[Seqinr-forum] problems with connecting to the database

[Leonor Palmeira]

On 03/11/11 09:53, stacy xu wrote:
> Hi, Leo,
>
> Thanks very much for quick reply! I checked with my colleague, I rerun
> the program with "verbose=TRUE", and below is the output：
> # Verbose mode is on, parameter values are:
> #   bank =  NA
> #   host = "pbil.univ-lyon1.fr <http://pbil.univ-lyon1.fr>"
> #   port =  5558
> #   timeout =  5 seconds
> #   infobank =  FALSE
> #   tagbank =  NA
> # I'm ckecking that sockets are available on this build of R...
> # ... yes, sockets are available on this build of R.
> # I'm trying to open the socket connection...
> # Error in socketConnection(host = host, port = port, server = server,
> blocking = blocking,  :
> #   cannot open the connection
> # In addition: Warning message:
> # In socketConnection(host = host, port = port, server = server,
> blocking = blocking,  :
> # pbil.univ-lyon1.fr:5558 <http://pbil.univ-lyon1.fr:5558> cannot be opened
> # Error in choosebank(verbose = TRUE) :
> #   I wasn't able to open the socket connection:
> #    o Check that your are connected to the internet.
> #    o Check that port 5558 is not closed by a firewall.
> #    o Try to increase timeout value (current is 5 seconds).
>
> I think you are right that the port 5558 may be disabled on my computer.
> Can you kindly suggest how to open it?

Dear Stacy,

I am answering to the list again, in order to archive the thread. This 
might help people experiencing the same problem.

You should check with your system administrator if the 5558 port is 
closed on your machine only or if it comes from the firewall 
configuration (which is much more likely). I suspect you are not running 
a Linux system, so I will not be able to help you more than this, but 
your system administrator should :-)

> By the way, I also saw on SeqinR
> manual that I can set up the database from my own sever without
> connecting to the internet. However, I could not connect to
> ftp://pbil.univ-lyon1.fr/pub/seqinr/demoacnuc/acnucdatabase.tar.Z as
> well. Is the address correct for the database download? Thanks!

The address is correct and the server is up and running, so there is no 
problem on our side.
Could you check this again?

Best,
Leo.

> Thanks,
> Stacy