Thank you Hervé Pagès for your reply and Happy New Year!

Regarding why am I re-installed the packages, long story short, I have a project in Rmarkdown which I was working on it for the last six months. The project (under version control ) uses different packages from bioconductor. I took a week break from the project at the end of December, then came back to it. At the time I came back to it, I didn't upgrade to Big Sur, was using macOS Catalina.

The first problem I encountered was When I tried to load ggiob, using library (ggbio), my console will show this message:

Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

then, the console will stuck forever, even after pressing Ctrl + C unless restarted again. So, I tried to clear the cache and remove ggbio from RFrameworks and re-install it again but the same problem occurred. So, I removed RStudio, R, all packages and re-install them but the same problem occurred (this time also had a problem installing TxDb.Hsapiens.UCSC.hg19.knownGene). I tried to solve the problem myself for a few days and googled to look if anyone having the same problem, found this forum, so I posted for the first time my two questions (regarding ggbio and TxDb.Hsapiens.UCSC.hg19.knownGene).

I tried it on my Sister's Mac but unfriendly I encountered the same problem. Please note my sister's mac doesn't have R, so installed R and then just installed ggbio and TxDb.Hsapiens.UCSC.hg19.knownGene from R without RStudio but had a problem with both packages and this is the sessionInfo() from my sister's Mac:

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.1

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

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.0.3

Then. I upgraded to macOS Big Sur and tried again to install R and the packages but no luck.

To replicate the problem: Just install R and then run:

BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene") but it will reach

* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

and I left it for 18 hours but it never continues, it only pause indefinitely.

Then, you can also try (as I mentioned in a different question):

BiocManager::install(`ggbio`)
library(ggbio)

Please note that ggbio is installed fine but once it's loaded with library(ggbio), it shows:

Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

and the console then stuck forever. All this without using RStudio and I don't recall changes in my local machine that might affect the installation this much.

To summarise, I re-installed the packages because of the problem I was having with ggbio. Thank you again for your patience.