Hi Bioconductor team,

I noticed an install issue with the current DESeq2 1.40.0 binary build on macOS x86. The package is failing to load unless gfortran is installed at /opt/gfortran, from the macOS tools installer. Weirdly I'm only seeing this error inside of RStudio but not R running in the terminal.

BiocManager::install("DESeq2")
library(DESeq2)

Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library/DESeq2/libs/DESeq2.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library/DESeq2/libs/DESeq2.so, 0x0006): Library not loaded: /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib
  Referenced from: <C3CB82F6-4A9D-3B4B-A615-F82E978977AC> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library/DESeq2/libs/DESeq2.so
  Reason: tried: '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib' (no such file), '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)
Backtrace:
    ▆
 1. └─base::library(DESeq2)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)

Session info:

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: America/New_York
tzcode source: internal

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

other attached packages:
 [1] SummarizedExperiment_1.30.0 Biobase_2.60.0             
 [3] MatrixGenerics_1.12.0       matrixStats_0.63.0         
 [5] GenomicRanges_1.52.0        GenomeInfoDb_1.36.0        
 [7] IRanges_2.34.0              S4Vectors_0.38.0           
 [9] BiocGenerics_0.46.0         AcidDevTools_0.6.5         

loaded via a namespace (and not attached):
 [1] Matrix_1.5-4            gtable_0.3.3           
 [3] dplyr_1.1.2             compiler_4.3.0         
 [5] tidyselect_1.2.0        Rcpp_1.0.10            
 [7] bitops_1.0-7            parallel_4.3.0         
 [9] later_1.3.0             scales_1.2.1           
[11] BiocParallel_1.34.0     lattice_0.21-8         
[13] ggplot2_3.4.2           R6_2.5.1               
[15] XVector_0.40.0          generics_0.1.3         
[17] tibble_3.2.1            DelayedArray_0.25.0    
[19] munsell_0.5.0           GenomeInfoDbData_1.2.10
[21] pillar_1.9.0            rlang_1.1.0            
[23] utf8_1.2.3              cli_3.6.1              
[25] magrittr_2.0.3          zlibbioc_1.46.0        
[27] locfit_1.5-9.7          grid_4.3.0             
[29] rstudioapi_0.14         lifecycle_1.0.3        
[31] vctrs_0.6.2             glue_1.6.2             
[33] codetools_0.2-19        RCurl_1.98-1.12        
[35] fansi_1.0.4             colorspace_2.1-0       
[37] pkgconfig_2.0.3         tools_4.3.0

Best, Mike

The RStudio vs R thing is really puzzling. Definitely they are using same R version?

Edit: note that Mac binaries are being re-generated and will be available shortly, fixing this directly without users needing to customize anything locally.

Have you installed gfortran 12.2 from https://mac.r-project.org/tools/

That should fix Michael x2's problems. Although I do think that binaries are supposed to statically link against gfortran so that users should not have to install this package.

For Cynthia, it does not seem to be gfortran related, but I am a bit perplexed about why it is trying to load 4.2/Resources/lib/libR.dylib (wrong version).