[Primeusers] PrimeGSR installation

[Lars Arvestad]

I am running 2.3, which gives me warnings rather than errors. I have not 
been able to figure out how to correctly write error rules. The idea is 
that we should be able to interrupt parsing and give a, more or less, 
sensible error message.

One workaround would be to delete the difficult lines, 141, 177, and 
178, but I have not tested this. Please let me know how it works!

    Lars


jacky at ebi.ac.uk wrote:
> Hello,
>
> I am having trouble compiling PrimeGSR for use on our computing cluster.
>
> Initially there were some problems with incompatible Bison and M4 versions
> but I have come past that step in compilation now using Bison 2.4.1 and M4
> 1.4.9.
>
> However, compilation now stops at the following stage:
>
> bison -d -y -p yytree_ NHXparse.y
> NHXparse.y:141.30-31: $$ for the midrule at $3 of `subtree' has no
> declared type
> NHXparse.y:177.96-97: $$ for the midrule at $3 of `ext_annotation' has no
> declared type
> NHXparse.y:178.97-98: $$ for the midrule at $3 of `ext_annotation' has no
> declared type
> NHXparse.y:141.11-89: warning: type clash on default action: <v> != <>
> NHXparse.y:177.18-128: warning: type clash on default action: <a> != <>
> NHXparse.y:178.18-130: warning: type clash on default action: <a> != <>
> make: *** [NHXparse.c] Error 1
>
> It looks like it could still be a Bison issue. Which version of Bison are
> you running your installation with?
>
> Thanks very much,
>
> Jacky
>
>
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-- 
School of Computer Science and Communication
and Stockholm Bioinformatics Center
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