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

[Uwe Ligges]

As alternative, just use R itself for it:


chooseBioCmirror()
setRepositories() # select BioC repositories here
install.packages("vsn")


Which should so the trick without any additional tools not shiped with R 
directly.

Best,
Uwe Ligges


On 18.05.2014 07:38, Jeff Newmiller 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.
>
> 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.
>