From dtenenba at fhcrc.org  Mon Sep 23 21:55:40 2013
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Mon, 23 Sep 2013 12:55:40 -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: <1600338441.876350.1379965703448.JavaMail.root@fhcrc.org>
Message-ID: <220141431.876438.1379966140031.JavaMail.root@fhcrc.org>

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



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