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rmacosopenmpseurat

R package 'Seurat' crashes with openMP error

I've been stuck in this problem for a while. I've installed a package Seurat on my Mac (Catelina), but when calling this library, R will crash with the following message:

OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized. OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/ Abort trap: 6

I googled around, and it seems to be a MacOS problem, and might be conda related. But I do not have conda on my machine.

I also brewed llvm, didn't work.

Please help me with this problem.

Thanks!

Solution

  • Found a possible answer to my own question.

    1. Remove ~/Library/r-miniconda
    2. Remove Seurat
    3. Install Seurat, when asking to instal r-miniconda, choose no

    Seurat package could be loaded successfully. But still don't know if r-miniconda is essential to run further analyses with Seurat.