On 18 May 2014, at 07:38 , Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> Then you had best not do it again if you don't like that result.
>
> 1) This is not the right mailing list for issues having to do with
> bioconductor. Please go to the bioconductor mailing list for that.
Hmm, this is one case where I'd really rather not scare people off R-help.
Non-BioC users do use BioC packages from time to time and what Juergen did is
what the BioConductor web pages tells new users to do (probably minus the
as-root bit). A warn-off on R-help seems entirely warranted. Good to see that
Martin Morgan is taking the issue very seriously in his post below.
>
> 2) Running random scripts straight from the internet as root without
> reviewing them is exactly the kind of thing any experienced *nix user would
> never do. That is why user-level accounts have limits on the things they can
> do. I doubt you are supposed to be running anything with your current
> directory set to /, ever, especially not logged in as root.
> ---------------------------------------------------------------------------
> Jeff Newmiller The ..... ..... Go Live...
> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
> Live: OO#.. Dead: OO#.. Playing
> Research Engineer (Solar/Batteries O.O#. #.O#. with
> /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On May 17, 2014 10:16:46 PM PDT, Juergen Rose <r...@rz.uni-potsdam.de> wrote:
>> 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.
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd....@cbs.dk Priv: pda...@gmail.com
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