[Seqinr-forum] Problems connecting to ACNUC databases

[Alejandro Gonzalez V]

Hello,

I am new to seqinr, I discovered the package through a colleague and hope to use it to download sequences for a list of species. I am trying to write a script in the hope to teach myself to use seqinr, but have all too quickly run into a problem. I think it may have to do with the configuration of my machine, I am using Mac OS X 10.6.2. The problem I have is with the connection to the ACNUC databases using choosebank(). I tried several times, with different databases and kept getting the following message: Error in if (res[1] != "0") { : argument is of length zero
I tried again using verbose = TRUE in the choosebank command and got the following:

Verbose mode is on, parameter values are:
  bank =  "genbank" 
  host =  "pbil.univ-lyon1.fr" 
  port =  5558 
  timeout =  45 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...
... yes, I was able to open the socket connection.
I'm trying to read answer from server...
... answer from server is:  
clientid(): sending clientid&id=seqinr_2.0-7 
... answer from server is:  
parser.socket received: --><--
character(0) detected returning NULL
Error in if (res[1] != "0") { : argument is of length zero

I did not have the firewall turned on at the time in my machine but I am trying to do all this from our research centre.

Any assistance would be appreciated.

Thank you,

Alejandro
__________________________________

Alejandro Gonzalez Voyer
Post-doc

NEW ADDRESS & NEW E-MAIL

Estación Biológica de Doñana (CSIC)
Avenida Américo Vespucio s/n
41092 Sevilla 
Spain

E-mail: alejandro.gonzalez at ebd.csic.es

Tel: +34- 954 466700, ext 1749






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