Question: Can't install the correct version of bioconductor, keeps using old version
0
gravatar for colin.kern
4 months ago by
colin.kern0
colin.kern0 wrote:

I feel like I'm going in circles here. I have R 3.6.0 installed, and it clearly shows this is the version I'm using when I enter the interpreter:

$ R

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

Next, I follow the instructions on the Bioconductor website for installing BiocManager:

> install.packages("BiocManager")
Installing package into ‘/share/apps/rmodules’
(as ‘lib’ is unspecified)
Warning in install.packages("BiocManager") :
  'lib = "/share/apps/rmodules"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘~/R/x86_64-pc-linux-gnu-library/3.6’
to install packages into? (yes/No/cancel) yes
trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.4.tar.gz'
Content type 'application/x-gzip' length 242304 bytes (236 KB)
==================================================
downloaded 236 KB

* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)

The downloaded source packages are in
    ‘/tmp/RtmpFDxU5w/downloaded_packages’

But then when I try install a package from Bioconductor, it says I'm on an old version and sends me to the exact same website I used to install it in the first place:

> BiocManager::install("normr")
Error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install

How can I get it so it's using version 3.9? I'm on a computing cluster which is why I have to install to a personal library. Is that causing this issue?

ADD COMMENTlink modified 4 months ago by Martin Morgan ♦♦ 23k • written 4 months ago by colin.kern0
Answer: Can't install the correct version of bioconductor, keeps using old version
1
gravatar for Martin Morgan
4 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Is there a package 'BiocVersion' already installed, perhaps in /share/apps/rmodules? Use "BiocVersion" %in% rownames(installed.packages()) If so, remove.packages("BiocVersion"), but probably this indicates that you're trying to re-use the R-3.5 library with R-3.6, which is generally not a good idea. You might instead investigate how to set .libPaths() (see ?.Rprofile) so that it does not include that path.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Martin Morgan ♦♦ 23k

Thanks for your answer. I think this is the issue. I still haven't gotten it working, but I think I'm on the right track at least.

ADD REPLYlink written 4 months ago by colin.kern0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 170 users visited in the last hour