I am having trouble installing DESeq2:
biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
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 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/S4Vectors_0.12.2.tgz'
Content type 'application/x-gzip' length 1130228 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/DESeq2_1.14.1.tgz'
Content type 'application/x-gzip' length 1781581 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
The downloaded binary packages are in
/var/folders/bt/j1th0gjn1mbdgcr1xh1x3bgw0000gn/T//RtmpmPeLAW/downloaded_packages
> 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
IF I DETACH S4VECTORS I GET THIS ERROR WHEN I TRY TO LOAD DESEQ2:
> remove.packages('S4Vectors')
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
(as ‘lib’ is unspecified)
library(DESeq2)
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
status
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!
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!
Why don't you want to update to a newer R (e.g. 3.4.1 is current)?