Error Information: Hi! I'm relatively new to R, so I might be missing something super obvious here. But since updating RStudio, packages I used to have have disappeared and I'm unable to reinstall them. Here is what happens when I try:
> install.packages("BiodiversityR")
also installing the dependency ‘Rcmdr’
There are binary versions available but the source versions are later:
binary source needs_compilation
Rcmdr 2.6-2 2.7-1 FALSE
BiodiversityR 2.11-3 2.13-1 FALSE
installing the source packages ‘Rcmdr’, ‘BiodiversityR’
trying URL 'https://cran.rstudio.com/src/contrib/Rcmdr_2.7-1.tar.gz'
Content type 'application/x-gzip' length 4817926 bytes (4.6 MB)
==================================================
downloaded 4.6 MB
trying URL 'https://cran.rstudio.com/src/contrib/BiodiversityR_2.13-1.tar.gz'
Content type 'application/x-gzip' length 689008 bytes (672 KB)
==================================================
downloaded 672 KB
* installing *source* package ‘Rcmdr’ ...
** package ‘Rcmdr’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: X11 library is missing: install XQuartz from xquartz.macosforge.org
ERROR: lazy loading failed for package ‘Rcmdr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcmdr’
Warning in install.packages :
installation of package ‘Rcmdr’ had non-zero exit status
ERROR: dependency ‘Rcmdr’ is not available for package ‘BiodiversityR’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BiodiversityR’
Warning in install.packages :
installation of package ‘BiodiversityR’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/n1/p8rtxp4d1lvb0wgmbv2t63740000gn/T/Rtmp3azpQY/downloaded_packages’
The output of running sessionInfo() is as follows:
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 ggsci_2.9 viridis_0.5.1 viridisLite_0.3.0 ggordiplots_0.4.0 glue_1.4.2
[7] factoextra_1.0.7 forcats_0.5.1 stringr_1.3.1 dplyr_1.0.7 purrr_0.3.4 readr_1.3.1
[13] tidyr_1.0.0 tibble_3.1.2 tidyverse_1.2.1 ggplot2_3.3.3 vegan_2.5-2 lattice_0.20-35
[19] permute_0.9-4
loaded via a namespace (and not attached):
[1] tidyselect_1.1.1 haven_2.1.0 colorspace_1.3-2 vctrs_0.3.8 generics_0.0.2 yaml_2.2.0 mgcv_1.8-24
[8] utf8_1.1.4 rlang_0.4.11 pillar_1.6.1 withr_2.1.2 DBI_1.0.0 modelr_0.1.4 lifecycle_1.0.0
[15] munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0 rvest_0.3.4 labeling_0.3 parallel_3.5.1 fansi_0.4.0
[22] broom_0.7.8 Rcpp_1.0.7 scales_1.0.0 backports_1.1.4 jsonlite_1.5 gridExtra_2.3 hms_0.4.2
[29] digest_0.6.15 stringi_1.2.4 ggrepel_0.8.2 grid_3.5.1 cli_1.0.0 tools_3.5.1 magrittr_1.5
[36] cluster_2.0.7-1 crayon_1.3.4 pkgconfig_2.0.2 MASS_7.3-50 ellipsis_0.3.2 Matrix_1.2-14 xml2_1.2.0
[43] lubridate_1.7.4 assertthat_0.2.1 httr_1.4.0 rstudioapi_0.10 R6_2.4.0 nlme_3.1-137 compiler_3.5.1
Can anyone help?