Re: [Rd] bug in R CMD INSTALL do_install under OS X

From: David Rossell <david.rossell_at_irbbarcelona.org>
Date: Tue, 16 Dec 2008 10:14:39 +0100

You're right William, unsetting the CDPATH variable does the trick. The R INSTALL script should unset it to avoid the problem.

Thanks a lot,

David

On Mon, Dec 15, 2008 at 9:29 PM, William Dunlap <wdunlap_at_tibco.com> wrote:

> This problem could be caused by having CDPATH set. E.g.,
>
> % env CDPATH=. ~/R-svn/r-devel/R/bin/R CMD INSTALL -l Rlib
> testCMacros
> /homes/bill/packages/Rlib
> /homes/bill/R-svn/r-devel/R/bin/INSTALL: line 948: cd:
> /homes/bill/packages/testCMacros
> /a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/testCMacros:
> No such file or directory
> /bin/sed: can't read DESCRIPTION: No such file or directory
> ERROR: no 'Package' field in 'DESCRIPTION'
> /bin/sed: read error on /homes/bill/packages/testCMacros: Is a
> directory
> (It works fine if I set 'CDPATH='.)
>
> The happens because, from 'man cd' in
> http://www.linuxhowtos.org/manpages/1p/cd.htm:
>
> If a non-empty directory name from CDPATH is used, or if
> cd - is used, an absolute pathname of the new working
> directory shall be written to the standard output as follows:
> "%s\n", <new directory>
> Otherwise, there shall be no output.
>
> and INSTALL uses the idiom
> `cd ${dir} && /bin/pwd`
> to convert the directory name dir to a full path.
>
> libtools explicitly unsets CDPATH, presumably to avoid this
> sort of problem. All the R scripts should do so.
>
> Bill Dunlap
> TIBCO Software Inc - Spotfire Division
> wdunlap tibco.com
>
> > -----Original Message-----
> > From: r-devel-bounces_at_r-project.org
> > [mailto:r-devel-bounces_at_r-project.org] On Behalf Of David Rossell
> > Sent: Monday, December 15, 2008 2:05 AM
> > To: r-devel_at_r-project.org
> > Subject: [Rd] bug in R CMD INSTALL do_install under OS X
> >
> > Hi, I believe I've encountered a bug in the do_install function in the
> > script used by R CMD INSTALL. I'm using R 2.8.0 under OS X
> > 10.5.5. I was
> > trying to install a package from source (the package gaga
> > which I maintain,
> > which I checked and builds correctly for R 2.8.0) when I get the error
> > message
> >
> > * Installing to library '/Users/drossell/Desktop/R-2.8.0/library'
> > /Users/drossell/Desktop/R-2.8.0/bin/INSTALL: line 950: cd:
> > /Volumes/biostats/projects/routines/R/gaga
> > /Volumes/biostats/projects/routines/R/gaga: No such file or directory
> > sed: DESCRIPTION: No such file or directory
> > ERROR: no 'Package' field in 'DESCRIPTION'
> >
> > I get this same error for any other package that I try to install.
> >
> > Upon debugging the script, I've found that the script is
> > trying to cd to
> > "/Volumes/biostats/projects/routines/R/gaga\n/Volumes/biostats
> /projects/routines/R/gaga".
> > That is, the directory is repeated twice, which causes the
> > installation to
> > fail. To temporarily fix the bug I commented out the 1st two
> > lines in the
> > do_install function and manually specified the directory.
> > After doing this
> > the package installs just fine.
> >
> > # cd "${1}"
> > # pkg_dir="${1}"
> > cd "/Volumes/biostats/projects/routines/R/gaga" #line added
> > pkg_dir="/Volumes/biostats/projects/routines/R/gaga" #line added
> >
> > Thanks,
> >
> > David
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel_at_r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>

-- 
David Rossell
Manager, Bioinformatics and Biostatistics unit
IRB Barcelona
Tel (+34) 93 402 0217
Fax (+34) 93 402 0257

	[[alternative HTML version deleted]]

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