Upgrading directly from Ubuntu Maverick to Oneiric Alpha 3.

First of all, this is my experience on macbook pro.  Let me begin by saying this is not recommended, my notes are practically non-existent (I’m just typing this from memory and the “history” command) and Oneiric Alpha three isn’t officially ready for production systems.  That is to say, DO NOT TRY THIS AT HOME!

The other issue that you must be aware of is the ability to put your computer in a non-bootable state very easily.  If you start this process, you must finish it.  If you turn off your computer part way through or before all of the dependencies are configured, you may find yourself with an inoperable computer, or with some subsystems (such as networking) in a completely unusable state – forcing a complete reinstall.

Ok, those disclaimers out of the way, it IS possible to go directly from Maverick (Ubuntu 10.10) to Oneiric (Ubuntu 11.11), but I don’t recommend it.  The process took hours (for me, 5 hours) of (learning how to) manually straighten out dependencies.  It was absolutely not worth the pain.  (It took approximately 500 install/remove/configure commands to straighten out, so consider yourself forewarned!)

To get it started, I brute forced the upgrade by opening my /etc/apt/sources.list file and doing a global search and replace, changing “maverick” to “oneiric”.  At that point, you can issue the command:

sudo apt-get update; sudo apt-get dist-upgrade

That will get the upgrade started.  If you’re ready for 5 hours of agony, press Y.  Before your trial by fire can begin, you may have to wait about while the nearly 1.3Gb of updated packages download. It took about 2 hours for me.

At first, the process will look fine, installing packages quickly, with the update manager doing what it should. However, at some point, the whole upgrade crapped out on me with unresolvable dependencies.  At this point, I used two tools:

sudo apt-get dist-upgrade


sudo dpkg --install [deb filename]
sudo dpkg --remove [package name]

Between those two tools (and three commands), you can work through all but one of the broken package problems you’ll face. (I used synaptic to bypass that one, as mentioned below.)

Unfortunately, I don’t have any screen captures, but if you try, you’ll see a message that reads something like:

Package [name1] can't be installed, depends: [name2] (>version).
  [name2] not configured.

Each time, you’ll need to manually try to add package [name2] yourself.  The trick is that all of these files are already downloaded, so you can add them relatively easily by moving into the directory in which apt downloaded them:

cd /var/cache/apt/archives/

The (not so hard) challenge is to figure out the name of the .deb file you need to install – which is surprisingly easy.  Once you’re in the apt archives directory, all of the packages will start with the name of the package as described by the error message above.

The bigger problem is that the dependency relations can be pretty deep.  Sometimes trying to install one package will result in another message that it, in turn, depends on another package.  One by one, you have to follow each lead to figure out what the right package is, and worse, the right order to install them in.

The bigger issue is that periodically, you will find that there is a set of dependencies that you just can’t resolve, in which case, you need to remove the blocking package from the system, install the new package, then re-install the new version of the one you’ve just un-installed.  For instance, I found I had to remove the kubuntu-desktop package to get some of the kdebase packages to install.  It’s not a big deal to do this (although you need to be aware you can accidentally remove a lot of important stuff if you aren’t careful), but you’ll need to be aware of what you remove so you can add it back if (and only if!) there is an updated package for it in the archives directory.

I also found, at one point, that there were packages I could not resolve (icedtea-6-jre-jamvm and openjdk-6-jre, if I remember right) and ended up turning to synaptic. There was a simple “resolve broken packages” command or some such. That was able to get around the set I couldn’t fix manually. I still have no idea how. However, when Synaptic works, it can finish an install for you – while it can’t/doesn’t fix everything, it can be an incredibly useful tool for navigating some complex dependency nightmares.

Periodically, you’ll also discover that you have a bunch of things that are installed, but not configured because their dependencies weren’t satisfied.  You can either re-install them manually, or use the command:

sudo dpkg --configure -a

that will reconfigure any packages in that state.

Other notes – I had to remove xserver-xorg-video-all and xserver-xorg-video-nouveau to get X to work again, as well as blacklist the nouveau driver.  You can see my post here, where I describe it in more detail.  I also had to reinstall kubuntu-desktop at the end, as it was removed earlier.

Finally, I also found I needed to recompile my kernel modules (eg, for nvida-current)at some point when I did a further dist-upgrade.  For those who are familiar with the process, I discovered this on a later reboot when x refused to restart and had to drop to the terminal to make that change.

To give the complete picture, even now, not everything is now working.  Adjusting KDE plasma panels can cause significant instability in compiz (driving it up to 100% cpu), and I had to reset the compiz settings to default before compiz would stop becoming unstable. (I have a diff between the before and after settings, and nothing jumps out at me other than the active plugins and the s0_outputs resolution:

< s0_active_plugins = core;bailer;detection;composite;opengl;imgjpeg;
> s0_active_plugins = core;bailer;composite;opengl;debugspew;decor;


< s0_outputs = 1680x1050+0+0; 
> s0_outputs = 640x480+0+0;

I can’t see that helping anyone, but perhaps one of the packages previously enabled was the cause of the instability.

Hopefully the above is useful to someone else, either by pointing you in the right directions if you follow my footsteps, OR, by keeping someone from following. Either one would be a good outcome!

