there
I am facing a strange problem and would welcome some help

My colleague is able to run a command that does not work on my machine and we haven’t been able to figure out why

I am pasting below the command lines and then the sessionInfo from my machine and from my colleague’s
Thank you so much for any help you can provide!


The command is its simple as 

## Multilevel model
vcov_mat <- impute_covariance_matrix(es_data$g_var, 
                                       cluster = es_data$Paper,                            
                                       r = 0.8) 
mlma_model<- metafor::rma.mv(g ~ 1, # Intercept only MLMA model
                  V = vcov_mat, 
                  random = ~ 1 | Paper / ES_ID,# NOT WORKING WE COULD ADD COGNITIVE DOMAIN TOO!?
                  # random = list(~ 1 | Paper, ~ 1 | ES_ID),# 
                  # random = ~ 1 | ES_ID,# WORKING
                  sparse = TRUE,
                  data = es_data, 
## Add RVE using clubSandwich
CHE_model <- clubSandwich::coef_test(mlma_model, vcov = "CR2")  

>Error in if (!all(nested)) stop("Random effects are not nested within clustering") : 
  missing value where TRUE/FALSE needed

R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] matrixStats_0.57.0 doMC_1.3.7         iterators_1.0.13   foreach_1.5.1      partitions_1.10-2  DescTools_0.99.38  ggsci_2.9          RColorBrewer_1.1-2 plotly_4.9.2.1    
[10] ggthemes_4.2.0     scales_1.1.1       wesanderson_0.3.6  ggExtra_0.9        ggstatsplot_0.6.5  metafor_2.4-0      Matrix_1.3-2       clubSandwich_0.5.3 robumeta_2.0      
[19] zoo_1.8-9          kableExtra_1.3.1   knitr_1.30         summarytools_0.9.6 plyr_1.8.6         forcats_0.5.0      stringr_1.4.0      dplyr_1.0.3        purrr_0.3.4       
[28] readr_1.4.0        tidyr_1.1.2        tibble_3.1.0       ggplot2_3.3.3      tidyverse_1.3.0    lavaan_0.6-8       data.table_1.13.6  reshape2_1.4.4     pacman_0.5.1      

