Cannot install snpStats packages
3
1
Entering edit mode
4.8 years ago
zwang10 ▴ 20

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?

r bioconductor snpStats • 4.5k views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

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'
ADD REPLY
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
4.8 years ago
Guangchuang Yu ★ 2.4k

'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
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
17 months ago

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
0
Entering edit mode
10 months ago
UMen • 0

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
ADD COMMENT

Login before adding your answer.

Traffic: 1874 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6