I am having trouble with the seqinr package and "maintainer('seqinr')" pointed me in your direction. Specifically, I'm trying to retrieve the genome sequence for Dengue virus from NCBI. I am working on the 'Retrieving genome sequence data using SeqinR' section from page 15 (PDF page 19) of 'A Little Book of R for Bioinformatics, Release 0.1', which can be found here: http://www.cs.ukzn.ac.za/~hughm/bio/docs/a-little-book-of-r-for-bioinformatics.pdf. The exact code that I am using can be found here: https://github.com/DaveHalvorsen/R_for_Bioinformatics/blob/master/getncbiseq.R The error I receive is:

"""

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 cannot be opened
Error in choosebank(db, timeout = 55) : 
  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 55 seconds).

"""

I am working on Ubuntu 16.04. Here is what I have tried to fix the error:

• choosebank(db, timeout=55)
• sudo ufw allow 5558
• sudo iptables -A INPUT -m state --state NEW -m tcp -p tcp --dport 5558 -j ACCEPT

Do you have any ideas on getting this code working?

> maintainer("seqinr") says that you should contact "Simon Penel <simon.penel@univ-lyon1.fr>" for support of this non-Bioconductor package. It looks like the SERVER (not your computer) is not configured to accept incoming connections.