> you can do it as 4x uniform vec4s, then stick them together into a mat4 in 
> the shader. There's probably a small overhead in doing this, but it works 
> fine, in my experience.
>> The 'uniform mat3 rotationMatrix;' is defined and used within the fragment 
>> shader but the inputs for the parameter doesn't appear in the patch editor.
>> Is this possible?

Can either of you file a bug report requesting exposure to mat2s, mat3s, and 
mat4s?  seems silly to kludge it like this in 2010...

>> BTW: I am currently creating the rotation matrix in the vertex shader and 
>> passing it to the fragment shader via a varying parameter as to reduce the 
>> calculations within the fs. However, along with other precalculations I've 
>> hit upon the limit for the number of varying inputs for older GPUs!

Another way to provide lots of data to the FS is to use several textures.  This 
doesn't work so well when the texture sizes are different (another bug to 
file), but if they're all the same you can add 8 4-channel per-pixel inputs, 
which is pretty handy :)
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