Question: DESeq2 installing error: S4Vectors cannot be unloaded; anyone?
gravatar for nidz91
22 months ago by
nidz910 wrote:

I am having trouble installing DESeq2:


Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘DESeq2’
also installing the dependency ‘S4Vectors’

trying URL ''
Content type 'application/x-gzip' length 1130228 bytes (1.1 MB)
downloaded 1.1 MB

trying URL ''
Content type 'application/x-gzip' length 1781581 bytes (1.7 MB)
downloaded 1.7 MB

The downloaded binary packages are in
> library("DESeq2", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
Loading required package: S4Vectors
Error in unloadNamespace(package) : 
  namespace ‘S4Vectors’ is imported by ‘IRanges’, ‘Biostrings’, ‘XVector’ so cannot be unloaded
In addition: Warning message:
package ‘S4Vectors’ was built under R version 3.3.3 
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,  : 
  Package ‘S4Vectors’ version 0.12.1 cannot be unloaded



> remove.packages('S4Vectors')
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
(as ‘lib’ is unspecified)

Error: package ‘S4Vectors’ required by ‘DESeq2’ could not be found
In addition: Warning message:
In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
  cannot open compressed file '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/DESCRIPTION', probable reason 'No such file or directory'


My R version:

platform       x86_64-apple-darwin13.4.0   
arch           x86_64                      
os             darwin13.4.0                
system         x86_64, darwin13.4.0        
major          3                           
minor          3.2                         
year           2016                        
month          10                          
day            31                          
svn rev        71607                       
language       R                           
version.string R version 3.3.2 (2016-10-31)
nickname       Sincere Pumpkin Patch 


Is there no other way but to update R to 3.3.3 to use DESeq2? 

ANY DESeq2 users suggestions appreciated!


deseq2 installation • 2.4k views
ADD COMMENTlink modified 22 months ago by Martin Morgan ♦♦ 23k • written 22 months ago by nidz910

Ok, Martin Morgan was right, I had to start a new session. R --vanilla did not work for some reason so I started new project. I loaded DESeq2 first and then phyloseq. So far so good!

ADD REPLYlink written 22 months ago by nidz910

Why don't you want to update to a newer R (e.g. 3.4.1 is current)?

ADD REPLYlink written 22 months ago by Wolfgang Huber13k
Answer: DESeq2 installing error: S4Vectors cannot be unloaded; anyone?
gravatar for Martin Morgan
22 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Make sure you do not have any R sessions running.

Start R from the command line, using R --vanilla

Run BiocInstaller::biocValid() and follow directions to update / downgrade individual packages.

Use BiocInstaller:biocLite("S4Vectors") to re-install S4Vectors.

Use library(DESeq2) (no library path) to load DESeq2.

If for some reason you want to install and use packages from a particular library location, do so consistently and in a way that avoids duplicate package installations across active library paths. For instance, set .libPaths() to contain a 'session-specific' library path (e.g., Bioc version 3.4 packages) and a 'system' library path (base and recommended packages only)

ADD COMMENTlink written 22 months ago by Martin Morgan ♦♦ 23k

This exactly works!

ADD REPLYlink written 19 months ago by elximo0
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