scenario
Hi, when I try to install Bioconductor package 'affy' Experience below error
input
BiocManager::install("affy")
output
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://c r a n .rst ud io. com/ ## The space was created to prevent a link
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: 'affy'
scenario
So then i try to use 'force=TRUE', the installation was done, but still could not call the library
input*
BiocManager::install("affy",force = TRUE)
output*
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https. ://cran. rstudio. com/ ## The space was created to prevent a link
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. . o rg/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/affy_1.76.0.tgz' ## The space was created to prevent a link
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
scenario*
but the library(affy) still could not be call
input*
library(affy)
output*
Error: package or namespace load failed for ‘affy’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/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)
May I know how do I fix above error? 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)