I had the following files in /:
root@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@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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