CODEWITHSUNDEEP
rbioconductor
Programming Noob
Programming Noob

Reputation: 1332

is there any way to download Deseq1 package in R?

I'm trying to load some RData files with the function load, but I get this message:

Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘cds3’
Loading required package: DESeq
Error in .requirePackage(package) : 
  unable to find required package ‘DESeq’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DESeq’

Which means that this file can only be opened if I have the old DEseq package installed. I know it's an old package, but I have looked everywhere and searched the bioconductor guide for this package, and tried this code:

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq")

and got this error

Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

I already have DEseq2 but I need the first DEseq. I really need to load those files, what can I do ?

Upvotes: 0

Views: 282

Answers (1)

Joe Cursons
Joe Cursons

Reputation: 11

Unfortunately, the lack of backwards compatibility in R packages is one of the major pain points but this probably isn't the right forum for that argument!

It's far from a perfect solution as you will need to mess around with installing dependencies, but it is possible to download the .tar.gz file (e.g. from here) and then if you set your working directory as the folder containing the downloaded file you can run:

install.packages("DESeq_1.38.0.tar.gz", repos=NULL)

You will likely get some errors about missing dependencies on the first attempt, hopefully you can install the dependencies using BiocManager::install() or install.packages() and then try to install from the .tar.gz again.

There is a non-zero chance that you will break other packages through changes to dependencies (yay R!) so proceed with caution (and maybe make a fresh R install to try this on). I would suggest using e.g. a conda environment, but this is also usually a nightmare with R.

Upvotes: 1

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