R devel - Feb 2016 - R Package Installation Ignores libPaths Setting

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

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

Good day,

I believe from the documentation that folders in R_LIBS should appear in the
output of .libPaths, but they do not. The documentation contains "The
library search path is initialized at startup from the environment variable
R_LIBS ..."

However,

$ export R_LIBS=/users/stgrad/dario/tmp/
$ Rscript -e ".libPaths()"
[1] "/dskh/nobackup/biostat/Bioconductor"
"/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"            
"/usr/lib/R/library"

Is there some other crucial information which I have missed ?

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia