On 2014-05-18 20:43, peter dalgaard wrote:
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.
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.
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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.
______________________________________________
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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.
______________________________________________
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.
