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
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