solving DESeq2 installation issues

At work a colleague asked me to do a system-wide installation of the R module DESeq2 in one of our internal servers.
The installation procedure is quite straight-forward:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Unfortunately I had some issues on my system, in fact I got:

…
Warning in fun(libname, pkgname) :
couldn't connect to display "localhost:12.0"
* DONE (maSigPro)

The downloaded source packages are in
	‘/tmp/RtmpfdD2RC/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I then tried to install manually the various dependencies, like XML. Still no luck. After a quick Google search I found that I was missing a couple of -dev packages on my Ubuntu machine, so I installed them:

root@server:~# apt-get install libcurl4-openssl-dev libxml2-dev

… and then re-tried to install DESeq2. This time everything was ok. Problem solved!

using graphical software on Ubuntu as root after you’ve logged in remotely

Sometimes I find myself in the situation of having to lauch some graphical software like synaptic, gedit, baobab while already using the server as root from the command line. I do not want to ‘exit’ my session and use the previous methods of which I’ve written in the past.

This is how I did it.

koolinus@localhost:~$ ssh -Y koolinus@remote.server.it
koolinus@remote:~$ sudo -i
root@remote:~# touch .Xauthority
root@remote:~# xauth merge /home/koolinus/.Xauthority 

And that’s all. Now I can launch the needed program without interrupting my root session, for example:

root@remote:~# baobab &
Aside

Ubuntu 13.10 (Saucy Salamander) released

Fwd: Ubuntu 13.10 (Saucy Salamander) released

The Ubuntu team is very pleased to announce the release of Ubuntu 13.10 for Desktop, Server, Cloud, Phone, and Core products.

Codenamed “Saucy Salamander”, 13.10 continues Ubuntu’s proud tradition of integrating the latest and greatest open source technologies into a high-quality, easy-to-use Linux distribution. The team has been hard at work through this cycle, introducing new features and fixing bugs.

Ubuntu 13.10 introduces the first release of Ubuntu for phones and Ubuntu Core for the new 64-bit ARM systems (the “arm64″ architecture, also known
as AArch64 or ARMv8), and improved AppArmor confinement. In addition to these flagship features there are also major updates throughout.

Ubuntu Server 13.10 includes the Havana release of OpenStack, alongside deployment and management tools that save devops teams time when
deploying distributed applications – whether on private clouds, public clouds, x86 or ARM servers, or on developer laptops. Several key server
technologies, from MAAS to Ceph, have been updated to new upstream versions with a variety of new features.

Maintenance updates will be provided for Ubuntu 13.10 for 9 months, through July 2014.

To get Ubuntu 13.10
——————-

In order to download Ubuntu 13.10, visit:

http://www.ubuntu.com/download

getting packages info on Ubuntu

Recently we’ve decided to move all our CentOS 5 server installations to a more modern, and bioinformatics friendly, environment. So the choose was on Ubuntu, in it’s 12.04 LTS version.

Some commands are different, especially those for exploring packages, their releases and such.

For example to see what packages install $something now I do a:

sudo apt-file search $package

while to see a package’s details, for example nano, I give a:

sudo apt-cache show nano

Package: nano
Priority: standard
Section: editors
Installed-Size: 604
Maintainer: Ubuntu Developers 
Original-Maintainer: Jordi Mallach 
Architecture: amd64
Version: 2.2.6-1
Replaces: pico
Provides: editor
Depends: libc6 (>= 2.11), libncursesw5 (>= 5.7+20100313), dpkg (>= 1.15.4) | install-info
Suggests: spell
Conflicts: pico
Breaks: alpine-pico (<= 2.00+dfsg-5)
Filename: pool/main/n/nano/nano_2.2.6-1_amd64.deb
Size: 194014
MD5sum: ce845269d2dac9b74ab02bd4f874beed
SHA1: 79a41964d1b14a2a0eb700b54e474e00b9d5de08
SHA256: a8dba08696a1ffdfbb15b617880b2b7bbe05ac9f7d690574000fe569b2298efa
Description-en: small, friendly text editor inspired by Pico
 GNU nano is an easy-to-use text editor originally designed as a replacement
 for Pico, the ncurses-based editor from the non-free mailer package Pine
 (itself now available under the Apache License as Alpine).
 .
 However, nano also implements many features missing in pico, including:
  - feature toggles;
  - interactive search and replace (with regular expression support);
  - go to line (and column) command;
  - auto-indentation and color syntax-highlighting;
  - filename tab-completion and support for multiple buffers;
  - full internationalization support.
Homepage: http://www.nano-editor.org/
Description-md5: b7e1d8c3d831118724cfe8ea3996b595
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu
Supported: 5y
Task: standard, kubuntu-active

That’s all (for now).