Sorry I had to:

Java for the win!


Michiel Van Bel wrote:
Avoid PHP references wherever possible. That's my advise :-)

Frederik Delaere wrote:
  
he means that the BOGAS staff is deprecated and that you will be 
replaced by the
next update

Lieven Sterck wrote:
  
    
can somebody comment on this?

L.

-------- Original Message --------
Subject: 	BOGAS: Deprecated: Assigning the return value of new by 
reference
Date: 	Wed, 10 Nov 2010 18:08:30 +0300
From: 	Alexander Osypov <aosypov@gmail.com>
To: 	Lieven Sterck <lieven.sterck@psb.vib-ugent.be>



Dear Lieven,

After I installed Bogas on my new system on the notebook, it issued
many commentaries looking like this:
"Deprecated: Assigning the return value of new by reference is
deprecated in <filename>"
After googling I've found that it's because in the current last
version of php the construction like
$something = & new Something_else();
with the ampersand is deprecated. And the cake (and some Bogas staff)
is full of them.
adding  "& ~E_DEPRECATED" to "error_reporting(E_ALL)" helps the situation now:
error_reporting(E_ALL & ~E_DEPRECATED);
but beware of it - it may be not in the future. Think of fixing it in
your code and switching to a new Cake.

Yours truly, ao

P.S. how about the full Bogas file to make a direct link to a locus page?
  
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-- 
Sofie Van Landeghem
PhD Student
VIB Department of Plant Systems Biology, Ghent University
Bioinformatics and Systems Biology
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Website: http://bioinformatics.psb.ugent.be