soaplab-users

[Soaplab-users] acd2xml

[allan <al...@im...>]

Hi
I'm trying to use soaplab in a miRNA research project but have run  
into a problem with acd2xml

allan 09:43 AM> ./generator/acd2xml -d -l test.xml miranda
Processing miranda...
         using /home/allan/projects/soap2/analysis-interfaces/ 
metadata/miranda.acd
Can't use an undefined value as an ARRAY reference at ./generator/ 
acd2xml line 218.

I have  tried some of the other acd files in 'metadata' as well, but  
they all give the same error. I hope somebody has a suggestion to  
what can go wrong.

Best wishes

Allan Lind-Thomsen

Re: [Soaplab-users] acd2xml

[Martin S. <mar...@gm...>]

> Can't use an undefined value as an ARRAY reference at ./generator/
> acd2xml line 218.


The problem is with the newer version of Perl (you are using). I have a
fix for this bug but have not committed it yet (actually I thought I did but
apparently not, sorry for that). Here it is: please edit
your generator/acd2xml perl script by adding the following line:

   $app{'input'} = [] unless defined $app{'input'};

Put the line just before the line:

   my ($input);  # a reference to a hash

This should fix it.

Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger

Re: [Soaplab-users] acd2xml

[Peter E. <P....@dk...>]

On Tue, 26 Sep 2006, Martin Senger wrote:

> > Can't use an undefined value as an ARRAY reference at ./generator/
> > acd2xml line 218.
> 
> 
> The problem is with the newer version of Perl (you are using). I have a
> fix for this bug but have not committed it yet (actually I thought I did
> but apparently not, sorry for that).

I copied the fix a few months ago to:

http://soaplab.sourceforge.net/jar-storage/acd2xml.tar.gz

However, in order to update your local cache, you must run the Ant target 
"gather". (or use "build.sh" instead of "build-dev.sh").

Kind regards,

	Peter