[Haskell-cafe] SYB3 codebase

Mads Lindstrøm mads_lindstroem at yahoo.dk
Fri Oct 19 13:59:37 EDT 2007

Hi Greg

To the best of my knowledge it is not maintained anymore :(

If you want to use it, you should properly make use of this patch:
The patch was made by Kido Takahiro (aka. Shelarcy). The patch makes
SYB3 compile with GHC 6.6 and GHC 6.8.

However, I do not _think_ anybody else currently uses SYB3 with this
patch. As far as I know, I was the only user and I have recently
migrated to
http://hackage.haskell.org/cgi-bin/hackage-scripts/package/syb-with-class-0.3 (hereafter know as HappS-SYB3). HappS-SYB3 is based on the SYB3 code you mention, but the code has been changed quite a bit compared to using the Shelarcy patch. So it will properly require some more work. On the other hand, I think the http://hackage.haskell.org/cgi-bin/hackage-scripts/package/syb-with-class-0.3 version is better maintained, as it is used in HappS project.

I have not been able to find any documentation for HappS-SYB3. I _think_
it is because the HappS folks main focus is to use it to support the
HappS project.

I've have emailed the HappS maintainer about my usage of HappS-SYB3, but
I am yet to receive an answer. Thus I have no idea of his position on my
usage of HappS-SYB3.

If I was you, I would use the Shelarcy patch first, as it will require
less work. When everything is working I would migrate to HappS-SYB3, as
they have an interest in maintaining their version.


Mads Lindstrøm

P.s. if you decide using the Shelarcy patch then apply it with:

> patch -u -dSYB3 <SYB3_Shelarcy.diff

Greg Meredith:
> Haskellians,
> Does anyone know the status of SYB3 codebase? It appears that FreshLib
> critically depends on it, but the code downloadable from
> http://homepages.cwi.nl/~ralf/syb3/code.html dies in make test on the
> first test with
> lgmaclt:~/work/src/projex/biosimilarity/HS1/Process/haskell/SYB3 lgm$
> make test
> make test1 stem=geq1
> ghci -fglasgow-exts -fallow-overlapping-instances
> -fallow-undecidable-instances -v0 geq1.hs < Main.in > geq1.out
> geq1.hs:27:34:
>     Inferred type is less polymorphic than expected
>       Quantified type variable `a1' escapes
>     Probable cause: `geq'' is applied to too few arguments 
>     In the first argument of `gzipWithQ', namely `geq''
>     In the first argument of `and', namely `(gzipWithQ geq' x y)'
> <interactive>:1:0: Not in scope: `main'
> diff -b geq1.out geq1.ref
> 0a1,4
> > True
> > False
> > False
> > True
> make[1]: *** [test1] Error 1
> make: *** [test] Error 2
> lgmaclt:~/work/src/projex/biosimilarity/HS1/Process/haskell/SYB3 lgm$ 
> Is there a newer version of this codebase? Has this functionality been
> folded into mainline Haskell tree somewhere?
> Best wishes,
> --greg
> -- 
> L.G. Meredith
> Managing Partner
> Biosimilarity LLC 
> 505 N 72nd St
> Seattle, WA 98103
> +1 206.650.3740
> http://biosimilarity.blogspot.com 
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