Fixing the proxy problem in Mendeley Developer preview 1.7 on Ubuntu 12.04 LTS

I am a big fan of Mendeley (www.mendeley.com) as a tool for storing and organizing my references. In particular the pretty robust extraction of bibliographic data from PDFs saves me a couple of steps in the workflow that I was used to when doing this with Endnote.
I recently received my new (proper) workstation and I have switched from running Ubuntu 10.04LTS in a virtual machine to using Ubuntu 12.04LTS as the main OS and rather running a virtual machine instance of Windows 7 for the few remaining pieces of software which need a Windows OS. Since switching over to Linux, I have not been able to use the Linux version of Mendeley, as it steadfastly refuses to connect to the internet via our work proxy server. While it is possible to configure the proxy settings under "Tools/Options/Connection" the connection test (which can be invoked by pressing Ctrl+Shift+D to bring up the debug console - "Test Internet Connection") reported that it wasn't able to provide proxy authentication. I tried several fixes as outlined in the Mendeley support forums (e.g. http://feedback.mendeley.com/forums/4941-general/suggestions/1051563-generic-linux-bug-connecting-through-proxy-does-n) but none of them worked...

Eventually a combination of defining system wide proxy settings as described here:

http://askubuntu.com/questions/150210/how-do-i-set-systemwide-proxy-servers-in-xubuntu-lubuntu-or-ubuntu-studio

and here some GNOME specific settings:

http://developer.gnome.org/ProxyConfiguration/

and setting the "Tools/Options/Connection" settings in Mendeley to

"No Proxy"

have fixed this problem.

Now Mendeley uses the system-wide proxy setting for connecting to the server and nicely syncs my library the way I was used to. Unfortunately I cannot tell which environment variable is relevant to Mendeley, but as I am using a number of applications which need internet access and everyone of them seems to read out different variables the best way seems to be to set all possible PROXY variables with the relevant connection information.

Installing "mixOmics" under R-2.15.1 - fixing missing dependencies

mixOmics

The package "mixOmics" depends on a nunber of packages which render some of the 3D graphics output, among them "rgl" which in turn needs a OpenGL libraries/header files for successful compilation. These can be installed by issuing following command in a separate terminal window:

sudo apt-get install libglu1-mesa-dev libgl1-mesa-dev

 Once the system packages have been installed, issuing following command in your R session will install the "mixOmics" package:

install.packages("mixOmics")

Installing R-2.15.1 source package on Ubuntu 12.04 LTS

When attempting to install R-2.15.1 from source on a freshly installed Ubuntu 12.04.1 desktop I ran into several problems stemming from unmet dependencies. The by far most challenging to resolve was the missing of "libg2c0" which is required to run mixed C/FORTRAN code.

The error message from running ./configure in the R source directory:

checking whether mixed C/Fortran code can be run... configure: WARNING: cannot run mixed C/Fortan code
configure: error: Maybe check LDFLAGS for paths to Fortran libraries?

 After spending approximately two hours trying to resolve this unmet dependency by several different approaches, the command which brought the solution to this was:

sudo apt-get install cfortran

And some additional packages to resolve issues with HTML and PDF format R manuals:

apt-get install texlive-fonts-extra fig2ps

"fig2ps" in particular will install a lot of dependencies if TEX has not previously been installed on the system.