Bioconductor package run time
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mohit • 0
@mohit-9667
Last seen 6.2 years ago

Hi,

I am trying to install and run few of the bioconductor packages but coming across the library path issue.

Could any one help me to solve this problem???

 

################################################################
A new version of Bioconductor is available after installing the most
  recent version of R; see http://bioconductor.org/install
Installing package(s) 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
Calls: source ... eval.parent -> eval -> eval -> eval -> eval -> install.packages
Execution halted

 

#################################################################

 

 

Best,

M

 

support.bioconductor.org • 1.2k views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

There are two problems here. First you apparently have an old version of R installed, so you should probably upgrade. Second, your R is installed in a dir that is not user-accessible. There are many ways around this problem. Two possibilities are

  1. Install the new R in /usr/local, like the current one, providing you have sudo. Or get your sysadmin to do it for you. And then you can set up a local lib (see ?.libPaths, and do note that there is a dot pre-pended to that function name) where your personal packages will be installed.
  2. Install the new R in your home dir, or another dir within which you have write privileges. It's actually simple to do. There are instructions in the R Installation and Administration manual. The only difference is you would set a different prefix dir at the configure step.

I personally prefer the latter, as it doesn't require sudo privileges, I can upgrade at will, it's easy to have multiple different versions of R/BioC floating around, etc. But ymmv.

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