DESeq2 Error: package or namespace load failed for 'DESeq2'
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Entering edit mode
2.6 years ago
ATCG ▴ 370

Hi I am unable to run DESeq2

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 image not found • 4.2k views
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Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

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Why not do this in R following the workflow?

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2
Entering edit mode
2.6 years ago

The error message says you're missing libopenblasp-r0.3.7.dylib. Installing openblas could fix it, and there's several suggestions to reinstall R itself to gather the assumed dependencies. https://stackoverflow.com/questions/50634727/dyld-library-not-loaded-usr-local-opt-openblas-lib-libopenblasp-r0-2-20-dylib

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Yes, this fixed the problem! Thank you so much!

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