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...
UPDATED PACKAGES INSTALLATION:
> 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
locale:
[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
OLD PACKAGES INSTALLATION:
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
locale:
[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