EdgeR installation in Mac 1 Pro (M1 chip) using Studio
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Entering edit mode
11 weeks ago
ralbero ▴ 10

Good morning,

I tried to install edgeR in my Mac M1 laptop. In Rstudio, I do:

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

And I receive the message:

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) Warning message: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'edgeR'

So, I try again with force=T;

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("edgeR", force=T)

And I get:

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) Installing package(s) 'edgeR' trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/edgeR_3.40.0.tgz' Content type 'application/x-gzip' length 2314825 bytes (2.2 MB)

downloaded 2.2 MB

The downloaded binary packages are in /var/folders/hl/h48_66xn2xzb1d3x29d3dpwr0000gn/T//RtmpGcQntR/downloaded_packages

However, when I try to get the library:

Error: package or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so': dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so, 0x0006): Library not loaded: /opt/R/arm64/gfortran/lib/libgfortran.5.dylib Referenced from: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so Reason: tried: '/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)

On the other hand, this is not happening when I try other packages (for example, this one: ChIPQC)

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

BiocManager::install("ChIPQC",force=T)

Do you have any clue/ any help?

Thanks

edger r studio Mac • 473 views
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Entering edit mode

Are you using R for ARM64 or for Intel?

This may be useful: https://support.bioconductor.org/p/9138121/

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Entering edit mode
11 weeks ago

Had a few people run into this here, think the solution was installing gfortran.

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