Unable to install a Bioconductor package to local directory
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tagirdzh • 0
@tagirdzh-15769
Last seen 3.4 years ago

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

error biocinstaller • 985 views
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@james-w-macdonald-5106
Last seen 17 hours ago
United States

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.

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0
Entering edit mode

This worked. Thanks!

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