A quantum leap (CoRe in CiRM [4])

Today, as I was trying to install SpatialEpi to use the Scotland lip cancer data in the last chapter of Bayesian Core, I realised my version of R, R Version 2.6.1, was hopelessly out of date! As I am also using Hardy Heron, a somehow antiquated version of Ubuntu on my Mac, upgrading R took some effort as well. I eventually found that adding the line

deb http://cran.cict.fr/bin/linux/ubuntu hardy/

in /etc/apt/sources.list worked nicely. So I now moved two years forward in time!!! On top is my first attempt at plotting the dataset with my modified version of mapvariable. As it happens, another blog appeared today on R-bloggers about color gradients using ggplot2.

karmic-mac (2)

At this stage the Ubuntu 9.10 system installed on my Mac had not yet crashed! The current post was actually started and posted from that very Mac…Things that are working properly are ethernet and wireless connections (obviously!), suspend functions, basic functions like pdflatex and R, Skype, USB connections, screensaver, multiple screens, DVD and camera handling. Things not working are brightness and keyboard backlight control from the keyboard. Things I have not yet tested are sound and driver add-ons. But then I copied the sound and video instructions from the Kamic documentation for MacBook Pro 5.3, including the fateful

sudo add-apt-repository ppa:mactel-support

and then rebooted. This (or maybe the sound related command

sudo aptitude reinstall linux-headers-`uname -r` linux-image-`uname -r`

that was alluded to on a forum) created a nvidia error

NVIDIA(0): Failed to load the NVIDIA kernel module

and an almost empty xorg.conf file… I tried to reinstall the xorg.conf using various sources and the repair live cd, to no avail. So I eventually went back to reinstall Ubuntu 9.10 for the third time in three days… It is working again but I have not tried to reinstall the sound following the instructions on the documentation. I have reinstalled Skype, it seems to work, even the webcam is working but not the sound! I also installed the pommed package that should control brightness and the backlit keyboard. It does not work as

sudo pommed -f

returns

E: Unknown Apple machine: MacBookPro5,3

and changing values in /etc/pommed.conf does not have any impact… I would like to see those major points solved without any further manipulation from the user, we are talking the sound system of a Mac, not a third generation obscure software..! I am thus quite disappointed with the continuing inability of Linux distributions to keep track of on-going hardwares…

karmic-mac

Having purchased a new MacBook Pro [5.3] thanks to the support of our most recent ANR EMILE grant, and prodded by Jean-Michel Marin to give it a try, I first attempted using the local Mac software, i.e. the Unix system behind the Snow Leopard OS, but I could not get my terminal environment to work properly for my ten basic Unix commands to operate seamlessly enough. Presumably for not trying hard enough…

Thus, this weekend, I started on the “big” move to a rEFIt dual boot with Ubuntu 9.10 (Karmic koala!) installed on the second half of the partition. The whole process is fairly well described on Ubuntu forums and I followed the steps there so that the installation first succeeded. I then tried to install KDE 4.3 from the original Gnome environment and this did not produce an acceptable working platform. I reluctantly switched back to Gnome and cut down as many features of this environment as possible to obtain a minimalist working space. At this stage, I was asked to update various packages  of Karmic and then disaster stuck when I accepted to switch between versions of Grub2: later attempts to rescue and even to reinstall Ubuntu 9.10 failed. When I booted from anything but the Mac OS, on the rEFIt panel, I was getting an infinite sequence of GRUB on the screen… The forums being also full of contradictory and failing suggestions, this drove me mad the whole afternoon!!! I eventually erased everything including rEFIt and managed once again to access  the Ubuntu OS. I cannot say I have  yet reached a point where I trust the stability of the system.