R devel - Sep 2013 - tar warnings in R-3.0.2 RC when R is installed by a different (non-root) user

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

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.

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