DESEQ2 on R cannot be installed on server

Question

[Kai_Qi]

Hi all:

I am using sever to analyze RNA-seq data. I am in Anaconda3. Under Anaconda3 I called R, it shows it is R 3.5.1

R version 3.5.3 (2019-03-11) -- "Great Truth" Copyright (C) 2019 The R
Foundation for Statistical Computing Platform:
x86_64-conda_cos6-linux-gnu (64-bit)

Then I tried to install DESeq2 on R following the bioconductor instructions:

But I got the error like this: ERROR: dependency 'latticeExtra' is not
available for package 'Hmisc'
* removing '/home/caiqi/anaconda3/lib/R/library/Hmisc' ERROR: dependency 'Hmisc' is not available for package 'DESeq2'
* removing '/home/caiqi/anaconda3/lib/R/library/DESeq2'

The downloaded source packages are in
    '/tmp/RtmpJxuJxt/downloaded_packages' Updating HTML index of packages
in '.Library' Making 'packages.html' ... done Old packages: 'vctrs'
Update all/some/none? [a/s/n]: a trying URL
'https://cran.rstudio.com/src/contrib/vctrs_0.3.0.tar.gz'
.....
The downloaded source packages are in
    '/tmp/RtmpJxuJxt/downloaded_packages' Updating HTML index of packages
in '.Library' Making 'packages.html' ... done Warning messages: 1: In
install.packages(...) :   installation of package 'Hmisc' had non-zero
exit status 2: In install.packages(...) :   installation of package
'DESeq2' had non-zero exit status
> library(DESeq2) Error in library(DESeq2) : there is no package called 'DESeq2'

I searched around and see it is advised to update my R. So I typed conda update R

Everything goes smoothly but when I call R. I see the version is still 3.5, and of course I still cannot use DESeq2

I cannot understand why this happens.

I appreciate a lot for your help,

[Ram]

If you're using conda to manage R, I'd recommend using conda to install packages as well. conda search -c bioconductor deseq2 should give you the name of the package to install (most probably bioconductor-deseq2).

[Kai_Qi]

Thank you very much, it worked. But it downgrade my R version to 3.2.

Will it affect the already installed packages?

Appreciate a lot for your constructive advice.

[Ram]

It might. It should not have affected your R version. It might affect other packages, but conda R does not mix well with system-level R in my experience.

If you're using module load R, you should be able to use a user-level library for most packages.

[Kai_Qi]

It affect my packages in R somehow:

 > library(Rsubread)

Warning message: package 'Rsubread' was built under R version 3.5.3

I guess I should copy the files into my hard-disk and do them locally.

Thank you, I have contacted our administrator to install DESeq2 so that I can use module load R and library(DESeq2)

[Ram]

Having your sysadmin install it is the best solution, although I can't understand why you're unable to use a local library.

[Kai_Qi]

Oh. I did not explain well. I mean it will downgrade the R version in conda. I also have other packages installed there.

Thanks a lot,

[GenoMax]

I see the version is still 3.5

Looks like there is a system-wide R that is taking precedence over one you installed using conda. Amend you $PATH to your local conda directory appears first. That may do the trick. If there is a system-wide R then you could request sys admins to install DESeq2 there. It is a common package that should be of use to many.

[Kai_Qi]

Thank you, for the reply. Actually, I tried to use module load R, and i see it has R at version 3.6; but I can not library(DESeq2) because it is not installed.

But I already sent a message to see if they can install it there.

Thank you for your advice.