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Question: R:Cannot install snpStats packages
0
gravatar for zwang10
3.0 years ago by
zwang10 • 0
United States
zwang10 • 0 wrote:

I follow the instruction from https://www.bioconductor.org/install/. But I got error as following

> source("http://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
  'lib = "/share/apps/R/3.1.1/intel/2013.0.028/lib64/R/library"' is not writable
Error in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : 
  unable to install packages
Calls: source ... eval.parent -> eval -> eval -> eval -> eval -> install.packages
Execution halted

Can someone help me here?
bioconductor R • 2.5k views
ADD COMMENT • link •
modified 3.0 years ago by Guangchuang Yu • 2.2k • written 3.0 years ago by zwang10 • 0

Follow this:

#To install core packages:
source("https://bioconductor.org/biocLite.R")
biocLite()
#To install specific packages
source("https://bioconductor.org/biocLite.R")
biocLite("snpStats")
ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Pranavathiyani G • 240
3
gravatar for Guangchuang Yu
3.0 years ago by
Guangchuang Yu • 2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu • 2.2k wrote:

'lib = "/share/apps/R/3.1.1/intel/2013.0.028/lib64/R/library"' is not writable

Obviously, you don't have the permission to install package to the R library folder.

  1. add the following lines to ~/.Renviron: R_LIBS_USER='~/R/library'

  2. try again:

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

You should be able to install any package you want.
ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Guangchuang Yu • 2.2k

you may need to mkdir -p ~/R/library if it complained that the folder does not exists.

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Guangchuang Yu • 2.2k
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