From wdunlap at tibco.com  Mon Dec 15 21:29:33 2008
From: wdunlap at tibco.com (William Dunlap)
Date: Mon, 15 Dec 2008 12:29:33 -0800
Subject: [Rd] bug in R CMD INSTALL do_install under OS X
In-Reply-To: <376b783d0812150204h551df587t51ab032a4f980a72@mail.gmail.com>
References: <376b783d0812150204h551df587t51ab032a4f980a72@mail.gmail.com>
Message-ID: <77EB52C6DD32BA4D87471DCD70C8D70053609B@NA-PA-VBE03.na.tibco.com>

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
> 



[Rd] bug in R CMD INSTALL do_install under OS X
William Dunlap