Question: Unable to install a Bioconductor package to local directory
0
gravatar for tagirdzh
12 months ago by
tagirdzh0
tagirdzh0 wrote:

Hi, I am trying to install Biostrings package. The problem is that I am working on a server where I don't have sudo privileges, so I install all packages into my directory. Fist, when I followed the installation instructions, I got this message

source("http://bioconductor.org/biocLite.R")

use 'source("https://bioconductor.org/biocLite.R")' or

  'source("http://bioconductor.org/biocLite.R")' to update

  'BiocInstaller' after library("utils")

bioClite()

Error in bioClite() : could not find function "bioClite"

When, I tried to specify my local utils library, and got this error:

library(utils,lib.loc='/local/path')

source("http://bioconductor.org/biocLite.R")

Installing package into ‘/usr/local/lib/R/site-library’

(as ‘lib’ is unspecified)

Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :

  'lib = "/usr/local/lib/R/site-library"' is not writable

Error in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : 

  unable to install packages

 

I tried to specify 'lib', but the source function doesn't take this argument.

Is there a way to install Bioconductor to my folder?

Thanks!

Gulnara

biocinstaller error • 521 views
ADD COMMENTlink modified 12 months ago by James W. MacDonald50k • written 12 months ago by tagirdzh0
Answer: Unable to install a Bioconductor package to local directory
3
gravatar for James W. MacDonald
12 months ago by
United States
James W. MacDonald50k wrote:

You can use .libPaths  (note that this function has a prepended period) to create a library path that is writeable, and then when you source biocLite it should install there.

ADD COMMENTlink written 12 months ago by James W. MacDonald50k

This worked. Thanks!

ADD REPLYlink written 12 months ago by tagirdzh0
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