Library Error using DESeq2 in R
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
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2 answers
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.
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This has been discussed on bioconductor:
https://support.bioconductor.org/p/9141859/
detailing the gfortran issue...
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