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Question: Bioconductor - not updating
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gravatar for gdembins
7 months ago by
gdembins0
gdembins0 wrote:

Ok everyone, I'm new to this so please be nice.  I am trying to update Bioconductor in my R.  I have R 3.3.0.  I followed the troubleshooting instructions to load with R --vanilla and remove.packages (biocInstaller) etc. and it still doesn't work. And I have looked at other posts where other people have struggled and I still can't seem to figure it out.


R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

I have done the following:

R -- vanilla

remove.packages("BiocInstaller")

Removing package from ‘C:/Users/Gina D/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘BiocInstaller’

source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite.  for help
BiocInstaller version 3.0 is too old for R version 3.3.0;
  remove.packages("BiocInstaller") then
  source("http://bioconductor.org/biocLite.R")
A new version of Bioconductor is available after
  installing the most recent version of R; see
  http://bioconductor.org/install

I have tried this in several R sessions.  Also, I run biocValid() and the same packages (179 of them) are out of date every time, so it's not saving the updated ones after running biocLite() ?

Please any advice at what I am doing wrong would be great.

 

 

ADD COMMENTlink modified 7 months ago by Martin Morgan ♦♦ 20k • written 7 months ago by gdembins0
0
gravatar for Martin Morgan
7 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

It seems likely that your R was installed as 'Administrator', that there are at least two library paths

.libPaths()

and that one of them is not writable by the user you are currently running as. The R error message "there is no package called 'BiocInstaller'" is I think R's way of saying "...that I can remove".

I would suggest simply starting with a new R installation, installed as a regular user.

The alternative is to run R as an 'Administrator' and update your Administrator packages, then switch back to your usual user and update the out-of-date packages. But this only perpetuates the problem, and you'll have to run as Administrator periodically.

ADD COMMENTlink written 7 months ago by Martin Morgan ♦♦ 20k

Thank you for sharing that! There are 2 paths -one under the Program Files (administrator) which has a library and the exe files, and one where I have my package library under my user.  I think I have to re-install R because trying to move things I caused the 'fatal error: no base package' message.  Is it regular practice to have two copies of the library like that? Maybe I've just been updating my R wrong every time...

ADD REPLYlink written 7 months ago by gdembins0

There is always a library path associated with the location R is installed, e.g., under Program Files. If R detects that the current user can't install packages at that location, it will ask whether it is OK to create a second path, and will remember that the second path exists. So two paths are normal when R has been installed as one user, and used as another.

For individual workstations, it is better to install R under your regular user account. There will then be a single library path, and all packages can be updated by the regular user.

ADD REPLYlink written 7 months ago by Martin Morgan ♦♦ 20k

Ah I see.  I just installed it with the rest of my programs, but I can see it making more sense to install it in the user path.  Thanks Martin, this was very helpful information!

ADD REPLYlink written 7 months ago by gdembins0
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