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Question: How do I stop DESeq2 from loading and additional errors related to the package.
0
gravatar for mdi3
4 months 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 4 months ago by Axel Klenk920 • written 4 months ago by mdi30
0
gravatar for Axel Klenk
4 months 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 4 months 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 4 months ago by Michael Love20k

 

I am not sure how it has nothing to do with DESeq2 if it's the only package that RStudio loads up with the message 

 

Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

 

I have multiple objects from different packages in my workspace, but it's only DESeq2 that's nagging me. 

ADD REPLYlink written 4 months ago by mdi30
1

It sounds like what is happening is your have saved some DESeq2 objects to automatically load when you start R, and this is triggering the package that is needed to show and work with the objects.

Then you removed the DESeq2 package so you are getting an error.

What I meant was that, what you are experiencing isn’t a special property of DESeq2 but would happen if you repeated the above procedure with another package. DESeq2 doesn’t have any special auto-loading behavior.

Why don’t you try to either reinstall DESeq2 or remove these objects from the autoloaded workspace.

ADD REPLYlink written 4 months ago by Michael Love20k
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