Error in loading DESeq2

Question

[a.basitkhan1990]

Hi all

I have been using DESeq2 no problem for a while including earlier today

Now, whenever I load it I get the below error message. I tried re-downloading DESeq2 and restarting my computer and R, but no dice.

Any thoughts?

Error: package or namespace load failed for ‘SummarizedExperiment’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Matrix/libs/Matrix.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Matrix/libs/Matrix.so, 0x0006): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <DCE2B2F5-3FA9-326F-9575-E14C849466CD> /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Matrix/libs/Matrix.so
  Reason: tried: '/System/Volumes/Preboot/Cryptexes/OS@rpath/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)
Error: package ‘SummarizedExperiment’ could not be loaded

I also tried to download SummarizedExperiment package, but this did not help load DESeq2.

Additional info:

> sessionInfo(package = NULL)
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] Biobase_2.58.0        MatrixGenerics_1.10.0 matrixStats_0.63.0    GenomicRanges_1.50.2  GenomeInfoDb_1.34.9   IRanges_2.32.0        S4Vectors_0.36.2     
[8] BiocGenerics_0.44.0   sp_1.6-0             

loaded via a namespace (and not attached):
 [1] XVector_0.38.0         zlibbioc_1.44.0        MASS_7.3-58.3          munsell_0.5.0          colorspace_2.1-0       lattice_0.21-8         R6_2.5.1              
 [8] rlang_1.1.0            tools_4.2.2            grid_4.2.2             gtable_0.3.3           KernSmooth_2.23-20     cli_3.6.1              lifecycle_1.0.3       
[15] GenomeInfoDbData_1.2.9 RColorBrewer_1.1-3     bitops_1.0-7           RCurl_1.98-1.12        glue_1.6.2             pheatmap_1.0.12        compiler_4.2.2        
[22] scales_1.2.1          
> 

[rpolicastro]

The error message seems to be complaining about a fortran compiler, which would be a system and not R dependency. Try (re)installing gcc on your computer.

If you're using some debian flavor of linux you could install build-essential which includes gcc and a bunch of other useful compilers.

sudo apt-get update
sudo apt-get install build-essential

[a.basitkhan1990]

Thanks, I tried to re-download gfortran but that did not seem to work

Any other thoughts?

Thanks!

Edit: I use MacOS not linux

[ATpoint]

There is a specific section on CRAN that covers gfortran and other required tools for macOS: https://mac.r-project.org/tools/

Please go through that, be sure that XCode and the gfortran compiler are properly installed as described there.

Answer 1

[a.basitkhan1990]

Thanks all as an update

I think I updated my computer and my Fortran libraries moved

I used this command line code to fix:

locate libgfortran.5.dylib

returns:

/usr/local/gfortran/lib/libgfortran.5.dylib

corrected by:

ln /usr/local/gfortran/lib/libgfortran.5.dylib /usr/local/lib/libgfortran.5.dylib