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

[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 ->
> /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. 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



> 
>  -- output of sessionInfo():
> 
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=C
>  [5] LC_MONETARY=C              LC_MESSAGES=de_DE.UTF-8
>  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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