DESeq2 won't load
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Entering edit mode
Naomi • 0
@dd97877a
Last seen 20 months ago
United States

I just updated R, RStudio and Bioconductor (sessionInfo at the end). I reinstalled DESeq2 with no error messages. But I cannot load it.

Thanks.

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/4.2-arm64/Resources/library/DESeq2/libs/DESeq2.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/DESeq2/libs/DESeq2.so, 6): Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
  Referenced from: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/DESeq2/libs/DESeq2.so (which was built for Mac OS X 13.0)
  Expected in: /usr/lib/libc++.1.dylib


sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.5

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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    
[6] datasets  methods   base     

other attached packages:
[1] SummarizedExperiment_1.28.0 Biobase_2.58.0             
[3] MatrixGenerics_1.10.0       matrixStats_0.63.0         
[5] GenomicRanges_1.50.2        GenomeInfoDb_1.34.9        
[7] IRanges_2.32.0              S4Vectors_0.36.2           
[9] BiocGenerics_0.44.0        

loaded via a namespace (and not attached):
 [1] KEGGREST_1.38.0        locfit_1.5-9.7        
 [3] lattice_0.20-45        colorspace_2.1-0      
 [5] vctrs_0.5.2            utf8_1.2.3            
 [7] blob_1.2.3             XML_3.99-0.13         
 [9] rlang_1.0.6            pillar_1.8.1          
[11] glue_1.6.2             DBI_1.1.3             
[13] BiocParallel_1.32.5    bit64_4.0.5           
[15] RColorBrewer_1.1-3     GenomeInfoDbData_1.2.9
[17] lifecycle_1.0.3        zlibbioc_1.44.0       
[19] Biostrings_2.66.0      munsell_0.5.0         
[21] gtable_0.3.1           codetools_0.2-19      
[23] memoise_2.0.1          geneplotter_1.76.0    
[25] fastmap_1.1.1          parallel_4.2.2        
[27] AnnotationDbi_1.60.0   fansi_1.0.4           
[29] Rcpp_1.0.10            xtable_1.8-4          
[31] BiocManager_1.30.20    scales_1.2.1          
[33] cachem_1.0.7           DelayedArray_0.24.0   
[35] annotate_1.76.0        XVector_0.38.0        
[37] bit_4.0.5              ggplot2_3.4.1         
[39] png_0.1-8              grid_4.2.2            
[41] cli_3.6.0              tools_4.2.2           
[43] bitops_1.0-7           magrittr_2.0.3        
[45] RCurl_1.98-1.10        RSQLite_2.3.0         
[47] tibble_3.2.0           pkgconfig_2.0.3       
[49] crayon_1.5.2           Matrix_1.5-3          
[51] httr_1.4.5             R6_2.5.1              
[53] compiler_4.2.2        
DESeq2 load • 662 views
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0
Entering edit mode
@mikelove
Last seen 11 hours ago
United States

The issue I believe is that it's built for OS X 13 and you are running 11. You can use an older version of R/DESeq2.

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