DEseq R code problem

[theokirkland]

I have Deseq installed using Bioconductor and RStudio.

When I try to use the following wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq1.r it does not load an R script I get dyld: Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib Referenced from: /usr/local/bin/wget Reason: image not found Abort trap: 6

Any ideas?

Thx Theo

[ialbert]

This looks like some sort of conflict with OpenSSL when installed in different ways

https://github.com/kelaberetiv/TagUI/issues/86

if your wget is not working the whole installation is suspect.

[kensoh]

Adding on, it looks like wget is using OpenSSL v1.0, which is deprecated from Homebrew, and also macOS newer versions don't come with OpenSSL anymore. An ideal solution would be getting an updated version of wget if available that works with the newer macOS releases.

If that's not viable, then maybe use the curl command which can also download files from the internet. If that's not possible, then following will install OpenSSL v1.0 on macOS. I created below custom solution to solve this problem for an open-source project that I maintain, so that users don't have to install Xcode and build the OpenSSL if using the existing Homebrew solution.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew update && brew upgrade
brew uninstall openssl; brew uninstall openssl; brew install https://github.com/tebelorg/Tump/releases/download/v1.0.0/openssl.rb

[theokirkland]

You’re absolutely right. Once I downloaded wget with home-brew I got the script. However the line of code will not run. I have R open in RStudio and DESeq installed, but the error is

cat simple_counts.txt | Rscript deseq1.r 3x3 > results.txt Error in library(DESeq) : there is no package called 'DESeq' Execution halted

I’m clearly having a problem running R from the command line. I tried running the script in RStudio but couldn’t get that to work either.

Thanks for your help.

Theo

Begin forwarded message:

From: Ken Soh notifications@github.com Subject: Re: [biostars/biostar-handbook-issues] DEseq R code problem (#97) Date: December 19, 2019 at 5:04:13 PM PST To: biostars/biostar-handbook-issues biostar-handbook-issues@noreply.github.com Cc: theokirkland tkirkland@ucsd.edu, Author author@noreply.github.com Reply-To: biostars/biostar-handbook-issues reply@reply.github.com

Adding on, it looks like wget is using OpenSSL v1.0, which is deprecated from Homebrew, and also macOS newer versions don't come with OpenSSL anymore. An ideal solution would be getting an updated version of wget if available that works with the newer macOS releases.

If that's not viable, then maybe use the curl command which can also download files from the internet. If that's not possible, then following will install OpenSSL v1.0 on macOS. I created below custom solution to solve this problem for an open-source project that I maintain, so that users don't have to install Xcode and build the OpenSSL if using the existing Homebrew solution.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" brew update && brew upgrade brew uninstall openssl; brew uninstall openssl; brew install https://github.com/tebelorg/Tump/releases/download/v1.0.0/openssl.rb — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biostars/biostar-handbook-issues/issues/97?email_source=notifications&email_token=AGHKSXVBHZOYOPI77O5PX53QZQKY3A5CNFSM4J4UVWL2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHLRK5Y#issuecomment-567743863, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHKSXUD4T2BYVZOBU52QNTQZQKY3ANCNFSM4J4UVWLQ.

[ialbert]

looks like wget has now been installed correctly. That solves the original problem.

For the R script to work, you need to install the libraries into R. The chapter:

• https://www.biostarhandbook.com/rnaseq-statistics.html

has more details

[kadavesh]

looks like wget has now been installed correctly. That solves the original problem.

For the R script to work, you need to install the libraries into R. The chapter:

• https://www.biostarhandbook.com/rnaseq-statistics.html

has more details

Following the instructions in the Biostar Handbook, I run into the sample problem: Error in library(DESeq) : there is no package called 'DESeq' Execution halted

I have RStudio globally installed. I installed DEseq, DEseq2, edgeR, pasilla, and gplots in the RStuio. The Rscript deseq1.r was downloaded successfully in the root directory.

R version: 3.6 Bioconductor version: 3.9

[ialbert]

these problems usually have to do with multiple R versions on the system.

The book has been updated with installation instructions from the command line to ensure the same R version is used.