Just back from a trip home to Ireland and am pooped. Got up at 6am (1am EST) and drove up to Dublin Airport from Donegal Town via Omagh. Got there about 10.30am, would have been earlier but the car was running on fumes and I had to stop for petrol. As I was whizzing down the M1, my cousin John, whom I gave a lift to the airport, said there’s no services on that motorway. Which lead us on a 30 minute detour trying to find some petrol pumps in the wastes of Louth!

Got to the airport at 10.30am, dropped off the car, had a ciggie, met my friend Eamon L. who dropped out to see me off and had a nice big (expensive) breakfast before going through security. Had 3 jumbo sausages, 2 rashers, 2 slices of thick toast, 1 egg, 1 hash brown, 1/2 a fried tomato, and numerous backed beans.:) A good end to a long drive, and a nice fill-up before a long flight.

On the plane I got 2 seats to meself and dosed off for about 2 hours or more after they served “dinner”. Woke up somewhere over the Canadian north and got to watch the lame ending to the last Harry Blouter film.

At Logan (Boston’s airport), I got through everything quickly, and didn’t have to wait too long for a shuttle bus to the blue line on the subway. And it wasn’t too busy considering it was rush hour. I guess most of the commuters were heading the other way. I changed Gov Center for the Green Line that goes near the house, and lucky enough I got a local train going to Kenmore (never seen one of those before) which was nice and quiet and not full of rush-hour nasties. And got home in time to see the sunset.

So now I’m pooped, as it’s 11:45pm Irish Time, and I need dinner … pics will appear on Flickr at some point.

Update: Here’s one!
More via this Flickr search.

These are rough notes on how to compile Eigensoft 3 on Ubuntu Jaunty.

Update, Eigensoft 4 is available and should compile on more recent versions of Ubuntu:
http://www.hsph.harvard.edu/faculty/alkes-price/software/

Create a location to build the code:

Warning: /tmp is for temporary files, and any files & directories you create there will be remove upon some subsequent reboot.

cd /tmp;

mkdir EIGEN;

cd  EIGEN;

Get the Eigensoft source code:

wget  http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG3.0.tar.gz;

tar xzvf EIG3.0.tar.gz;

Install required dependences: Continue reading ‘Compiling EIGENSOFT on Ubuntu Januty’

This is a brief HOWTO on compiling OSRA, (Optical Structure Recognition) on Ubuntu Jaunty. To quote the OSRA home page, OSRA is

… is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES (Simplified Molecular Input Line Entry Specification – see http://en.wikipedia.org/wiki/SMILES) or SD file – a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick – including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or SDF representation of the molecular structure images encountered within that document …

Update: I’ve a newer document that shows how to install Osra on Ubuntu 11.10 (Oneiric):

• http://timony.com/mickzblog/2012/03/24/build-install-osra-1-3-8/

Make a directory to compile the source:

mkdir /tmp/OSRA; cd /tmp/OSRA;

Be careful doing this in /tmp is cleaned upon reboot the directory may be removed.

Install dependencies needed by the OS:

sudo apt-get install libgraphicsmagick1-dev libmagick++-dev libgraphicsmagick++1-dev potrace gocr  libtclap-dev libopenbabel-dev libopenbabel3 openbabel libnetpbm10 libnetpbm10-dev

Don’t install ocrad and remove it if it’s on your system (you can probably reinstall if you need to after you get Osra to compile):
sudo apt-get remove –purge ocrad;

Source Code:

Instead of manually getting the source packages download the sources used to build the packages for Ubuntu if available.  Make sure the src lines are commented in, in your /etc/apt/sources.list . This will automatically download and extract the code into the current directory:

cd /tmp/OSRA; apt-get source gocr ocrad potrace;

This downloads Gocr 0.46 which the OSRA docs say may not work:

- GOCR/JOCR, optical character recognition library, version 0.43 or later (version 0.45 recommended, do not use 0.46! See special instructions for 0.47 compilation below) Continue reading ‘Compiling Osra on Ubuntu Jaunty’

I won’t be in Boston for the fireworks show on July 4th. But if you show up at the last minute to see the fireworks, they start at 10.30pm, you can head onto to Harvard Bridge, commonly know as Mass Ave Bridge and get some decent view of the fireworks.

The last time I watched the fireworks from the bridge was in 2007, and I was near the middle at the 200 smoot mark:

The views of the fireworks was quite good, not as good as being on the river banks. Considering you could show up 5 minutes before the start of the display instead of 12 hours before is a good tradeoff in viewing quality. Continue reading ’4th of July Fireworks!’

The view from my desk at my new job isn’t bad:

Much better than looking at the tweed walls of the cube in the cube farm of my old workplace. And, non-Donegal Tweed at that, sure even the Donegal Tweed is now made in Morocco, and the only native Donegal Tweed is made by artisans.

On Ubuntu it used to be that ctrl-alt-backspace would kill X (the backend of the various graphical user interfaces on Linux). In an aim to be user friendly this is now disabled by default. This can be a real pain if X locks up, you can’t kill it nor change to a console.

On Debian and Ubuntu you can install the dontzap command which will allow you to kill X:

sudo apt-get install dontzap

Then run dontzap:

sudo dontzap -d

Or you can the following section to your /etc/X11/xorg.conf file (which is what the dontxzap command does):

Section "ServerFlags"
        Option  "DontZap"       "False"
EndSection

See Alberto Milone’s blog for more info:
http://albertomilone.com/wordpress/?p=335

I use Kayak.com whenever I’m planning a trip any where, it’s a good source to determine who flies to what destination and whose got the lowest price. Today, there’s a wee bug on their website where they tell me I should upgrade to Firefox 2.0.0.16, this would be sound advise except for the fact that I’m using a newer version of Firefox:

So I think someone needs to look at the math used here, because 3.0.8 is greater than 2.0.0.16. This is using Firefox on Ubuntu Linux.

Update: This may not be a Kayak.com problem and may be a problem with how Ubuntu build Firefox. In the Firefox “about:” page (type about: in the URL bar). It reports the following:

There is a Ubuntu bug that may be related to this, and I’ve added a comment and the screen-shot that’s immediately above.

Great tool for converting KDE3 settings to KDE4 on Debian. Also, it’s works well to merge KDE4 settings from .kde4 with KDE3 settings in .kde. This is useful as KDE4 1st used .kde4 to save personal KDE configuration data. KDE4 is now using .kde for config data, which mean early KDE4 users will have problems with new KDE4 apps. Fear not, Kaboom will help!

http://pkg-kde.alioth.debian.org/kaboom.html

I’d advise saving back-up copies of both .kde and .kde4 .

I have a Red Hat 9 server that I have to support for a wee while longer. I needed to install some packages and I didn’t have the original install CD’s nor access to Red Hat’s repositories.

After lot’s and lot’s of searching I found the ISO images at:
ftp://archive.download.redhat.com/pub/redhat/linux/9/en/iso/i386/

But, there’s too many users on Red Hat’s FTP server and I can’t get access … thankfully rpmfind.net have a mirror:
http://fr.rpmfind.net/linux/redhat/9/en/iso/i386/

So now I can download the ISO images, and mount them on the Linux box using the loop-back interface and install the packages I need.

I expect to have new hardware within a month or so, and I’ll probably be using BU Linux or Ubuntu 8.04.