R Package Installation Ignores libPaths Setting

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 .

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

Works for me. Which shell are you using? Are you setting .libPaths elsewhere?

Peter-Dalgaards-MacBook-Air:F pd$ R_LIBS=~/tmp Rscript -e '.libPaths()'
[1] "/Users/pd/tmp"                                                 
[2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"

Peter-Dalgaards-MacBook-Air:F pd$ export R_LIBS=~/tmp 
Peter-Dalgaards-MacBook-Air:F pd$ Rscript -e '.libPaths()'
[1] "/Users/pd/tmp"                                                 
[2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"

-pd

On 20 Feb 2016, at 10:00 , Dario Strbenac <dstr7320 at uni.sydney.edu.au> wrote:

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

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

Good day,

Thank you for the suggestions. I had a .libPaths command in my .Rprofile file. I have now removed it and specified R_LIBS in .Renviron.

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