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Question: How do I stop DESeq2 from loading and additional errors related to the package.
0
gravatar for mdi3
6 days ago by
mdi30
mdi30 wrote:

Hello,

As far as I understand the DESeq2 package is automatically loaded when R is started up. I am not interested in using DESeq2 anymore, so how can I stop it from automatically loading? It's been interfering with the installation of other R packages, as sometimes I need to restart my session so that the package I am attempting to install would first update an already existing package. Because DESeq2 masks so many packages and loads first, I get basically stuck in a loop. 

The other issue is errors related to DESeq2 popping up when I don't have the package installed. I am using the same RStudio project file on both the PC and laptop. However, I have DESeq2 "installed" on the PC but not on the laptop. I guess that some settings in the RStudio project file attempt to load the DESeq2 package when I have the project open on my laptop, but to no avail because I don't have the package on it. The errors are

 

Loading required package: DESeq2
Error in .requirePackage(package) :
  unable to find required package ‘DESeq2’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DESeq2’

Loading required package: DESeq2

Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DESeq2’

 

They pop up randomly, even when the packages that are loaded at the moment are not associated with DESeq2 (e.g. ggplot2). 

So how do I uninstall DESeq2 and stop the errors? It's been my most frustrating experience with a package yet.  

ADD COMMENTlink modified 5 days ago by Axel Klenk920 • written 6 days ago by mdi30
0
gravatar for Axel Klenk
5 days ago by
Axel Klenk920
Switzerland
Axel Klenk920 wrote:

(Hmmm... not sure what happened to my previous answer. Anyway:)

No, DESeq2 is not normally loaded on R startup. I think this could be an issue with your RStudio project or R may restore a previously saved worksapce on startup that contains a DESeq2 object. The latter can be avoided by starting R like

> R --no-restore

which is generally a good idea.

Hope this helps.

 

ADD COMMENTlink written 5 days ago by Axel Klenk920

Yes, to affirm Axel's answer, this has nothing to do with the DESeq2 software but something about your R or RStudio setup.

Somewhere you are attempting to load DESeq2 by default when you start R, and it's most likely from the RStudio project settings.

ADD REPLYlink written 5 days ago by Michael Love18k
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