Good luck, and happy migrating.

Compiz running on Ubuntu 11.10 (Oneiric)

NOTE: October 18, 2011.  I see that this page is the top hit on my blog this week.  I think if you’re looking for more up to date information, you should see my current opinion on Compiz on Kubuntu here.

After months of waiting for things to be resolved with the nvidia drivers and such, I finally buckled down to see if I could get compiz running again smoothly on Ubuntu 11.10.  Happily, I can report that the answer is yes!

Using the latest packages, the trick was to follow some advice in this thread.

First, you need to blacklist the nouveau driver.  It hasn’t been working for me, and it has been preventing the nvidia driver from being loaded.

sudo nano /etc/modprobe.d/blacklist.conf

add “blacklist nouveau” to the end of the file, then save and close it.

Next, you do need to update initramfs and  reinstall the nvidia-current driver:

sudo update-initramfs -u -v
sudo apt-get install --reinstall nvidia-current

From that point on, a simple reboot (and making sure that your xorg.conf actually uses the nvidia driver) should be enough to get you back into Xorg with the Nvidia binary blob… and by opening a terminal and typing:

compiz --replace

You should be good to go again. Things appear to be stable, but I’m sure this will need a lot more testing before I switch back to compiz/kde/nvidia as my default setup.

“bioinformatics is in decline”

Actually, the original post said “Is bioinformatics on decline?”  That lack of consideration for English grammar might be a bit of a foreshadowing for the flavour of the arguments that I’ll relay below.  (Granted, I would never ignore a post solely because of bad grammar and the author is clearly not a native English speaker, so lets not dwell on that point.)

Let me summarize the original post:

  • A link to a post that indicates the author is upset that some people have to ask what fields are encompassed by bioinformatics.
  • A link to a blog post that says “Less people are searching for the word bioinformatics using google”.
  • Some ambiguous claim that this applies to India, which is later clarified to mean “northern India”, which is never explained.
  • The author, by the way, claims to be a Search Engine Optimization (SEO) “expert” on his blog.

The last point is a great indication to me about the quality of the information you’re about to hear from him, in my opinion.  Anyone who claims to be interested in search engine optimization is all about hits, not about quality of information disseminated.  That’s a simple guarantee –  and I’m certain that Mr Brij has gotten a lot of hits on his web page by making what is not a controversial statement, but an obtuse one.

In essence, I believe this whole claim is likely more about driving traffic to his blog than making a valid contribution to a discussion.  I regret having visited it already, and I certainly won’t be linking to it.

In any case, lets deal with his first two points.  The first is that “People are asking what bioinformatics is about.”  To me, that indicates that more people are interested in the field, rather than that fewer people are interested.  If he never had to answer the question about bioinformatics, then I might be concerned that he’d either saturated the world with people knowledgeable about the field, or that no one new was hearing about it.  Clearly the first is impossible.  (So long as I have family members, I can guarantee first hand knowledge that there are people who are clueless about what bioinformatics really is.)

In reality,  this is just anecdotal evidence that the author is relaying.  We’re better off ignoring it and assuming that the conclusions drawn by Mr. Brij are just inaccurate extrapolations from bad data.

Lets move on to the second claim that Mr. Brij makes about the decline of bioinformatics on google trends.  I’m going to ignore the  wonderful comment someone made about how all searches on google trends have to be considered in relation to the growing number of searches for “porn”.  I don’t know if it’s true or not, though it seems plausible, but it’s perhaps not the best refutation for Mr. Brij’s assertion that bioinformatics is declining.

Instead, lets look at a different set of words:  {bioinformatics, biotech, pharma and antibody}. This will give us a control experiment, as there are magazines and entire industries devoted to watching biotech and pharma for trends.  If either of those were in steep decline, it would undoubtedly be all over the front pages of every industry publication.

Guess what?  They all show exactly the same downward trend!  (Even down to the little dip over the North American winter holidays.  I’d definitely be interested in hearing more about that phenonmenon!)  Does that mean that the pharma and biotech industries are going to be extinct in the near future?  Not so much – it’s simply a function of the overall traffic on google.

I surmise that in order to predict the decline of something on the web, you’ll need much more useful information than the proportion of google searches that include a specific term.  People haven’t stopped using antibodies over the past decade and bioinformatics sure as heck hasn’t gotten any less popular.  Frankly, I doubt most bioinformaticians spend their time googling for “bioinformatics” anyhow, which makes this a pretty moot point.  We all have better things to do.

The third point from the original author is that this somehow relates specifically to bioinformatics in India.  I’m not even going to deal with this point other than to say that the data presented doesn’t support this claim.  No statistics are presented on Mr. Brij’s blog and the excerpt from an excel spreadsheet that is given only demonstrates that there is fluctuation in the frequency of the search terms by month.  It’s not at all enlightening.

So, if I may pass along one piece of advice to the “SEO expert” Mr. Brij: Instead of trying to get more traffic to your site by placing links to your blog next to poorly phrased questions on popular web sites, I suggest you try to produce quality analyses and insightful observations.  That will drive up the number of hits you get in the long term far more than trying to suck people in with ridiculous claims.

In the meantime, I won’t be visiting your page again.