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 <wdun...@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 ${dir} && /bin/pwd` > to convert the directory name dir to a full path. > > libtools explicitly unsets CDPATH, presumably to avoid this > sort of problem. All the R scripts should do so. > > Bill Dunlap > TIBCO Software Inc - Spotfire Division > wdunlap tibco.com > > > -----Original Message----- > > From: r-devel-boun...@r-project.org > > [mailto:r-devel-boun...@r-project.org] On Behalf Of David Rossell > > Sent: Monday, December 15, 2008 2:05 AM > > To: r-devel@r-project.org > > Subject: [Rd] bug in R CMD INSTALL do_install under OS X > > > > Hi, I believe I've encountered a bug in the do_install function in the > > script used by R CMD INSTALL. I'm using R 2.8.0 under OS X > > 10.5.5. I was > > trying to install a package from source (the package gaga > > which I maintain, > > which I checked and builds correctly for R 2.8.0) when I get the error > > message > > > > * Installing to library '/Users/drossell/Desktop/R-2.8.0/library' > > /Users/drossell/Desktop/R-2.8.0/bin/INSTALL: line 950: cd: > > /Volumes/biostats/projects/routines/R/gaga > > /Volumes/biostats/projects/routines/R/gaga: No such file or directory > > sed: DESCRIPTION: No such file or directory > > ERROR: no 'Package' field in 'DESCRIPTION' > > > > I get this same error for any other package that I try to install. > > > > Upon debugging the script, I've found that the script is > > trying to cd to > > "/Volumes/biostats/projects/routines/R/gaga\n/Volumes/biostats > /projects/routines/R/gaga". > > That is, the directory is repeated twice, which causes the > > installation to > > fail. To temporarily fix the bug I commented out the 1st two > > lines in the > > do_install function and manually specified the directory. > > After doing this > > the package installs just fine. > > > > # cd "${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@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]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
