error in installing R packages

savecancel

$ sage -f r
Calling sage-spkg on 'r'
r-2.14.0.p3

Oops! That is totally unrelated to installing R packages. You are trying there to reinstall the complete R installation inside of Sage.

I'm surprised that your initial method didn't work, but you should be able to try the following:

sage: r.install_packages("coda")
<various messages>
sage: r.library('coda')

to use it. There is a warning about restarting Sage, but this seems to be unnecessary in my experience.

Thank you for your answer. But it fails as follows:

$ sage
----------------------------------------------------------------------
| Sage Version 5.2, Release Date: 2012-07-25                         |
| Type "notebook()" for the browser-based notebook interface.        |
| Type "help()" for help.                                            |
----------------------------------------------------------------------
sage: 
sage: r.install_packages("coda")

R version 2.14.0 (2011-10-31)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin10.8.0 (64-bit)
 :
 :
> options(repos="http://cran.r-project.org/"); install.packages("coda")
trying URL 'http://cran.r-project.org/src/contrib/coda_0.15-2.tar.gz'
Content type 'application/x-gzip' length 73937 bytes (72 Kb)
opened URL
==================================================
downloaded 72 Kb

* installing *source* package ‘coda’ ...
** package 'coda' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Error in if (file.info(codeFile)["size"] == file.info(loaderFile)["size"]) warning("package seems to be using lazy loading already") else { : 
  missing value where TRUE/FALSE needed
ERROR: lazy loading failed for package ‘coda’
* removing ‘/Applications/sage/local/lib/R/library/coda’

The downloaded packages are in 
    ‘/private/var/folders/c7/qc6d0rs88xlbfy00r6by6by00000gn/T/Rtmp4MMxZq/downloaded_packages’ 
Warning message:
In install.packages("coda") :
   installation of package 'coda' had non-zero exit status 
> 

real    0m4.736s
user    0m1.791s
sys 0m0.137s
Please restart Sage in order to use 'coda'.
sage: quit
Exiting Sage (CPU time 0m0.63s, Wall time 0m10.44s).
$ ls  /Applications/sage/local/lib/R/library/ 
KernSmooth  cluster     graphics    nnet        stats4
MASS        codetools   grid        parallel    survival
Matrix      compiler    lattice     rpart       tcltk
base        datasets    methods     spatial     tools
boot        foreign     mgcv        splines     utils
class       grDevices   nlme        stats
$
$ sage
----------------------------------------------------------------------
| Sage Version 5.2, Release Date: 2012-07-25                         |
| Type "notebook()" for the browser-based notebook interface.        |
| Type "help()" for help.                                            |
----------------------------------------------------------------------
sage: 
sage: r.library('coda')
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
 :
 :