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

[Dan Tenenbaum]

----- Original Message -----
> From: "Juergen Rose" <rose at rz.uni-potsdam.de>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Juergen Rose [guest]" <guest at bioconductor.org>, "vsn Maintainer" <huber at ebi.ac.uk>, bioconductor at r-project.org
> Sent: Sunday, May 18, 2014 10:39:03 AM
> Subject: Re: [BioC] R-3.1.0: biocLite("vsn") removes all files in /
> 
> Am Sonntag, den 18.05.2014, 10:32 -0700 schrieb Dan Tenenbaum:
> > 
> > ----- Original Message -----
> > > From: "Juergen Rose" <rose at rz.uni-potsdam.de>
> > > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> > > Cc: "Juergen Rose [guest]" <guest at bioconductor.org>, "vsn
> > > Maintainer" <huber at ebi.ac.uk>, bioconductor at r-project.org
> > > Sent: Sunday, May 18, 2014 3:38:34 AM
> > > Subject: Re: [BioC] R-3.1.0: biocLite("vsn") removes all files in
> > > /
> > > 
> > > Am Sonntag, den 18.05.2014, 00:03 -0700 schrieb Dan Tenenbaum:
> > > > Hi Juergen,
> > > > 
> > > > ----- Original Message -----
> > > > > From: "Juergen Rose [guest]" <guest at bioconductor.org>
> > > > > To: bioconductor at r-project.org, rose at rz.uni-potsdam.de
> > > > > Cc: "vsn Maintainer" <huber at ebi.ac.uk>
> > > > > Sent: Saturday, May 17, 2014 11:09:44 PM
> > > > > Subject: [BioC] R-3.1.0: biocLite("vsn") removes all files in
> > > > > /
> > > > > 
> > > > > 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
> > > > > ->
> ...
> > > > > 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/
> ...
> > > > > -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   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 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. I know it is a risk to run scripts from the internet
> > > > > as
> > > > > root. But what would be the alternative to install a
> > > > > bioconductor
> > > > > package for all users?
> > > > > 
> > > > 
> > > > I don't know why this happened. We'll need to investigate
> > > > further.
> > > > 
> > > > However, you could install BiocInstaller (the package that
> > > > provides
> > > > biocLite()) as follows (you don't need to be root):
> > > > 
> > > > install.packages("BiocInstaller",
> > > > repos="http://bioconductor.org/packages/3.0/bioc")
> > > > 
> > > > Then you can install packages as follows:
> > > > library(BiocInstaller)
> > > > biocLite("vsn")
> > > > 
> > > > Note that you don't have to be root to install packages tha are
> > > > accessible to all users.
> > > > You just have to install them to a directory that you have
> > > > permissions to write to.
> > > > 
> > > > You can start R (as any user) and see where it will look for
> > > > packages by doing:
> > > > 
> > > > .libPaths()
> > > > 
> > > > Then arrange to give yourself (a non-root user) write
> > > > permissions
> > > > to that directory, and then install packages with biocLite() as
> > > > described above. If the installation is indeed removing files
> > > > from
> > > > /, it should now not be able to do so if it doesn't have
> > > > permission to do so.
> > > > 
> > > > Dan
> > > 
> > > Thanks Dan,
> > > 
> > > I tried this.  I am belonging to group portage and the R-packages
> > > are
> > > installed under /usr/lib64/R/library. Therefore I changed the
> > > group
> > > of /usr/lib64/R/library to portage and made it writable by
> > > portage:
> > > 
> > > root at lynx2:/root(21)# ll -d /usr/lib64/R/library
> > > drwxrwxr-x 40 root portage 4096 May 18 12:10
> > > /usr/lib64/R/library/
> > 
> > 
> > Maybe try changing permissions recursively?
> > 
> > sudo chgrp -R portage /usr/lib64/R/library
> > 
> > Dan
> 
> Maybe I should do this only for bioconductor R-packages. Is there an
> easy way to find out, which installed R-packages are installed with
> 'biocLite("pkg")'?
> 

Bioconductor packages can have dependencies on CRAN packages so you need to be able to install those too.

biocLite() installs CRAN as well as Bioconductor packages. 

BTW, I think Kasper's suggestion is a good one.

Dan


> Juergen
> 
>  
> 
> 
>