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