loaded via a namespace (and not attached):
  [1] coda_0.19-4               multcomp_1.4-15           inline_0.3.16             generics_0.1.0            callr_3.5.1               cowplot_1.1.0            
  [7] TH.data_1.0-10            correlation_0.4.0         webshot_0.5.2             xml2_1.3.2                lubridate_1.7.9.2         httpuv_1.5.4             
 [13] StanHeaders_2.21.0-6      assertthat_0.2.1          WRS2_1.1-0                xfun_0.20                 hms_0.5.3                 evaluate_0.14            
 [19] promises_1.1.1            tidyBF_0.4.0              fansi_0.4.2               dbplyr_2.0.0              readxl_1.3.1              DBI_1.1.0                
 [25] tmvnsim_1.0-2             htmlwidgets_1.5.2         reshape_0.8.8             kSamples_1.2-9            stats4_4.0.4              Rmpfr_0.8-2              
 [31] paletteer_1.2.0           ellipsis_0.3.1            crosstalk_1.1.0.1         selectr_0.4-2             rcompanion_2.3.26         ggpubr_0.4.0             
 [37] backports_1.2.1           V8_3.4.0                  pbivnorm_0.6.0            insight_0.10.0            ggcorrplot_0.1.3          rapportools_1.0          
 [43] RcppParallel_5.0.2        libcoin_1.0-6             vctrs_0.3.6               abind_1.4-5               withr_2.4.1               pryr_0.1.4               
 [49] metaBMA_0.6.5             bdsmatrix_1.3-4           checkmate_2.0.0           prettyunits_1.1.1         fastGHQuad_1.0            mnormt_2.0.2             
 [55] lazyeval_0.2.2            crayon_1.4.1              labeling_0.4.2            pkgconfig_2.0.3           SuppDists_1.1-9.5         nlme_3.1-152             
 [61] statsExpressions_0.6.0    rematch_1.0.1             rlang_0.4.10              lifecycle_1.0.0           miniUI_0.1.1.1            LaplacesDemon_16.1.4     
 [67] MatrixModels_0.4-1        sandwich_3.0-1            mathjaxr_1.0-1            EMT_1.1                   modelr_0.1.8              cellranger_1.1.0         
 [73] tcltk_4.0.4               broomExtra_4.1.0          lmtest_0.9-38             loo_2.3.1                 mc2d_0.1-18               carData_3.0-4            
 [79] boot_1.3-26               reprex_0.3.0              base64enc_0.1-3           processx_3.4.5            viridisLite_0.3.0         PMCMRplus_1.7.0          
 [85] parameters_0.9.0          rootSolve_1.8.2.1         debugme_1.1.0             pander_0.6.3              multcompView_0.1-8        coin_1.3-1               
 [91] rstatix_0.6.0             ggsignif_0.6.0            memoise_1.1.0             magrittr_2.0.1            compiler_4.0.4            rstantools_2.1.1         
 [97] bbmle_1.0.23.1            lme4_1.1-25               cli_2.3.1                 pbapply_1.4-3             ps_1.5.0                  TMB_1.7.18               
[103] Brobdingnag_1.2-6         MASS_7.3-53               mgcv_1.8-33               tidyselect_1.1.0          stringi_1.5.3             highr_0.8                
[109] yaml_2.2.1                ggrepel_0.8.2             bridgesampling_1.0-0      grid_4.0.4                polynom_1.4-0             tools_4.0.4              
[115] lmom_2.8                  rio_0.5.16                rstudioapi_0.13           foreign_0.8-81            gridExtra_2.3             ipmisc_4.1.0             
[121] gld_2.6.2                 pairwiseComparisons_3.1.0 farver_2.1.0              RcppZiggurat_0.1.6        digest_0.6.27             shiny_1.5.0              
[127] nortest_1.0-4             BWStest_0.2.2             Rcpp_1.0.6                car_3.0-10                broom_0.7.3.9000          ez_4.4-0                 
[133] BayesFactor_0.9.12-4.2    performance_0.5.1         metaplus_0.7-11           later_1.1.0.1             httr_1.4.2                rsconnect_0.8.16         
[139] effectsize_0.4.0          colorspace_2.0-0          rvest_0.3.6               fs_1.5.0                  splines_4.0.4             statmod_1.4.35           
[145] rematch2_2.1.2            expm_0.999-5              Exact_2.1                 xtable_1.8-4              gmp_0.6-1                 jsonlite_1.7.2           
[151] nloptr_1.2.2.2            rstan_2.21.2              Rfast_2.0.1               zeallot_0.1.0             modeltools_0.2-23         R6_2.5.0                 
[157] broom.mixed_0.2.6         pillar_1.5.1              htmltools_0.5.1           mime_0.9                  DT_0.16                   glue_1.4.2               
[163] fastmap_1.0.1             minqa_1.2.4               class_7.3-18              codetools_0.2-18          pkgbuild_1.2.0            mvtnorm_1.1-1            
[169] utf8_1.2.1                lattice_0.20-41           numDeriv_2016.8-1.1       curl_4.3                  gtools_3.8.2              magick_2.5.2             
[175] logspline_2.1.16          zip_2.1.1                 openxlsx_4.2.3            survival_3.2-7            rmarkdown_2.6             munsell_0.5.0            
[181] e1071_1.7-4               haven_2.3.1               gtable_0.3.0              bayestestR_0.7.5         

