http://forum.lazy8studios.com/index.php?PHPSESSID=h1d37r13a2d2ccnk5c5j6b2c94&topic=475.msg837#msg837

This is a fix for the bug where Cogs launches with the following output:

Shader compile log for data/effects/TextureBumpCubemap.fsh:
Fragment shader failed to compile with the following errors:
ERROR: 0:41: error(#132) Syntax error: ‘smooth’ parse error
ERROR: error(#273) 1 compilation errors.  No code generated

Apparently the word “smooth” is reserved, but only on ATI cards in Linux.  The fix is to modify the following file.

~/games/cogs/data/effects/TextureBumpCubemap.fsh

Just do a global replace of the word “smooth” with “Smooth”.

A huge thanks to Renee Marie Jones, who figured this one out

I wasn’t seeing that particular output on the console, and the screen was just blank/black and I could hear the music. But, this fix did work for me on Ubuntu Linux 10.10 (Maverick).

I suspected that this was an issue with ChemDraw 12.0.2 (I’m using 12.0.1 and so are other CMLD members for the research lab I support). I suggested that he create a new user on his Mac and see if ChemDraw works correctly. I reasoned that ChemDraw was upgraded sometime in the past, and that there may have been some user preferences causing issues after upgrading, or some preferences settings were corrupted.

If a new user was able to use ChemDraw, then this would indicate that the installation is valid and working, and the issue is with the user’s preferences. If ChemDraw didn’t work, then the issue is probably with the installation, and we would need to install the application, and hunt down any remnants of the installation that may be in /Library or /System and then reinstall 12.0.1 to see if that would resolve the problem.
In this case, ChemDraw worked for the new user, thus indicating that the issue was not with the installation, but with the user’s setting. Deleting any files whose name started with com.cambridgesoft files in

/Users/[Your User Name]/Library/Preferences

resolved the problem.

Friday before I left work I kicked off the upgrade to Mac OS 10.6.3 on the MacBook Pro (MBP)  I use at work. I’d already upgrade my personal MacBook at home (that I got a deal on at MicroCenter) and I didn’t have any observeable problems or issues and I was confident that I could upgrade and not bork my work environment.

When I arrived back into work on Monday it looked like the upgrade had completed. I logged into the MBP and  my Bluetooth MagicMouse wasn’t working, and all  bluetooth settings were unavailable and grayed out (both on the status bar, and in System Preferences).

I figured something had gotten out of sync during the upgrade and I thought a reboot would fix the problem. Rebooting didn’t fix the problem, but manually reinstalling the upgrade did solve the problem and Bluetooth is active and settings are accessible.

You can manually get the upgrade at:

http://support.apple.com/kb/DL1017

However, when I tried to sync with my phone, a Sony Ericsson C902, the connection keeps dropping. So Bluetooth in 10.6.3 might be a bit flaky.

Wp-supercache now supports the wp-mobile plugin. What isn’t obvious from the wp-supercache settings is that you need to install the wp-mobile plugin. Get it at http://wordpress.org/extend/plugins/wordpress-mobile-edition/ unzip it, and then read the included README.txt to configure it properly.

See David Byrne’s site for more details.

1. Download the RPM package and install using rpm (not advisable).
2. Download the RPM package and convert to a DEB package using alien
3. Download the ZIP file titled “Oracle SQL Developer for other platforms” and manually install
4. Use the make-sqldeveloper-package to convert the ZIP file into a DEB package

I used the make-sqldeveloper-package, which is available for Debian and Ubuntu and it’s derivatives. However, the man page and the instructions are little unclear on how to use it. You need to download the zip file available at Oracle’s (and not the RPM file nor any of the other packages) and then use the make-sqldeveloper-package to convert it to a DEB which you can then install using the dpkg command.

This is preferable to using rpm or alien as you can more easily manage the package using Debian’s and Ubuntu package management tools, plus it will integrate SQL Developer into Gnome’s Menu System . Plus, when Oracle updates their version you can use make-sqldeveloper-package to create an updated DEB package and easily update the version you have installed. The procedure outlined below works on Ubuntu Karmic and should also work on any Debian version that has the make-sqldeveloper-package.

