ChemBioDraw/ChemDraw segfault on Mac OS X.

A user at work reported that ChemDraw suddenly started segfault-ing (crashing) on startup on his Mac. He’d opened a support ticket with CambridgeSoft and tried their suggestions, basically deleting every file associated with ChemDraw and reinstalling, which didn’t correct the problem.

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.

Bluetooth Stops working After upgrade to Mac OS 10.6.3

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 & Wp-mobile plugin

Recently I updated the wp-supercache plugin. It’s a plugin for WordPress which is the blogging software that runs this site. Wp-supercache is used to cache pages and is very useful if this blog should happen to get Slashdotted.

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.

Install Oracle SQL Developer on Ubuntu Karmic & Lucid

If you want to install Oracle’s SQL Developer on Ubuntu (or another DEB based system such as Debian) you can do one of the following:

  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 home

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! 🙂
BackstrandsMore via this Flickr search.

Compiling EIGENSOFT on Ubuntu Januty

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

Compiling Osra on Ubuntu Jaunty

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):

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

Linux, Python, Boston, Donegal.