MareesAT / GWA_tutorial

A comprehensive tutorial about GWAS and PRS

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problem solved: download site of qqman

Clemence50421 opened this issue · comments

**** Problem solved ****
As stated in the tutorial, changing the CRAN mirror to your own VPN would solve this problem.
**** Problem solved ****

I got an error when downloading qqman package from http://cran.cnr.berkeley.edu/ (which is written in Manhattan_plot.R of the tutorial), and I believe it is because there is problem in the download source.

I'm using R version 4.1.1 (2021-08-10), which meets the prerequisite of qqman installation.

Could you guide me to the currently available download site of qqman package? Thank you!

--------- My input ----------
(plink) Rscript --no-save Manhattan_plot.R

--------- Full text of the error ----------
Warning: unable to access index for repository http://cran.cnr.berkeley.edu/src/contrib:
cannot open URL 'http://cran.cnr.berkeley.edu/src/contrib/PACKAGES'
Warning: unable to access index for repository http://cran.cnr.berkeley.edu/bin/macosx/contrib/4.1:
cannot open URL 'http://cran.cnr.berkeley.edu/bin/macosx/contrib/4.1/PACKAGES'
Warning message:
package ‘qqman’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Error in library("qqman", lib.loc = "~") :
there is no package called ‘qqman’
Execution halted