[R] dev-lang/R-3.1.0: biocLite("vsn") removes all files in /
Henric Winell
nilsson.henric at gmail.com
Mon May 19 10:09:02 CEST 2014
On 2014-05-18 20:43, peter dalgaard wrote:
>
> On 18 May 2014, at 07:38 , Jeff Newmiller <jdnewmil at 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.
As a non-BioC user using BioC packages I've always wondered why the
standard R functionality isn't enough. Can someone, please, tell me why
'biocLite()' should be used?
I've always succeeded installing BioC packages using the standard R
tools (as indicated by Uwe in his reply).
Henric Winell
>
>>
>> 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:<jdnewmil at 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 <rose at rz.uni-potsdam.de> 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.
>>>
>>> ______________________________________________
>>> R-help at 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 at 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.
>
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