Deseq2 error

Question

[sgadila]

Hello everyone,

I was performing deseq2 using R and I came across the following error. I have downloaded the R scripts and deseq2 as mentioned in the biostar sub-book RNAseq by Example.

cat simple_counts.txt | Rscript deseq2.r 2x2 > results.txt
dyld: Library not loaded: @rpath/libz.1.dylib
  Referenced from: /Users/sgadila/micromamba/envs/bioinfo/lib/R/lib/libR.dylib
  Reason: image not found
Abort trap: 6
(bioinfo)

Could anyone please help me with this issue? Also, could you please explain if this is an issue with the deseq2 or R?

[Ram]

What is this deseq2.r - where did you get it from and what are is contents?

[sgadila]

Thanks for your response. I was using Biostar handbook and looks like this is from the old version of the book.

[Ram]

Please edit your post and mention this there. Also paste the contents of deseq2.r in there.

[GenoMax]

deseq2.r code is now in a sub-book called RNAseq by Example which is part of biostar handbook. Are you using the instructions in that book?

[sgadila]

Yes, I did set up my computer as mentioned in the sub-book RNAseq by Example and also downloaded the RNAseq scripts from the book to perform the analysis.

[Ram]

Can you please edit your post and add the information I asked you to add?

[sgadila]

Sorry, I just edited my post.

[GenoMax]

What version of macOS are you using and did you install a different python than what came with your macOS.

[sgadila]

I am using version 10.13.6 of macOS and yes, I have installed Python 3.8.18.