Monday, November 30, 2009

Version control system inside Emacs

Emacs works with version control.

Here is something for using Git inside Emacs:

OpenMX, again

With help from Michael Spiegel, the lead developer of OpenMX, I was able to get it compiled and installed on my 64-bit Ubuntu system. Now it runs beautifully.


to synchronize between different computers:


It seems to be something I am looking for: an interface between R and C for Bayesian analysis.

Another juicy programming story

Sunday, November 29, 2009

Silly mistake

I was trying to run and debug a Fortran program within Emacs. Strangely, GDB refused to run and Emacs kept giving me error messages. I figured there might some comparabilities between gfortran, gdb, and emacs and spent quite some time trying to figure out. Finally, it turns out to be a problem with my directory name: Emacs's gdb mode cannot handle directories with spaces in their names.

Now I know.

Portable Ubuntu

Looks interesting:

Can't get the GDB plug-in for Geany to work

I have trouble to get Geany's GDB plug-in to work smoothly. For this, Emacs definitely wins.

Linux editor


Another TeX/LaTeX journal:

Saturday, November 28, 2009

TeX Daemon

This little TeX tool seems interesting:

Friday, November 27, 2009

I like the new Stata web site

much better than the earlier one.

PBSadmb for R

This package bridges ADMB and R. It was once Windows-only and now has matured and become platform-independent. I will check it out and comment more about it.

And here is yet another R to ADMB interface:

Thursday, November 26, 2009

This is also very neat: GDB inside Emacs

ECB with Emacs

The ECB package for Emacs seems useful. Here is a screenshot.

Different ways to setup Emacs window size

Wednesday, November 25, 2009

Coders at Work: Reflections on the Craft of Programming

by Peter Seibel. Really cool book, helpful to even the non-programmers.

Various wasy to improve the "compile" command in Emacs

Tuesday, November 24, 2009

LaTeX to HTML solution

The best solution seems to be TeX4ht.

It converts a manuscript I am working on flawlessly, including tables (using the booktabs package). Wow...

A good introduction of Linux/Unix to students

If I want to teach a class on data analysis using R/Emacs/Linux, I can simply refer students to this site.

Friday, November 20, 2009

Geany and LaTeX

I just realized that Geany can handle LaTeX really well.

Nobel Peace Prize to Linus Torvalds

It makes sense to me.

Another Ubuntu review

This long review ( made several good points.

Thursday, November 19, 2009

Zim: a desktop wiki

Zim is appealing, part because its built-in LaTeX-based equation editor. It is suitable for everyday writing: sorting ideas, recording references, etc.

Here is the most recent version:

Some good Ubuntu tips

Tuesday, November 17, 2009

2009 ranking of sociology deparment

Don't know how meaningful it is:

Sunday, November 15, 2009


Looks promising:

Right now it cannot be build from source because there are some comparabilities between OpenMx and R 2.10.0, but I assume this will be resolved soon.

And the development seems to be quite active.

Saturday, November 14, 2009

Virtual machine

With 8 GB ram and fast core2 extreme processor, it is natural to have a Linux hosting Windows virtual machines on my Precision mobile workstation so I don't have to book back to Windows whenever I need to work with my colleagues using Word. There are several alternatives such as VMware, VirtualBox. It is worthwhile to try them out.

Wow, this is hard to believe

Thursday, November 12, 2009

Numeric library for Mono

Looks promising:

Tuesday, November 10, 2009

MCMC in Python

The Python library "PyMC" looks promising ( Also, here are some demos:

This is convinient

Negative reviews of Ubuntu 9.10

I myself did not experience any of the problems. Everything works flawlessly on my Precision M4400, even the webcam!


The idea of creating an IDE for ADMB is great. The currently one, which is based on Emacs, works well out-of-the-box. For a new Emacs user, it is great - the IDE has been tweaked in the way people who are not used to Emacs key binding can use immediately. But for people who use Emacs on daily basis, and have a long .emacs file, the idea of making heavy changes on the Emacs configuration file (key bindings, etc.) might not be that attractive.

A better solution will be to offer three different sets of configuration files: the one is for completely Emacs newcomers, the second one is for people who have some familiarity with Emacs but are willing to make some changes to their work habit, the third is for those diehard Emacs user who only want a syntax highlighting and maybe a key binding for compiling a .tpl file.

Nov. 19:

Well, it turns out that the "minimal IDE" I was talking about is already there: the ADMB Emacs editing mode. Simply put this file in the include directory and put two lines in the .emacs file, it works like charm. All other customizations are entirely optional. This seems to be a perfect solution.


It is Nov. 10 now and the Photran web site is stilling saying that the new version will be made available by the end of Oct.

Monday, November 09, 2009

Good examaples for copy via ssh

R package for sequence analysis

Saturday, November 07, 2009

ssh with X11

I don't have Stata installed on my new 64-bit machine so I need to use the copy on my older machine via ssh. The simple command of "ssh -X" does the trick!

Friday, November 06, 2009

Why Linux does not need a disk defragmenter?

This is by far the most intuitive discussion I found:

Good tips on Emacs

Thursday, November 05, 2009

Winbugs 1.4 works really well under Ubunti 9.10 64-bit

via Wine. I had trouble getting it running on my 32-bit Ubuntu 9.04 box. I am quite pleased.

After adding ""/home/shige/bin/WinBUGS14/", program="WinBUGS", useWINE=TRUE" to each BUGS call using R2WinBUGS, I was able to run the radon example provided in Gelmam's book.

Wednesday, November 04, 2009

Scivews-K got updated again

With the recent update, I was able to get it working properly.

Interestingly, while it works on my Vista 64-bit, it does not work on my Ubuntu 64-bit. I have no idea what is going on.

64-bit aML

I was able to compile and run aML under 64-bit Ubuntu 9.10. The only problem was "maktab", so I replaced my binary with the one supplied by the official web site. I will do some benchmark and see if these binaries are faster.

Tuesday, November 03, 2009

Advances in Statistical Methods for the Health Sciences

A useful book