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

2014-05-19 Thread Henric Winell
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

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

2014-05-19 Thread Martin Morgan
On 05/19/2014 01:09 AM, Henric Winell wrote: 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

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

2014-05-18 Thread 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

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

2014-05-18 Thread Martin Morgan
This would be very bad and certainly unintended if it were the responsibility of biocLite. Can we communicate off-list about this? In particular can you report noquote(readLines(http://bioconductor.org/biocLite.R;)) ? Martin Morgan On 05/17/2014 10:16 PM, Juergen Rose wrote: I had the

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

2014-05-18 Thread peter dalgaard
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

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

2014-05-18 Thread jwd
On Sun, 18 May 2014 07:16:46 +0200 Juergen Rose r...@rz.uni-potsdam.de wrote: What disappeared are links and three files. The links are recreatable, although they would be better placed in user space rather than under /. Of the three files, the *bz2 appears to be part of a Gentoo release, the

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

2014-05-17 Thread Juergen Rose
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 root11 Jan 22 2011 data

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

2014-05-17 Thread Jeff Newmiller
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