As the man page states:

This utility will require you to download the “Oracle  SQL  Developer  for  other  platforms”  archive  from  <http://otn.oracle.com/software/prod‐ucts/sql/> to create the Debian package from.

1. Download the ZIP file from Oracle’s site

You will need to accept Oracle’s license agreement and download the ZIP file, titled “Oracle SQL Developer for other platforms”, from:

http://www.oracle.com/technology/software/products/sql/index.html

2. Install the make-sqldeveloper-package package

sudo apt-get install sqldeveloper-package

You will need Ubuntu’s multiverse software repository. See the instructions on how to do so.

2.a. Install the tofrodos package

sudo apt-get install tofrodos

Create symbolic links to the tofrodos commands to allow the sqldeveloper-package to work:

sudo ln -s /usr/bin/fromdos /usr/bin/dos2unix

sudo ln -s /usr/bin/todos /usr/bin/unix2dos

Thanks to Miles for the tofrodos tip.

3. Convert the ZIP file to .DEB package

The format of the command is:

make-sqldeveloper-package -b BUILD_LOCATION LOCATION_OF_ZIP_FILE

In my example, I’m going to use /tmp/ORA as the build location and the ZIP file has been download to my Desktop (~Desktop).

make-sqldeveloper-package -b /tmp/ORA/ ~/Desktop/sqldeveloper-2.1.0.63.73-no-jre.zip

The command will create the build directory and remove it when the command finishes. If the command completes successfully you’ll see the following output after a minute or two:

make-sqldeveloper-package: Building sqldeveloper package in "/tmp".

The DEB file will be created in the current directory. In my example I had changed directories to /tmp and that’s where the DEB file will be:

/tmp/sqldeveloper_2.1.0.63.73+0.2.3-1_all.deb

See the man page for more information about the tool:

man make-sqldeveloper-package

4. Install the package

sudo dpkg -i sqldeveloper_2.1.0.63.73+0.2.3-1_all.deb

5. Run SQL Developer

After installing there should he an entry in Gnome’s menu to start the SQL Developer. It’s located under:

Applications->Programming->SQL Developer

Note: You will need a JVM installed for the tool to run.

Obligatory Screen Shot:

Oracle SQL Developer

Updated September 27th 2010. Added instructions from Miles on installing dos2unix alternative for Ubuntu Lucid. The dos2unix command is not available in Ubuntu Lucid.

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.

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:

sudo apt-get install f2c libg2c0 libatlas-base-dev liblapack-dev;

This symbolic link is needed as the Makefile links looks for the static version of the library and not the shared version (correct me if I’m wrong, it’s late at night and I could be mistaken):

sudo ln -s /usr/lib/libg2c.so.0 /usr/lib/libg2c.so;

Build the code:

cd /tmp/EIGEN;

cd src;

Create a backup copy of the Makefile:

cp Makefile  Makefile.org;

Edit the Makefile:

emacs -nw Makefile;

Change this line (line 24):

FF=g77

To read as:

FF=”gfortran -std-legacy”

This is needed as the g77 fortran compiler is not longer included with Ubuntu, but you can use the gfortan compiler instead, but you must run it in legacy mode.

Run make:

make eigenstrat;

This next step is essential, because binaries are included in the bin directory that appear to have been build against a 64-bit kernel and are probably artefact’s left over from when the author was testing his code. Also, running “make clean” does not remove the binaries in the bin directory, but does remove those build in the src directory.

make install;

And that should be it run the example.perl in the EIGENSTRAT directory and you should see output like this:

./example.perl
smartpca.perl -i example.geno  -a example.snp  -b example.ind  -k 2  -o example.pca  -p example.plot  -e example.eval  -l example.log  -m 5  -t 2  -s 6.0
smartpca -p example.pca.par >example.log
ploteig -i example.pca.evec -c 1:2  -p Case:Control  -x  -y  -o example.plot.xtxt
evec2pca.perl 2 example.pca.evec example.ind example.pca
smarteigenstrat.perl  -i example.geno  -a example.snp  -b example.ind  -p example.pca  -k 1  -o example.chisq  -l example.log
smarteigenstrat -p example.chisq.par >example.loggc.perl example.chisq example.chisq.GC

If you run into problems running and compiling the code, the README suggests running the following:

make pcatoy;

And, as per the README, contact your sys admin if it doesn’t work.