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DescTools_0.99.37  ggsci_2.9          RColorBrewer_1.1-2 plotly_4.9.3       ggthemes_4.2.0     scales_1.1.1       wesanderson_0.3.6  ggExtra_0.9       
 [9] ggstatsplot_0.7.1  metafor_2.5-57     Matrix_1.2-18      clubSandwich_0.5.0 robumeta_2.0       zoo_1.8-8          kableExtra_1.1.0   knitr_1.29        
[17] summarytools_0.9.6 plyr_1.8.6         forcats_0.5.0      stringr_1.4.0      dplyr_1.0.0        purrr_0.3.4        readr_1.3.1        tidyr_1.1.0       
[25] tibble_3.0.3       ggplot2_3.3.3      tidyverse_1.3.0    lavaan_0.6-8       data.table_1.13.0  reshape2_1.4.4     pacman_0.5.1      

loaded via a namespace (and not attached):
  [1] readxl_1.3.1              pairwiseComparisons_3.1.3 backports_1.1.8           selectr_0.4-2             lazyeval_0.2.2            splines_4.0.2            
  [7] gmp_0.6-2                 kSamples_1.2-9            ipmisc_6.0.0              pryr_0.1.4                digest_0.6.25             SuppDists_1.1-9.5        
 [13] htmltools_0.5.0           magick_2.5.0              fansi_0.4.1               magrittr_1.5              checkmate_2.0.0           memoise_2.0.0            
 [19] paletteer_1.3.0           modelr_0.1.8              matrixStats_0.57.0        sandwich_2.5-1            colorspace_1.4-1          blob_1.2.1               
 [25] rvest_0.3.6               ggrepel_0.8.2             haven_2.3.1               xfun_0.16                 tcltk_4.0.2               crayon_1.3.4             
 [31] jsonlite_1.7.0            Exact_2.0                 zeallot_0.1.0             glue_1.4.1                gtable_0.3.0              webshot_0.5.2            
 [37] MatrixModels_0.4-1        statsExpressions_1.0.0    Rmpfr_0.8-3               rapportools_1.0           mvtnorm_1.1-1             DBI_1.1.0                
 [43] PMCMRplus_1.9.0           miniUI_0.1.1.1            Rcpp_1.0.5                viridisLite_0.3.0         xtable_1.8-4              performance_0.4.8        
 [49] tmvnsim_1.0-2             stats4_4.0.2              htmlwidgets_1.5.3         httr_1.4.2                ellipsis_0.3.1            farver_2.0.3             
 [55] pkgconfig_2.0.3           reshape_0.8.8             multcompView_0.1-8        dbplyr_1.4.4              labeling_0.3              tidyselect_1.1.0         
 [61] rlang_0.4.7               later_1.1.0.1             ggcorrplot_0.1.3          effectsize_0.4.4          munsell_0.5.0             cellranger_1.1.0         
 [67] tools_4.0.2               cachem_1.0.4              cli_2.0.2                 generics_0.0.2            broom_0.7.5               mathjaxr_1.0-1           
 [73] evaluate_0.14             fastmap_1.0.1             BWStest_0.2.2             yaml_2.2.1                rematch2_2.1.2            fs_1.4.2                 
 [79] pander_0.6.3              WRS2_1.1-1                pbapply_1.4-3             nlme_3.1-148              mime_0.9                  xml2_1.3.2               
 [85] correlation_0.6.0         compiler_4.0.2            rstudioapi_0.11           ggsignif_0.6.1            reprex_0.3.0              pbivnorm_0.6.0           
 [91] stringi_1.4.6             highr_0.8                 parameters_0.12.0         lattice_0.20-41           vctrs_0.3.2               pillar_1.4.6             
 [97] lifecycle_0.2.0           mc2d_0.1-18               insight_0.13.2            httpuv_1.5.4              patchwork_1.1.1           R6_2.4.1                 
[103] promises_1.1.1            BayesFactor_0.9.12-4.2    codetools_0.2-16          boot_1.3-25               MASS_7.3-51.6             gtools_3.8.2             
[109] assertthat_0.2.1          withr_2.2.0               mnormt_2.0.1              expm_0.999-5              mgcv_1.8-31               bayestestR_0.8.2         
[115] parallel_4.0.2            hms_0.5.3                 grid_4.0.2                coda_0.19-3               rmarkdown_2.3             shiny_1.5.0              
[121] lubridate_1.7.9           base64enc_0.1-3     

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