From dtenenba at fhcrc.org  Tue Sep 24 00:02:19 2013
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Mon, 23 Sep 2013 15:02:19 -0700 (PDT)
Subject: [Rd] tar warnings in R-3.0.2 RC when R is installed by a
 different (non-root) user
In-Reply-To: <5240B844.1080701@stats.ox.ac.uk>
Message-ID: <11859479.880715.1379973739174.JavaMail.root@fhcrc.org>



----- Original Message -----
> From: "Prof Brian Ripley" <ripley at stats.ox.ac.uk>
> To: r-devel at r-project.org
> Sent: Monday, September 23, 2013 2:53:08 PM
> Subject: Re: [Rd] tar warnings in R-3.0.2 RC when R is installed by a different (non-root) user
> 
> The issue is not the ownership (uname) but the uid.  A tarball can
> only
> store uids up to 'nobody' (usually 32767), and certainly larger ones
> cannot be unpacked portably.
> 

Thanks. I've changed the uid of this user and the warnings went away.
Dan


> The warnings did not occur before, but the tarball produced could
> cause
> problems when unpacking with other tools.
> 
> On 23/09/2013 20:55, Dan Tenenbaum wrote:
> > Hi,
> >
> > I created a package as follows:
> >
> >> a = 1
> >> package.skeleton()
> >
> > Then I got the following output when building the package:
> >
> > * checking for file ?anRpackage/DESCRIPTION? ... OK
> > * preparing ?anRpackage?:
> > * checking DESCRIPTION meta-information ... OK
> > * checking for LF line-endings in source and make files
> > * checking for empty or unneeded directories
> > * looking to see if a ?data/datalist? file should be added
> > * building ?anRpackage_1.0.tar.gz?
> > Warning: invalid uid value replaced by that for user 'nobody'
> > Warning: invalid uid value replaced by that for user 'nobody'
> > Warning: invalid uid value replaced by that for user 'nobody'
> > Warning: invalid uid value replaced by that for user 'nobody'
> > Warning: invalid uid value replaced by that for user 'nobody'
> > Warning: invalid uid value replaced by that for user 'nobody'
> > Warning: invalid uid value replaced by that for user 'nobody'
> >
> > One thing to note is that I am logged in as 'pkgbuild' and R was
> > installed by the user 'biocbuild'. I explicitly point to the R
> > that was installed by 'biocbuild' when building the package above.
> > (I used the command "~biocbuild/bbs-2.13-bioc/R/bin/R CMD build
> > anRpackage").
> >
> > There doesn't seem to be anything wrong with the ownership of the
> > files in anRpackage:
> >
> > $ ls -lR anRpackage
> > anRpackage:
> > total 20
> > drwxr-xr-x 2 pkgbuild users 4096 Sep 23 12:42 data
> > -rw-r--r-- 1 pkgbuild users  283 Sep 23 12:42 DESCRIPTION
> > drwxr-xr-x 2 pkgbuild users 4096 Sep 23 12:42 man
> > -rw-r--r-- 1 pkgbuild users   31 Sep 23 12:42 NAMESPACE
> > -rw-r--r-- 1 pkgbuild users  420 Sep 23 12:42 Read-and-delete-me
> >
> > anRpackage/data:
> > total 4
> > -rw-r--r-- 1 pkgbuild users 59 Sep 23 12:42 a.rda
> >
> > anRpackage/man:
> > total 8
> > -rw-r--r-- 1 pkgbuild users 1051 Sep 23 12:42 anRpackage-package.Rd
> > -rw-r--r-- 1 pkgbuild users  503 Sep 23 12:42 a.Rd
> >
> > These warnings did not appear with an earlier version of R-patched
> > (r63824).
> >
> > Thanks,
> > Dan
> >
> >
> >
> >> sessionInfo()
> > R version 3.0.2 RC (2013-09-17 r63944)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> >   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods
> >   base
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> 
> 
> --
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 



[Rd] tar warnings in R-3.0.2 RC when R is installed by a different (non-root) user
Dan Tenenbaum