Hello,

I have just upgraded to R v4.3 (R-4.3.0-x86_64, Intel) and the latest Rstudio release (RStudio-2023.03.0-386.dmg). I have installed BiocManager using the install.packages. Using this package, I have installed DESeq2 from Bioconductor using:

BiocManager::install("DESeq2",version=3.17)

Everything worked absolutely fine. However it looks that I cannot load the package because of GenomicRanges with the following output:

library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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: <FEFA222E-961F-34C6-A76C-85B8D4900B95> /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)
Error: package ‘GenomicRanges’ could not be loaded

This happens in Rstudio, the R console but not in terminal, where DESeq2 will load without any issue. The same applies with other packages like topGO. In both cases, it looks that the path chosen for libR.dylib is wrong (either refering to 4.2 or 4.3) instead of 4.3-x86_64.

sessionInfo( )
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

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Madrid
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.4.2        GenomeInfoDb_1.35.17 IRanges_2.33.1       S4Vectors_0.37.7    
[5] BiocGenerics_0.45.3 

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0        dplyr_1.1.2             blob_1.2.4             
 [4] bitops_1.0-7            fastmap_1.1.1           RCurl_1.98-1.12        
 [7] digest_0.6.31           lifecycle_1.0.3         RSQLite_2.3.1          
[10] magrittr_2.0.3          compiler_4.3.0          rlang_1.1.0            
[13] tools_4.3.0             utf8_1.2.3              data.table_1.14.8      
[16] bit_4.0.5               plyr_1.8.8              withr_2.5.0            
[19] grid_4.3.0              fansi_1.0.4             colorspace_2.1-0       
[22] scales_1.2.1            cli_3.6.1               crayon_1.5.2           
[25] generics_0.1.3          httr_1.4.5              reshape2_1.4.4         
[28] DBI_1.1.3               ape_5.7-1               cachem_1.0.7           
[31] stringr_1.5.0           zlibbioc_1.45.0         parallel_4.3.0         
[34] BiocManager_1.30.20     vctrs_0.6.2             bit64_4.0.5            
[37] glue_1.6.2              gtable_0.3.3            stringi_1.7.12         
[40] munsell_0.5.0           tibble_3.2.1            pillar_1.9.0           
[43] GenomeInfoDbData_1.2.10 R6_2.5.1                lattice_0.21-8         
[46] png_0.1-8               memoise_2.0.1           Rcpp_1.0.10            
[49] nlme_3.1-162            pkgconfig_2.0.3

Note that the BLAS location is wrong in this case, but not from Terminal where the same command yields:

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:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] C/UTF-8/C/C/C/C

time zone: Europe/Madrid
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.3.0

Last, the following woraround seems to do the trick under Rstudio:

system("Rscript -e 'library(DESeq2)'")

Any hints about how to correct this ?

Another workaround was to re-install faulty packages from source. This also requires to re-install dependencies from source. A bit long but works in the end.