From mtmorgan at fhcrc.org  Thu Oct 31 12:27:45 2013
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 31 Oct 2013 04:27:45 -0700
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>
References: <220141431.876438.1379966140031.JavaMail.root@fhcrc.org>
	<5240B844.1080701@stats.ox.ac.uk>
Message-ID: <52723EB1.1050908@fhcrc.org>

On 09/23/2013 02:53 PM, Prof Brian Ripley wrote:
> 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 many identical warnings can obscure useful messages, e.g., about invalid 
permissions on files. Can these be collapsed to a single warning, or one for 
each of uid / gid?

>
> 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
>>
>
>


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