R devel - Sep 2007 - installing packages (PR#9907)

Full_Name: Alexander Jerneck
Version: 2.4.0 (2006-10-03)
OS: Gentoo (2.6.17-custom kernel)
Submission from: (NULL) (130.91.92.78)


I had trouble installing R packages, either from inside R or from the
commandline, with R complaining about not finding /usr/bin/pwd
I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd and now
I can install packages. I do not know where the original problem is however.

On Wed, 12 Sep 2007, alexander.jerneck at gmail.com wrote:
> Full_Name: Alexander Jerneck
> Version: 2.4.0 (2006-10-03)
> OS: Gentoo (2.6.17-custom kernel)
> Submission from: (NULL) (130.91.92.78)
>
>
> I had trouble installing R packages, either from inside R or from the
> commandline, with R complaining about not finding /usr/bin/pwd
> I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd
and now
> I can install packages. I do not know where the original problem is
however.
This is NOT A BUG.

Likely, you do not have /bin on your path. Check

 	Sys.getenv("PATH")


install.packages() works fine on all my Gentoo boxes with R installed as 
per the instructions in

 	$R_HOME/doc/manual/R-admin.html
>
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>
Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

I don't think this is a bug in R.

I believe a (not too) recent change in Gentoo removed /usr/bin/pwd so 
that the only one left is /bin/pwd. R seems to remember from install 
time where to find these utilities, and probably found /usr/bin/pwd when 
you installed the not recent version of R. You found one workaround, and 
another would be a fresh install of R.

Paul

alexander.jerneck at gmail.com wrote:
> Full_Name: Alexander Jerneck
> Version: 2.4.0 (2006-10-03)
> OS: Gentoo (2.6.17-custom kernel)
> Submission from: (NULL) (130.91.92.78)
> 
> 
> I had trouble installing R packages, either from inside R or from the
> commandline, with R complaining about not finding /usr/bin/pwd
> I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd
and now
> I can install packages. I do not know where the original problem is
however.
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
===================================================================================
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alexander.jerneck at gmail.com wrote:
> Full_Name: Alexander Jerneck
> Version: 2.4.0 (2006-10-03)
> OS: Gentoo (2.6.17-custom kernel)
> Submission from: (NULL) (130.91.92.78)
>
>
> I had trouble installing R packages, either from inside R or from the
> commandline, with R complaining about not finding /usr/bin/pwd
> I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd
and now
> I can install packages. I do not know where the original problem is
however.
>   
Please don't report it as a bug then! Or at least do more of your 
homework first.

As far as I can see, this is handled by the configure script which goes 
looking for pwd and records the result in $GETWD (in Makeconf and the 
INSTALL and REMOVE scripts). If you compile on one system and run on 
another, strange things can and will happen if they do not have things 
in the same places.  There are a few other places where pwd is called 
directly (texi2dvi and libtool) but I don't think that can give the 
error message you describe.

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