Cannot install snpStats packages

Question

[zwang10]

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?

[Pranavathiyani G]

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")

[UMen]

Dear gemini,

sorry but that doesn't work for R 3.6.1

 if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
Installing package into ‘C:/Users/ugem/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://cran.uib.no/src/contrib:
  cannot open destfile 'C:\Users\ugem\AppData\Local\Temp\Rtmpmi2CkS\file641442e6cb5', reason 'No such file or directory'
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning messages:
1: package ‘BiocManager’ is not available (for R version 3.6.1) 
2: In gzfile(file, mode) :
  cannot open compressed file 'C:\Users\uwemenze\AppData\Local\Temp\Rtmpmi2CkS/libloc_196_fd84b67.rds', probable reason 'No such file or directory'

[curious]

One thing you could try is getting used to conda. Conda lets you manage many different environments with different versions of R. Usually installing packages are as simply as conda install [package]'. When using a new package the first thing I do these days is to look and see if it is install-able with conda

https://anaconda.org/bioconda/bioconductor-snpstats

Answer 1

[Guangchuang Yu]

'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.

[Guangchuang Yu]

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

Answer 2

[gemini.venkat]

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

Answer 3

[UMen]

Thanks for the answers, I found another solution by myself:

1. download "snpStats_1.38.0.zip" from Bioconductor
2. install.packages(file.choose(), repos = NULL, type="source") # choose zipfile downloaded