[R] dev-lang/R-3.1.0: biocLite("vsn") removes all files in /

[Martin Morgan]

This would be very bad and certainly unintended if it were the responsibility of 
biocLite. Can we communicate off-list about this? In particular can you report

   noquote(readLines("http://bioconductor.org/biocLite.R"))

?

Martin Morgan

On 05/17/2014 10:16 PM, Juergen Rose wrote:
> I had the following files in /:
>
> root at caiman:/root(8)# ll /
> total 160301
> drwxr-xr-x   2 root root      4096 May 16 12:23 bin/
> drwxr-xr-x   6 root root      3072 May 14 13:58 boot/
> -rw-r--r--   1 root root     38673 May 14 14:22 boot_local-d.log
> lrwxrwxrwx   1 root root        11 Jan 22  2011 data -> data_caiman/
> drwxr-xr-x   7 root root      4096 Mar  9 22:29 data_caiman/
> lrwxrwxrwx   1 root root        23 Dec 29 13:43 data_impala -> /net/impala/data_impala/
> lrwxrwxrwx   1 root root        21 Jan 27 08:13 data_lynx2 -> /net/lynx2/data_lynx2/
> drwxr-xr-x  21 root root      4040 May 14 14:40 dev/
> drwxr-xr-x 160 root root     12288 May 17 17:14 etc/
> -rw-------   1 root root     15687 Dec 26 13:42 grub.cfg_old
> lrwxrwxrwx   1 root root        11 Jan 23  2011 home -> home_caiman/
> drwxr-xr-x   5 root root      4096 Dec 26 11:31 home_caiman/
> lrwxrwxrwx   1 root root        23 Dec 29 13:43 home_impala -> /net/impala/home_impala/
> lrwxrwxrwx   1 root root        21 Jan 27 08:13 home_lynx2 -> /net/lynx2/home_lynx2/
> lrwxrwxrwx   1 root root         5 Mar 30 04:25 lib -> lib64/
> drwxr-xr-x   3 root root      4096 May 14 04:31 lib32/
> drwxr-xr-x  17 root root     12288 May 16 12:23 lib64/
> -rw-r--r--   1 root root   1797418 May 14 14:22 login.log
> drwx------   2 root root     16384 Jan 20  2011 lost+found/
> drwxr-xr-x   2 root root         0 May 14 14:21 misc/
> drwxr-xr-x  10 root root      4096 Nov  4  2013 mnt/
> drwxr-xr-x   4 root root         0 May 17 17:38 net/
> drwxr-xr-x  13 root root      4096 Feb 13 13:25 opt/
> dr-xr-xr-x 270 root root         0 May 14 14:21 proc/
> drwx------  36 root root      4096 May 17 15:00 root/
> drwxr-xr-x  30 root root       840 May 16 18:21 run/
> drwxr-xr-x   2 root root     12288 May 16 12:23 sbin/
> -rw-r--r--   1 root root 162191459 Jan 13  2011 stage3-amd64-20110113.tar.bz2
> dr-xr-xr-x  12 root root         0 May 14 14:21 sys/
> drwxrwxrwt  16 root root      1648 May 17 17:14 tmp/
> drwxr-xr-x  19 root root      4096 May  6 04:40 usr/
> drwxr-xr-x  16 root root      4096 Dec 26 11:17 var/
>
>
> Then I did as root:
> R
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("vsn")
>
> Save workspace image? [y/n/c]: n
> root at caiman:/root(15)# ll /
> total 93
> drwxr-xr-x   2 root root  4096 May 16 12:23 bin/
> drwxr-xr-x   6 root root  3072 May 14 13:58 boot/
> drwxr-xr-x   7 root root  4096 Mar  9 22:29 data_caiman/
> drwxr-xr-x  21 root root  4040 May 14 14:40 dev/
> drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
> drwxr-xr-x   5 root root  4096 Dec 26 11:31 home_caiman/
> drwxr-xr-x   3 root root  4096 May 14 04:31 lib32/
> drwxr-xr-x  17 root root 12288 May 16 12:23 lib64/
> drwx------   2 root root 16384 Jan 20  2011 lost+found/
> drwxr-xr-x   2 root root     0 May 14 14:21 misc/
> drwxr-xr-x  10 root root  4096 Nov  4  2013 mnt/
> drwxr-xr-x   2 root root     0 May 17 17:38 net/
> drwxr-xr-x  13 root root  4096 Feb 13 13:25 opt/
> dr-xr-xr-x 272 root root     0 May 14 14:21 proc/
> drwx------  36 root root  4096 May 17 15:00 root/
> drwxr-xr-x  30 root root   840 May 16 18:21 run/
> drwxr-xr-x   2 root root 12288 May 16 12:23 sbin/
> dr-xr-xr-x  12 root root     0 May 17 17:38 sys/
> drwxrwxrwt  19 root root  1752 May 17 18:33 tmp/
> drwxr-xr-x  19 root root  4096 May  6 04:40 usr/
> drwxr-xr-x  16 root root  4096 Dec 26 11:17 var/
>
> I.e., all not directory files in / disappeared. This happens on two systems.
>
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