I thought this warning from Gmail about an e-mail from Google Alerts was funny. Gmail and Google alerts are both Google services.
Taken with my HTC Sensation phone, which is an Android phone:
Osra is a a utility designed to convert graphical representations of chemical structures create by Igor Filippov at the National Cancer Institute. This page documents how to compile and install Osra on Ubuntu Linux 11.10. These instructions may work on other versions of Ubuntu Linux and on Debian Linux. Please leave a comment if you have compiled Osra using these instructions on a different version of Ubuntu, or on other Linux distributions.
At the time of writing this doc, March 2012, the Osra version is 1.3.8 and is available at:
I copied all the source to a directory in /tmp. If you need the source code at some later point in time, don’t use /tmp as files in /tmp are deleted upon reboot (if they’re older than 14 days). Also, at the time of writing Osra requires a patched version of Gocr for Osra to work. You need to install Gocr before you try to compile and install Osra, you also need to install other packages required for Osra to compile. Most are listed below, but see the Osra Homepage for more details.
An overview of the steps are:
- Install required Ubuntu packages
- Compile and Install Gocr
- Compile and Install Osra
I’ve also written instructions on how to install Osra 1.2.1 on Ubuntu 9.04, however that was written in 2009. Continue reading ‘Build & Install Osra 1.3.8 on Ubuntu 11.10′
See this forum posting for a potential fix, if your using an ATI graphics card:
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.
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).
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.
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:
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.
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.
See David Byrne’s site for more details.
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:
- Download the RPM package and install using rpm (not advisable).
- Download the RPM package and convert to a DEB package using alien
- Download the ZIP file titled “Oracle SQL Developer for other platforms” and manually install
- 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:
2. Install the make-sqldeveloper-package package
sudo apt-get install sqldeveloper-package
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-22.214.171.124.73-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:
See the man page for more information about the tool:
4. Install the package
sudo dpkg -i sqldeveloper_126.96.36.199.73+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:
Note: You will need a JVM installed for the tool to run.
Obligatory Screen Shot:
Updated September 27th 2010. Added instructions from Miles on installing dos2unix alternative for Ubuntu Lucid. The dos2unix command is not available in Ubuntu Lucid.