I am having trouble with the SeqinR package. 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?