Question

DESeq2 Error from Installing a Package

1

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johanna.shen ▴ 10

@johannashen-23496

Last seen 4.4 years ago

Dear Bioconductor team,

I am just getting started and learning about the basics of R. I have installed the package DESeq2 but every time I try to load the library this error shows up:

> 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/3.6/Resources/library/digest/libs/digest.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/digest/libs/digest.so, 6): Symbol not found: ___cxa_uncaught_exceptions
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
  Expected in: /usr/lib/libc++abi.dylib
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib

My Bioconductor is version 3.10 and my R is version 3.6.3. I am using a mac. I would appreciate any help on how to solve this error. Thanks!

deseq2 • 1.3k views

ADD COMMENT • link updated 4.4 years ago by Martin Morgan 25k • written 4.4 years ago by johanna.shen ▴ 10

Kevin Blighe · Answer 1 · 2020-05-09

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Kevin Blighe ★ 4.0k

@kevin

Last seen 5 weeks ago

Republic of Ireland

This does not seem to be an issue with DESeq2, specifically - it looks more like an issue related to the C libraries installed on your machine. Can you provide the output of sessionInfo() and also let us know how you normally install packages? Also, when was DESeq2 last functioning properly?

Edit: if you can, and have time, try upgrading to R 4.0.0 and Bioc 3.11 to see if that resolves it.

ADD COMMENT • link 4.4 years ago Kevin Blighe ★ 4.0k

0

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Thank you for your reply!

The output of:

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.2
Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel  stats4    stats     graphics  grDevices utils    
[7] datasets  methods   base     
other attached packages:
 [1] ggplot2_3.3.0               edgeR_3.28.1               
 [3] limma_3.42.2                SummarizedExperiment_1.16.1
 [5] DelayedArray_0.12.3         BiocParallel_1.20.1        
 [7] matrixStats_0.56.0          Biobase_2.46.0             
 [9] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[11] IRanges_2.20.2              S4Vectors_0.24.4           
[13] BiocGenerics_0.32.0        
loaded via a namespace (and not attached):
 [1] locfit_1.5-9.4         splines_3.6.3         
 [3] lattice_0.20-38        colorspace_1.4-1      
 [5] vctrs_0.2.4            base64enc_0.1-3       
 [7] survival_3.1-8         rlang_0.4.6           
 [9] pillar_1.4.4           withr_2.2.0           
[11] foreign_0.8-75         glue_1.4.0            
[13] RColorBrewer_1.1-2     jpeg_0.1-8.1          
[15] GenomeInfoDbData_1.2.2 lifecycle_0.2.0       
[17] zlibbioc_1.32.0        munsell_0.5.0         
[19] gtable_0.3.0           latticeExtra_0.6-29   
[21] Rcpp_1.0.4.6           acepack_1.4.1         
[23] BiocManager_1.30.10    scales_1.1.0          
[25] backports_1.1.6        checkmate_2.0.0       
[27] XVector_0.26.0         gridExtra_2.3         
[29] png_0.1-7              grid_3.6.3            
[31] tools_3.6.3            bitops_1.0-6          
[33] magrittr_1.5           RCurl_1.98-1.2        
[35] tibble_3.0.1           Formula_1.2-3         
[37] cluster_2.1.0          crayon_1.3.4          
[39] pkgconfig_2.0.3        ellipsis_0.3.0        
[41] Matrix_1.2-18          rstudioapi_0.11       
[43] R6_2.4.1               rpart_4.1-15          
[45] nnet_7.3-12            compiler_3.6.3

DESeq2 has not functioned properly at any point. To install DESeq2 I did the following:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("DESeq2")

Unfortunately I can't upgrade to R 4.0.0 because it's not compatible with my Mac OS.

ADD REPLY • link updated 4.4 years ago by Kevin Blighe ★ 4.0k • written 4.4 years ago by johanna.shen ▴ 10

1

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I am not a Mac user, unfortunately, but an update of your C++ libraries may help. You could start by trying to install / update the Rcpp package: https://cran.r-project.org/web/packages/Rcpp/index.html

Another possibility is to update your OS C++ libraries outside R. That would be via HomeBrew I presume.

Also try to re-install the digest package.

I would also do all of this in a fresh session without any other loaded packages, and after you have restarted your machine.

ADD REPLY • link 4.4 years ago Kevin Blighe ★ 4.0k

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Thank you again for your help! I have reinstalled the Rcpp package and the digest package. Unfortunately, DESeq2 still has the same problem. However, I think I have narrowed down the problem to the digest package. After reinstalling the digest package, I tried to run the library for it, but the following error came up:

install.packages("digest")
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/digest_0.6.25.tgz'
content type 'application/x-gzip' length 246357 bytes (240 KB)
downloaded 240 KB
The downloaded binary packages are in
    /var/folders/dl/b5_0s1fs1_bdj91_q78hlv9m0000gn/T//RtmpwySZ4G/downloaded_packages
library("digest")
Error: package or namespace load failed for ‘digest’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/digest/libs/digest.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/digest/libs/digest.so, 6): Symbol not found: ___cxa_uncaught_exceptions
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
  Expected in: /usr/lib/libc++abi.dylib
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib

When running the library for Rcpp there seems to be no issue. Do you have any advice? Thank you again for your help!

ADD REPLY • link updated 4.4 years ago by Kevin Blighe ★ 4.0k • written 4.4 years ago by johanna.shen ▴ 10

1

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I see. This problem has been reported previously but no concrete solution seems to exist. The next thing to try would be to install the package from source. So, download the tar.gz source file from HERE, and then, in R, do:

install.packages('digest_0.6.25.tar.gz', repos = NULL, type = 'source')

ADD REPLY • link 4.4 years ago Kevin Blighe ★ 4.0k