[Seqinr-forum] problems with connecting to the database

[stacy xu]

Hi, Leo,

You are right. I would ask our sys admin with the firewall issues.
Meanwhile I am able to retrieve the database through wget (somehow it does
not work for my browsers). Thanks very much for your help!

Thanks,
Stacy

On Thu, Nov 3, 2011 at 5:09 PM, Leonor Palmeira <mlpalmeira at ulg.ac.be>wrote:

> 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<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<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
>>
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