Saturday, May 30, 2009

More CMake

Printed out the complete documentation, and have been reading that. Have also managed to get .so files out of it. So I'm making progress...

Friday, May 29, 2009

CMake Progress

think I managed to compile utils with CMake, but I'm not 100% sure. It all came out with .a archive files, which seems to be CMake's default library file format. Trying to figure out how to do the .o, .lo, and .la files that the more traditional make configuration uses. Or perhaps it's not really necessary. Don't know. That's the next step, is figuring that out.

Otherwise, just spent today running through CMake tutorials of various kinds. Beginning to get a grip on how it all works. They're probably dreading me on the mailing list though, since I sound a bit like a naive idiot.

Thursday, May 28, 2009

And onto CMake...

Docs for SWIG mention CMake explicitly. Given that Pjotr also mentioned it, I'm thinking that the next step might be to try to get everything compiling with that. If I can do that, SWIG might follow really easily.

Main problem right now: CMake's docs are woefully vague. My main complaint is that their "basic tutorial" is written all in the passive voice, making it sound like everything is done automatically. (I suppose you probably have to at least think about it working, first.) Have just written to their mailing list asking for clarification. We'll see if they thought I was too bitchy. I tried to be nice, but I'm tired and annoyed right now.

It's nearing 2:00. Time to sleep.

Wednesday, May 27, 2009


Have downloaded SWIG, and it seems to be working. Now looking through documentation and examples. This is going to be a bit of a slog...

I worry a bit how far we're going to be able to get with SWIG. If the latest version of gcc had problems compiling due to scope issues, it seems that SWIG might choke as well. Oh well—no place to go but forward.

Compiling is all done. All five libraries are good. Took a little bit to get them to recognize each other, but wasn't too bad.

Tuesday, May 26, 2009


Had to add a couple of packages to my installation (automake and libtool), but I finally got to work.  So...I have working code now.  First step has been accomplished.

Problems Getting Started

A little annoyed right now with (non-) progress.

Essentially, the code downloadable from doesn't compile. There's a known issue with the most recent version of gcc, which is somehow a little more strict than previous versions.  There are some scoping issues, which make the thing just plain not work. They know about this, but won't have the fix up until June.

It is, apparently, fixed in the "CVS" version, which I haven't gotten the chance to find yet. Pjotr set up a Git repository as I was about to start searching, and I assume that that was the same thing. However, I can't get that to compile either. It has no make file. Tried using the one from the other version, in various combinations, but couldn't get it going.

At this point I backed off, and read a bunch of material on Git. If nothing else, I feel like I understand that better.

So...current plan of attack. First, find the explicit CVS version, and make sure that that's the same as our Git version. Maybe it even has a make file in there that'll work. Second, Pjotr suggests looking at cmake, of which I hadn't heard. Looked at it briefly, and maybe it'll work better than make. The long holiday weekend is behind us, and I'll get to focus on this in the morning.

Monday, May 25, 2009

Blog Created

Here is the first entry of this new blog, recording my progress on using SWIG to translate Bio++ to Java, R, and Python.