Unable to load edgeR with bioconductor
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@nancyjwahl7-11700
Last seen 6.0 years ago

Hi,

I have been trying to load edgeR on my laptop with Windows 10. This is what I get after typing the 2 recommended lines into my command window, and then copying and pasting into my console:

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

Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help

A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for

  help

> biocLite()

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).

Old packages: 'cluster', 'codetools', 'foreign', 'lattice', 'Matrix', 'mgcv',

  'survival'

Update all/some/none? [a/s/n]:

Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :

  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable

I don't understand what the problem is. I have R.3.3.1 installed, and used RStudio successfully in a class this past summer. But I can't get past this issue no matter what I try. Why is it saying this library is not writable? Thanks very much.

Nancy

 

edger • 3.6k views
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@wouterdecoster-10838
Last seen 20 months ago
Antwerp, Belgium

It's a warning, not necessarily an error. Doesn't it give you the opportunity to use a personal library instead? 

Either way, R has no permission to write in "C:/Program Files/R/R-3.3.1/library", perhaps you can start R as administrator on your computer?

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Hi,

Thank you for your suggestion. I did get further by answering yes to using a personal library, and it looked like everything was downloaded okay, but when I tried to type library('edgeR'), even after changing my path to what was provided, this is what I get:

The downloaded binary packages are in
    C:\Users\Wahl\AppData\Local\Temp\Rtmp6x3Gah\downloaded_packages
> library("edgeR")

Error in library("edgeR") : there is no package called ‘edgeR’

setwd('C:/Users/Wahl/AppData/Local/Temp/Rtmp6x3Gah/downloaded_packages')
> getwd()
[1] "C:/Users/Wahl/AppData/Local/Temp/Rtmp6x3Gah/downloaded_packages"

library("edgeR")
Error in library("edgeR") : there is no package called ‘edgeR’

I don't know how to start R as an administrator on my computer. I use no password or anything. Also, I have no trouble accessing it on my work computer where I do have a username and password. What's next?

Thanks again!

Nancy

 


 

 

 

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Have you installed edgeR (required the first time only) with biocLite("edgeR") ?

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Come to think of it, I haven't. When I get home I will try that instead of library("edgeR"). Thanks, I will let you know what happens.

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'as well as' -- you need to install the package once

biocLite("edgeR")

and then in each R session where you want to use it you need to load it

library("edgeR")
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I tried library("edgeR") after running through the whole procedure and it didn't work. I think I will install RStudio 3.3.2 (I have 3.3.1) and see if that works.

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