From ripley at stats.ox.ac.uk  Thu Feb 18 09:02:40 2016
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 18 Feb 2016 08:02:40 +0000
Subject: [Rd] R Package Installation Ignores libPaths Setting
In-Reply-To: <SN1PR0101MB14390FF9CD858614E238134BCDAE0@SN1PR0101MB1439.prod.exchangelabs.com>
References: <SN1PR0101MB14390FF9CD858614E238134BCDAE0@SN1PR0101MB1439.prod.exchangelabs.com>
Message-ID: <56C57AA0.2020503@stats.ox.ac.uk>

You misunderstand what .libPaths does: it changes the path in the 
current session only.  Installation uses a different R process.

Set R_LIBS to change the library path for new sessions: see ?.libPath .


On 18/02/2016 07:00, Dario Strbenac wrote:
> Good day,
>
> If the library path is changed with .libPaths, the command
>
> install.packages("/nb/dario/Biostrings_2.39.9.tar.gz", repos=NULL)
>
> fails with
>
> ** testing if installed package can be loaded
> Error : package ?S4Vectors? required by ?Biostrings? could not be found
>
> However,
>
> running library(S4Vectors) followed by sessionInfo() after the error shows that the package can indeed be found by R
>
> R version 3.2.3 Patched (2016-02-14 r70170)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 8 (jessie)
>      ...        ...
> other attached packages:
> [1] S4Vectors_0.9.34    BiocGenerics_0.17.3
>
> The new library path is being ignored when the package is attempted to be loaded at the end of the installation process. How can the installation be successful ?
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford



[Rd] R Package Installation Ignores libPaths Setting
Prof Brian Ripley