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!
Thank you for your reply!
The output of:
DESeq2 has not functioned properly at any point. To install DESeq2 I did the following:
Unfortunately I can't upgrade to R 4.0.0 because it's not compatible with my Mac OS.
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.
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:
When running the library for Rcpp there seems to be no issue. Do you have any advice? Thank you again for your help!
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: