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Any recommendation for calculating Fu and Li's D using RStudio?

I'm currently working on a project that requires me to calculate Fu and Li's D using RStudio. Previously I would use the package PopGenome. However, after I update my RStudio program which leads to me having to re-install every package. Unfortunately, I ran into problem downloading PopGenome again.

So my question is that: is there any other package in R that could calculate Fu and Li's D? and is there any other way to download PopGenome besides using "devtools" and "manual package installation"? I have tried both and fail.

The error is like this.

17 warnings and 12 errors generated.
make: *** [whopgenome/readdnapp.o] Error 1
ERROR: compilation failed for package ‘PopGenome’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PopGenome’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/8f/f796rj315876tvkpmhk_hw980000gn/T//RtmpJ0eJdy/filea8fb7ecf1ba1/PopGenome_2.7.7.tar.gz’ had non-zero exit status

Thank you in advance.

popgenome
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updated by Michael Dondrup Michael Dondrup • written by Chatchapon • Chatchapon

1 answer

I have recently experienced the same, also PopGenome was thrown out of CRAN a while ago. You might get it to work in combination with an older R-version, e.g. using conda. You can try:

micromamba create -n popgenome bioconda::r-popgenome
micromamba activate popgenome

Use whatever conda frontend you like (depending on how much time you have).

Then use the package inside the lagacy R. If you want to stick with RStudio, you can try changing its settings to use the R installation in the new conda environment, however, I have never tried this.

This is the R version I am getting:

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"

And loading the library works.

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written by Michael Dondrup Michael Dondrup

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