Library Error using DESeq2 in R

Question

[Artjola]

Hello, I am using the latest version of Bioconductor 13.6, R 4.2.1 (R console). I managed to install BiocManager, but when I try to install DESeq2, it shows at the end:

Warning messages:

1: package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'DESeq2' 
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘BiocParallel’ had non-zero exit status

> library("DESeq2")
Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/user/Library/R/arm64/4.2/library/genefilter/libs/genefilter.so':
  dlopen(/Users/user/Library/R/arm64/4.2/library/genefilter/libs/genefilter.so, 0x0006): Library not loaded: /opt/R/arm64/gfortran/lib/libgfortran.5.dylib
  Referenced from: <25917248-EA0A-30AB-BC08-38790335B68D> /Users/user/Library/R/arm64/4.2/library/genefilter/libs/genefilter.so
  Reason: tried: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

Please, can anybody help me with that? I have been trying heavily but nothing is working. I am using Mac M1

Answer 1

[Matthias Zepper]

It seems you are missing a Fortran compiler (some R functions are implemented in Fortran). You can test if which gcc returns something, but I guess not. In that case, try brew install gfortran and then try to reinstall the BiocParallel package in R.

Answer 2

[niels]

This has been discussed on bioconductor:

https://support.bioconductor.org/p/9141859/

detailing the gfortran issue...