Dear all,

I am installing the usual packages (edger, rtracklayer .., other packages) on a Mac M1 running Monterrey 12.5 OS, and I do encounter the following two issues :

1. I can not download the binaries for these packages, the message being :

"Warning: unable to access index for repository 

https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL

'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Package

which is only available in source form, and may need compilation of C/C++/Fortran: ‘edgeR’"

1. When I do compile edgeR from source, I am getting the following error messages :

a. shall I setup .libPaths() to a personal folder only :

 .libPaths("/Users/tanasab/Desktop/SOFTWARE/R")

the error message is :

The downloaded source packages are in
    ‘/private/var/folders/lx/q0dsb0_n2s3gx5jyzk2wkxwr0000gn/T/RtmpgerV9u/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library

b. OK, it is expected, but shall I setup .libPaths() to a personal folder + OS folders,

.libPaths(c("/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library", 
"/Users/tanasab/Library/R/arm64/4.2/library", 
"/Users/tanasab/Desktop/SOFTWARE/R"))

the error message is :

Warning in install.packages(...) :
  'lib = "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) 

and at the end of the compilation :

Installation paths not writeable, unable to update packages
  path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
  packages:
    cluster, foreign, MASS, Matrix, nlme, nnet, survival
Warning message:
In install.packages(...) :
  installation of package ‘edgeR’ had non-zero exit status

1. The R version that I am using is 4.2.1

2. I have checked many previous postings for example :

http://yiqingxu.org/public/BigSurError.pdf

those solutions did not work for me.

Thank you for your help,

Bogdan

ps : The R Version :

> R.Version()
$platform
[1] "aarch64-apple-darwin20"

$arch
[1] "aarch64"

$os
[1] "darwin20"

$system
[1] "aarch64, darwin20"

$status
[1] ""

$major
[1] "4"

$minor
[1] "2.1"

$year
[1] "2022"

$month
[1] "06"

$day
[1] "23"

$`svn rev`
[1] "82513"

$language
[1] "R"

$version.string
[1] "R version 4.2.1 (2022-06-23)"

$nickname
[1] "Funny-Looking Kid"