merge (all=T) error

I have two installations of RStudio with each different updates of the packages. On the recent packages I get two errors that I don't have with the previous packages. Can someone tell me what the problem is?

Error 1:

df_lofreq_3_DEL <- merge(df_lofreq_3_DEL, deletions_VAR_df_sub_freq, by.x="VAR_MUT", by.y="lofreq_del", all=T)

Error in if (all.x) all.x <- (nxx <- length(m$x.alone)) > 0L :  the condition has length > 1

Error 2

write.xlsx(T_dfCOVID_3, paste0(path,"/Results/Tables/",date,"Numbering_WW_fasta.xlsx"), rowNames=T)

Error: rowNames must be a logical vector with NAs

I don't understand what is wrong especially because with the older packages it still works...


> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

[1] LC_COLLATE=English_Belgium.utf8  LC_CTYPE=English_Belgium.utf8    LC_MONETARY=English_Belgium.utf8
[4] LC_NUMERIC=C                     LC_TIME=English_Belgium.utf8    

attached base packages:
 [1] stats4    parallel  splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] sqldf_0.4-11            RSQLite_2.3.0           gsubfn_0.7              proto_1.0.0            
 [5] purrr_1.0.1             rlist_0.4.6.2           ape_5.7-1               gdata_2.18.0.1         
 [9] openxlsx_4.2.5          Biostrings_2.64.1       GenomeInfoDb_1.32.4     XVector_0.36.0         
[13] IRanges_2.30.1          S4Vectors_0.34.0        BiocGenerics_0.42.0     viridis_0.6.2          
[17] viridisLite_0.4.1       cowplot_1.1.1           ggsankey_0.0.99999      RColorBrewer_1.1-3     
[21] rjson_0.2.21            lubridate_1.9.2         stringr_1.5.0           optparse_1.7.3         
[25] rnaturalearthdata_0.1.0 rnaturalearth_0.3.2     sf_1.0-10               ggspatial_1.1.7        
[29] betareg_3.1-4           scales_1.2.1            ggrepel_0.9.3           tmaptools_3.1-1        
[33] ggmap_3.0.2             gamlss_5.4-12           nlme_3.1-162            gamlss.dist_6.0-5      
[37] MASS_7.3-58.3           gamlss.data_6.0-2       data.table_1.14.2       dplyr_1.1.0            
[41] reshape2_1.4.4          ggplot2_3.4.1           tidyr_1.3.0            

loaded via a namespace (and not attached):
 [1] colorspace_2.1-0       class_7.3-21           modeltools_0.2-23      dichromat_2.0-0.1      rstudioapi_0.14       
 [6] proxy_0.4-27           farver_2.1.1           bit64_4.0.5            getopt_1.20.3          flexmix_2.3-18        
[11] fansi_1.0.4            R.methodsS3_1.8.2      cachem_1.0.7           knitr_1.42             Formula_1.2-5         
[16] jsonlite_1.8.4         png_0.1-8              R.oo_1.25.0            compiler_4.2.1         httr_1.4.5            
[21] Matrix_1.5-3           fastmap_1.1.1          cli_3.6.0              htmltools_0.5.4        tools_4.2.1           
[26] gtable_0.3.1           glue_1.6.2             GenomeInfoDbData_1.2.8 Rcpp_1.0.9             cellranger_1.1.0      
[31] vctrs_0.5.2            lmtest_0.9-40          lwgeom_0.2-11          xfun_0.37              timechange_0.2.0      
[36] lifecycle_1.0.3        gtools_3.9.4           XML_3.99-0.13          zlibbioc_1.42.0        zoo_1.8-10            
[41] ragg_1.2.5             sandwich_3.0-2         yaml_2.3.7             memoise_2.0.1          gridExtra_2.3         
[46] stringi_1.7.8          e1071_1.7-13           zip_2.2.1              chron_2.3-60           RgoogleMaps_1.4.5.3   
[51] rlang_1.1.0            pkgconfig_2.0.3        systemfonts_1.0.4      bitops_1.0-7           evaluate_0.20         
[56] lattice_0.20-45        labeling_0.4.2         bit_4.0.5              tidyselect_1.2.0       plyr_1.8.7            
[61] magrittr_2.0.3         R6_2.5.1               generics_0.1.3         DBI_1.1.3              pillar_1.8.1          
[66] withr_2.5.0            units_0.8-1            stars_0.6-0            survival_3.5-5         abind_1.4-5           
[71] RCurl_1.98-1.10        sp_1.6-0               nnet_7.3-18            tibble_3.2.0           crayon_1.5.2          
[76] KernSmooth_2.23-20     utf8_1.2.3             rmarkdown_2.20         jpeg_0.1-10            grid_4.2.1            
[81] readxl_1.4.1           blob_1.2.3             digest_0.6.29          classInt_0.4-9         R.utils_2.12.2        
[86] textshaping_0.3.6      munsell_0.5.0          tcltk_4.2.1       


R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

[1] LC_COLLATE=English_United Kingdom.utf8 
[2] LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

attached base packages:
[1] stats4    stats     graphics  grDevices utils    
[6] datasets  methods   base     

other attached packages:
 [1] reshape2_1.4.4      sqldf_0.4-11       
 [3] RSQLite_2.2.18      gsubfn_0.7         
 [5] proto_1.0.0         purrr_0.3.4        
 [7] rlist_0.4.6.2       ape_5.6-2          
 [9] gdata_2.18.0.1      stringr_1.4.0      
[11] openxlsx_4.2.5      RColorBrewer_1.1-3 
[13] tidyr_1.2.0         dplyr_1.0.9        
[15] ggplot2_3.3.6       Biostrings_2.62.0  
[17] GenomeInfoDb_1.30.1 XVector_0.34.0     
[19] IRanges_2.28.0      S4Vectors_0.32.4   
[21] BiocGenerics_0.40.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9             lattice_0.20-45       
 [3] gtools_3.9.3           assertthat_0.2.1      
 [5] digest_0.6.29          utf8_1.2.2            
 [7] chron_2.3-58           R6_2.5.1              
 [9] plyr_1.8.7             evaluate_0.15         
[11] pillar_1.8.0           zlibbioc_1.40.0       
[13] rlang_1.0.4            rstudioapi_0.13       
[15] data.table_1.14.2      blob_1.2.3            
[17] rmarkdown_2.14         RCurl_1.98-1.7        
[19] bit_4.0.4              munsell_0.5.0         
[21] compiler_4.2.1         xfun_0.31             
[23] pkgconfig_2.0.3        htmltools_0.5.3       
[25] tcltk_4.2.1            tidyselect_1.1.2      
[27] tibble_3.1.8           GenomeInfoDbData_1.2.7
[29] fansi_1.0.3            crayon_1.5.1          
[31] withr_2.5.0            bitops_1.0-7          
[33] grid_4.2.1             nlme_3.1-158          
[35] gtable_0.3.0           lifecycle_1.0.1       
[37] DBI_1.1.3              magrittr_2.0.3        
[39] scales_1.2.0           zip_2.2.0             
[41] cachem_1.0.6           cli_3.3.0             
[43] stringi_1.7.8          generics_0.1.3        
[45] vctrs_0.4.1            tools_4.2.1           
[47] bit64_4.0.5            glue_1.6.2            
[49] parallel_4.2.1         fastmap_1.1.0         
[51] yaml_2.3.5             colorspace_2.0-3      
[53] memoise_2.0.1          knitr_1.39    

The errors are consistent with T no longer having the value TRUE but it being a vector with two or more elements. Try substituting TRUE where you have T.

Thank you! That seems to be doing the trick!