[Bioperl-l] Example code in Bioperl Tutorial

Joel Martin j_martin at lbl.gov
Tue Jun 26 21:01:29 EDT 2007


Hello, 
  The tutorial code snippet is an endless loop, I think it's supposed
to remove the rid.  As the only print statement you added is after the
endless loop, you aren't seeing anything happen.   

Use the code from this instead,

perldoc Bio::Tools::Run::RemoteBlast

  The bptutorial.pl does have a note that it's not useful and to read the pod
for Bio::Tools::Run::RemoteBlast, it's in the next sentences after the code
snippet you used.  

  Though, as it's a tutorial example it might be nice to remove the while
loop .. or at least add the sleep(5) part.
http://www.bioperl.org/wiki/Bptutorial.pl#Running_BLAST_.28using_RemoteBlast.pm.29

  Aside from that, you may have network issues but www.ncbi.nlm.nih.gov
doesn't respond to ping as far as I can tell. 

Joel


On Tue, Jun 26, 2007 at 02:26:03AM -0700, don esteban wrote:
> 
> Try using the Proxyconfiguration in your script:
> 
> $ENV{"HTTP_PROXY"}="http://proxy.somewhere.org:8080";
> 
> 
> 
> 
> L Xu wrote:
> > 
> > I do have the internet connection bu not use the proxy server.
> > I tested the network connection with ping command (below). The ncbi
> > website 
> > does not response. Is there any special network setting needed for 
> > connecting the ncbi website?
> > Thank you so much.
> > 
> > C:\>ping www.yahoo.com
> > 
> > Pinging www.yahoo-ht3.akadns.net [69.147.114.210] with 32 bytes of data:
> > 
> > Reply from 69.147.114.210: bytes=32 time=363ms TTL=45
> > Reply from 69.147.114.210: bytes=32 time=319ms TTL=45
> > Reply from 69.147.114.210: bytes=32 time=312ms TTL=45
> > Reply from 69.147.114.210: bytes=32 time=360ms TTL=45
> > 
> > Ping statistics for 69.147.114.210:
> >     Packets: Sent = 4, Received = 4, Lost = 0 (0% loss),
> > Approximate round trip times in milli-seconds:
> >     Minimum = 312ms, Maximum = 363ms, Average = 338ms
> > 
> > C:\>ping www.ncbi.nlm.nih.gov
> > 
> > Pinging www.ncbi.nlm.nih.gov [130.14.29.110] with 32 bytes of data:
> > 
> > Request timed out.
> > Request timed out.
> > Request timed out.
> > Request timed out.
> > 
> > Ping statistics for 130.14.29.110:
> >     Packets: Sent = 4, Received = 0, Lost = 4 (100% loss),
> > 
> > 
> > 
> > = = = Original message = = =
> > 
> > Judging by the output it looks like you have no network access or? can't 
> > connect to the server (what remoteblast needs).? Make sure you? don't need 
> > proxy settings.
> > 
> > To preempt the next question, no, I'm not going to explain what a? proxy 
> > is.? The RemoteBlast docs show how to set them, and Google is a? wonderful 
> > tool...
> > 
> > chris
> > 
> > On Jun 13, 2007, at 7:16 AM, L Xu wrote:
> > 
> > 
> >    ...
> > -------------------- WARNING ---------------------
> > MSG: <HTML>
> > <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
> > <BODY>
> > <H1>An Error Occurred</H1>
> > 500 Can't connect to www.ncbi.nlm.nih.gov:80 (connect: Unknown error)
> > </BODY>
> > </HTML>
> > 
> > ---------------------------------------------------
> > ...
> > 
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