Hi, i have problem for DESeq2 install. I have change PC (windows) for new macbook pro (chip M1 Max). I have not problem bioconductor install. My results : in put

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.14")

out put

> if (!require("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install(version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)

in put

BiocManager::install("DESeq2")
library("DESeq2")

out put

> BiocManager::install("DESeq2")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'DESeq2'
also installing the dependencies ‘AnnotationDbi’, ‘annotate’, ‘genefilter’, ‘geneplotter’, ‘RcppArmadillo’

Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘genefilter’ ‘DESeq2’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.1/RcppArmadillo_0.10.8.1.0.tgz'
Content type 'application/x-gzip' length 1728276 bytes (1.6 MB)
==================================================
downloaded 1.6 MB


The downloaded binary packages are in
    /var/folders/2h/43w_ny0s7zj2hjdp5tn1bjjh0000gn/T//Rtmp5e9i3r/downloaded_packages
installing the source packages ‘AnnotationDbi’, ‘annotate’, ‘genefilter’, ‘geneplotter’, ‘DESeq2’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz'
Content type 'application/x-gzip' length 4330396 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/annotate_1.72.0.tar.gz'
Content type 'application/x-gzip' length 1723060 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/genefilter_1.76.0.tar.gz'
Content type 'application/x-gzip' length 807639 bytes (788 KB)
==================================================
downloaded 788 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/geneplotter_1.72.0.tar.gz'
Content type 'application/x-gzip' length 1437803 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DESeq2_1.34.0.tar.gz'
Content type 'application/x-gzip' length 2088431 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘rlang’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘AnnotationDbi’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/annotate’
ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/genefilter’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/DESeq2’

The downloaded source packages are in
    ‘/private/var/folders/2h/43w_ny0s7zj2hjdp5tn1bjjh0000gn/T/Rtmp5e9i3r/downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
7: In .inet_warning(msg) :
  installation of package ‘annotate’ had non-zero exit status
8: In .inet_warning(msg) :
  installation of package ‘genefilter’ had non-zero exit status
9: In .inet_warning(msg) :
  installation of package ‘geneplotter’ had non-zero exit status
10: In .inet_warning(msg) :
  installation of package ‘DESeq2’ had non-zero exit status
> library("DESeq2")
Error in library("DESeq2") : there is no package called ‘DESeq2’

For mme the problem it is can not connexion at URL. I watched the URL and is not defined...

I'm use 4.1.2 R version and i installed on my mac docker and Xquartz.

thanks for your help

I was having issues getting DESeq2 running as well and it ended up being that I had to install gfortran in order to get packages like genefilter working which made it possible to get DESeq2 running correctly... I installed gfortran from gcc: https://gcc.gnu.org/wiki/GFortranBinaries

and then followed advice from here: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran

to get R to access the gfortran install by creating a Makevars (~/.R/Makevars) file with the following:

# manual gfortran install from gcc
FLIBS   =-L/usr/local/gfortran/lib
F77     = /usr/local/gfortran/bin/gfortran
FC      = /usr/local/gfortran/bin/gfortran

and from there I was able to install the bioconductor packages that were breaking on the libgfortran loading... (I had to create the .R directory in my user location and create the Makevars file but after restarting my R instance it worked)...

Can you search the support site for the posts on how to install Bioconductor on M1.

You can search by adding "site:support.bioconductor.org" when using Google.