[Rd] Installation fails on FreeBSD (PR#9293)

Smith, Peter p.smith at auckland.ac.nz
Thu Oct 12 15:05:37 CEST 2006

Hi Peter,
Hmm, I thought so as well -- and so I did a chown and a chmod and set umask to 0000 and still the problem persists. Then I went wild and tried doing it as root, and still the problem remains.
So, I've now deleted everything in the ports tree and am kicking off the make again. But since it is now 2:00 in the morning, I'll leave it to run whilst I sleep.
Thanks for your prompt suggestions. Much appreciated.


From: pd at pubhealth.ku.dk on behalf of Peter Dalgaard
Sent: Fri 13/10/06 1:42
To: p.smith at auckland.ac.nz
Cc: r-devel at stat.math.ethz.ch; R-bugs at biostat.ku.dk
Subject: Re: [Rd] Installation fails on FreeBSD (PR#9293)

p.smith at auckland.ac.nz writes:

> Full_Name: Peter Smith
> Version: 2.3.1
> OS: FreeBSD 5.3
> Submission from: (NULL) (
> I'm installing R from the FreeBSD ports tree (i.e. running make from
> /usr/ports/math/R). During the make, the following error message is generated.
> <snip>
>      Formats: text html latex example
>  >>> Building/Updating help pages for package 'tcltk'
>      Formats: text html latex example
> building/updating package indices ...
> begin installing recommended package foreign
> * Installing *source* package 'foreign' ...
> eval: ./configure: Permission denied
> ERROR: configuration failed for package 'foreign'
> <snip>
> The problem seems to occur when the following command is executed.
> MAKE="make" R_LIBS= ../../../bin/R CMD INSTALL --no-lock -l "../../../library"
> foreign.tgz > foreign.ts.out 2>&1 || (cat foreign.ts.out && exit 1)
> The contents of foreign.ts.out is:
> * Installing *source* package 'foreign' ...
> eval: ./configure: Permission denied

I don't think this is a bug in R. More likely, you have a permission
problem in your setup, possibly a too restrictive umask setting. The
system is complaining that it cannot run the configure script.

[In principle, R could try and remedy such problems by overriding
system defaults. We have discussed this before and come down on the
side that if the user or the system adminstrator sets things up so
that there are things that users cannot do by default (such as running
arbitrary downloaded scripts), then it is not our business to fix it
behind their backs.]

> ERROR: configuration failed for package 'foreign'
> ** Removing '/usr/ports/math/R/work/R-2.3.1/library/foreign

   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

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