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Question: Cannot install snpStats packages
1
gravatar for zwang10
3.3 years ago by
zwang10 • 10
United States
zwang10 • 10 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?
snpstats bioconductor R • 3.0k views
ADD COMMENT • link •
modified 13 hours ago by zx8754 ♦ 8.4k • written 3.3 years ago by zwang10 • 10

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 3.3 years ago • written 3.3 years ago by Pranavathiyani G • 250
3
gravatar for Guangchuang Yu
3.3 years ago by
Guangchuang Yu • 2.3k
China/Guangzhou/Southern Medical University
Guangchuang Yu • 2.3k 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 3.3 years ago • written 3.3 years ago by Guangchuang Yu • 2.3k

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

ADD REPLY • link modified 3.3 years ago • written 3.3 years ago by Guangchuang Yu • 2.3k
1
gravatar for gemini.venkat
16 hours ago by
gemini.venkat • 20
gemini.venkat • 20 wrote:

With the latest update you have to do the same but install BiocManager : This is done only for version R > 3.4

  if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

and then :

BiocManager::install(c("snpStats"))

works for now
ADD COMMENT • link modified 13 hours ago by zx8754 ♦ 8.4k • written 16 hours ago by gemini.venkat • 20
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