Hi, when I try to install Bioconductor package 'affy' Experience below error\ May I know how do I fix this? I'm currently using R4.2.2 on MacBook Air, M1\ R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"\ Copyright (C) 2022 The R Foundation for Statistical Computing\ Platform: aarch64-apple-darwin20 (64-bit)
'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 tore-install: 'affy'
So then i try to use 'force=TRUE', the installation was done\
BiocManager::install("affy",force = TRUE)
'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) 'affy'\ trying URL 'http. s://bio. conductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/affy_1.76.0.tgz' \ Content type 'application/x-gzip' length 2072159 bytes (2.0 MB)\ downloaded 2.0 MB
The downloaded binary packages are in\ /var/folders/g3/fc92jylx5m53g0sxy2g0pq100000gn/T//RtmpODbIF8/downloaded_packages
But the library(affy) still could not be call\
Error: package or namespace load failed for ‘affy’ in dyn.load(file, DLLpath = DLLpath, ...):\ unable to load shared object \ '/Library/Frameworks/R.framework/Versions/4.2arm64/Resources/library/preprocessCore/libs/preprocessCore.so': dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/libs/preprocessCore.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/preprocessCore/libs/preprocessCore.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)
Did you restart R after performing the installation?
If that does not solve your problem you will likely have to delete homebrew components on your mac.
see the documentation at homebrew's github repo
This looks like a linking issue with
libgfortran.5.dylib. I'll see if we need to fix the binary to get it working.
There's a new binary available for
preprocessCore. Try installing