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:
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!
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 firstname.lastname@example.org 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 &
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:
This Luna release of the elementary OS GNU/Linux distribution seems and interesting project… I’m downloading it right now to play with it inside a VirtualBox instance …
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).
Matthew Paul Thomas ☞ System Settings for Ubuntu Phone
Ubuntu announced its 8.04 Desktop release almost 36 months ago, on April 24, 2008. For the LTS Desktop releases, Ubuntu committed to ongoing security and critical fixes for a period of 36 months. The support period is now nearing its end and Ubuntu 8.04 Desktop will reach end of life on Thursday, May 12, 2011. At that time, Ubuntu Security Notices will no longer include information or updated packages for Ubuntu 8.04 Desktop.
The supported upgrade path from Ubuntu 8.04 Desktop is via Ubuntu 10.04 Desktop. Instructions and caveats for the upgrade may be found at https://help.ubuntu.com/community/LucidUpgrades. Ubuntu 8.04 Server continues to be actively supported with security updates and select high-impact bug fixes. All announcements of official security updates for Ubuntu releases are sent to the ubuntu-security-announce mailing list, information about which may be found at
Ubuntu Release Manager
The Ubuntu team is proud to announce the release of Ubuntu 10.04.1 LTS,
the first maintenance update to Ubuntu’s 10.04 LTS release. This
release includes updated server, desktop, and alternate installation CDs
for the i386 and amd64 architectures.
Numerous updates have been integrated, and updated installation
media has been provided so that fewer updates will need to be downloaded
after installation. These include security updates and corrections for
other high-impact bugs, with a focus on maintaining stability and
compatibility with Ubuntu 10.04 LTS.
To Get Ubuntu 10.04.1 LTS
To download Ubuntu 10.04.1 LTS, or obtain CDs, visit:
We recommend that all users read the release notes, which document
caveats and workarounds for known issues. They are available at: