Need to derive (Binary,Serialize,FromJSON,ToJSON,NFData) for all the LimitType things

[Artoria2e5]

This is wanted by BiobaseInfernal in Biobase.SElab.HMM.Types and Biobase.SElab.CM.ModelStructure. I will try to do it tomorrow because I really want to compare some CMs (and no i don't want to downgrade the dependencies, what's the fun in that?)

[Artoria2e5]

The quad of Binary,Serialize,FromJSON,ToJSON all error out on Generic (V.Vector (Vector (PInt () StateIndex))) not being a thing when used in Biobase.SElab.CM.ModelStructure. This seems to happen via the bunch of Generic (v e) in Dense.hs, which does not look like a good idea considering v has no generic whatsoever?

[choener]

Checking these issues / any PRs would take me quite a while, since I am currently not working in bioinformatics anymore; but feel free to fork any and all repositories.

Some comments regarding the base problem: building CMCompare. This software is some 15 years old, and trying to update it and all dependencies will be quite an adventure. Parts of the libraries are in a semi-updated state, as I was actually in the process of writing a new version of CMCompare. But this never fully materialized.

If you really need CMCompare, you should consider getting the binary directly. It is mostly static and should still run after minor changes to its environment (probably just the library path). But also be aware that any new CMs might not run, if their model file can't be understood by CMCompare. In that case you probably have to filter out some things -- but I never checked if the current version of Infernal is incompatible.