[Bioperl-l] little wiki bug?

Mauricio Herrera Cuadra mauricio at open-bio.org
Tue Feb 3 00:21:24 EST 2009

The problem was the GeSHiHighlight.php file which needed to be updated 
to its latest version too (aside from the Geshi library), though no 
errors were thrown to the Apache logs...

Syntax highlighting is back to normal and apparently with the bug fixed, 
take a look to the Sandbox with Mark's example.


Mauricio Herrera Cuadra wrote:
> Permissions are fine (0755), in fact, PHP files don't need more than 
> 0644 when they're used as includes. If they need to run from the command 
> line, that's a different story. And yeah, highlighting seems to be 
> pretty bad on our side :(
> Smithies, Russell wrote:
>> I tried the latest version of Geshi on our wiki but saw no changes 
>> i.e. the coloring bug Mark demonstrated was still there. We certainly 
>> didn't lose _all_ our highlighting as you seem to have. Did you check 
>> file permissions on geshi.php? Should be 0755 I think.
>>> -----Original Message-----
>>> From: Mauricio Herrera Cuadra
>>> [mailto:mauricio.at.openbio.org at gmail.com] On Behalf Of Mauricio
>>> Herrera Cuadra
>>> Sent: Tuesday, 3 February 2009 1:43 p.m.
>>> To: Dave Messina
>>> Cc: Smithies, Russell; bioperl list; Mark A. Jensen
>>> Subject: Re: [Bioperl-l] little wiki bug?
>>> I found the 'NEW_geshi_in_here' directory inside the cross-site-stuff
>>> area and overwrote the previous Geshi installation with this one,
>>> reconfigured MediaWiki and other appropriate bits and restarted the
>>> webserver. Syntax highlighting seems even more screwed up now, just
>>> take
>>> a look to the Graphics HOWTO:
>>> http://bioperl.org/wiki/HOWTO:Graphics
>>> Are we sure this newer version fixes things? :)
>>> Mauricio.
>>> Dave Messina wrote:
>>>> This seems to be fixed in the latest version ( of the GeSHi
>>> library,
>>>> which underlies the plugin.
>>>> I think we can swap that in and resolve the problem.
>>>> I've uploaded the new library to the bioperl website, but I don't
>>> have perms
>>>> to move the existing geshi library dir. If one of the core devs has a
>>> sec
>>>> for this, email me off-list and I'll tell you where I put it.
>>>> Dave
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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