DESeq2 Error: package or namespace load failed for 'DESeq2'
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DataFanatic ▴ 10
@datafanatic-12212
Last seen 2.0 years ago

Hi, DESeq2 error while running, please help!

Installed

conda create -y -n test.DESeq2 python=3

conda activate test.DESeq2

conda install -y bioconductor-DESeq2

To Run

$ cat counts.txt | deseq2.r 3x3 > results2.csv

ERROR Error: package or namespace load failed for 'DESeq2' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Users/xx/opt/anaconda3/envs/test.gplots/lib/R/library/DESeq2/libs/DESeq2.dylib': dlopen(/Users/xx/opt/anaconda3/envs/test.gplots/lib/R/library/DESeq2/libs/DESeq2.dylib, 6): Library not loaded: @rpath/libopenblasp-r0.3.7.dylib Referenced from: /Users/xx/opt/anaconda3/envs/test.gplots/lib/R/library/DESeq2/libs/DESeq2.dylib Reason: image not found Execution halted (test.gplots)
RNA-Seq DESeq2 • 1.6k views
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if it's a conda installation, and DESeq2 can't be loaded in conda, isn't that a conda problem?

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User had posted on Biostars, too: https://www.biostars.org/p/432720/

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@ialbert
Last seen 5 days ago
United States

There is an ongoing problem with all packages that use certain libraries, the dependencies are not marked properly. Try this:

# Temporary solution on MacOS.
conda install -y libopenblas==0.3.7

See also:

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Thank you Istvan.

Also thanks again for making Biostars open source, this has really improved our interaction with users!

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