[Biococoa-dev] BioCocoa linux install

Scott Christley schristley at mac.com
Fri Mar 28 10:45:12 EDT 2008

Hello Paolo,

Yeah there are issues with Apple XML being read by GNUstep, so I  
created GNUstep compatible XML in BioCocoa.

Anyways, you created a suffix array file with your chromosome, try  
using the "print_sarray" command to output the contents of that  
suffix array.  That command needs to read an XML file (hold the  
suffix array meta data), so if it displays the suffix array data  
correctly then it should have read the XML fine.


On Mar 27, 2008, at 5:08 PM, paolo siniselli wrote:

> I installed all the XMl library I could but I've got
> the same errors. I found this googling around:
> NB. MacOS-X generates illegal XML for some strings -
> those which contain characters not legal in XML.
> GNUstep always generates legal XML, at the cost of a
> certain degree of compatibility. GNUstep XML property
> lists use a backslash to escape illegal chatracters,
> and consequently any string containing either a
> backslash or an illegal character will be written
> differently to the same string on MacOS-X.
> http://www.gnustep.org/resources/documentation/Developer/Base/ 
> ProgrammingManual/manual_13.html
> Do you think this is the problem?
> Thank you very much
> Paolo
> --- Scott Christley <schristley at mac.com> wrote:
>> These messages do not look good.  Seems to indicate
>> that something is
>> wrong with the XML parsing in GNUstep.  It is
>> necessary for the XML
>> parsing to be enabled and functional with GNUstep in
>> order for
>> BioCocoa to work.
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