Package won't load in Rstudio (but does in R console)

[gs12]

Hello,

I have upgraded my MacOs to Ventura 13.3.1, then Xquartz, before installing R v4.3 (Intel) and associated Rstudio from the posit website. After package installation through the BiocManager tool, it looks that a few packages can't load including GenomicFeatures
Loading required package: GenomicFeatures
Loading required package: GenomicRanges
Error: package or namespace load failed for ‘GenomicRanges’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/libs/XVector.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/libs/XVector.so, 0x0006): Library not loaded: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/libs/XVector.so
Reason: tried: '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no such file), '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no such file), '/usr/local/lib/libR.dylib' (no such file), '/usr/lib/libR.dylib' (no such file, not in dyld cache)
Failed with error: ‘package ‘GenomicRanges’ could not be loaded’

or

Biomart.
require(biomaRt)
Loading required package: biomaRt
Error: package or namespace load failed for ‘biomaRt’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biobase/libs/Biobase.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biobase/libs/Biobase.so, 0x0006): Library not loaded: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib
Referenced from: <738286D7-58BA-3BDB-AE28-2C8F205EB910> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biobase/libs/Biobase.so
Reason: tried: '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no such file), '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no such file), '/usr/local/lib/libR.dylib' (no such file), '/usr/lib/libR.dylib' (no such file, not in dyld cache)

The sessionInfo under Rstudio looks like:
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

Any help to circumvent this issue would be great !
cheers,
G

[EconProf]

I am definitely not an expert but it seems strange to be accessing frameworks for both R 4.3 and R 4.2.

[gs12]

Fully agree but I can't find any explanation for this. It seems to be associated with a few packages only, and this is associated with the Xvector or Biobase dependencies.

[papuco34]

I'm encounteering the same issue. I feel it may have something to do with the BLAS library, which is the only difference I can detect between the R console and Rstudio. I feel the BLAS Rstudio file path does not exist.

(in R console)
BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib

(in Rstudio)
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

[gs12]

Same inconsistency but not sure how it contribues to the issue.

[AlexisW]

Since the problem appears to be with BioConductor packages, maybe try to update BiocManager first, then use it to update all these BioConductor packages (maybe with checkBuilt = TRUE).