SeqinR socketConnection error? (I tried increasing timeout & opening port already)
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3.3 years ago

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?

seqinr accession ncbi sequence • 1.3k views
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What about this error:

pbil.univ-lyon1.fr:5558 cannot be opened

Is that a proxy server you are using? Or is that the name of your machine?

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"pbil.univ-lyon1.fr" is the host that I am trying to connect to. The choosebank function seems to default to "pbil.univ-lyon1.fr" as the host. Using host = "pbil.univ-lyon1.fr" as an argument replicates the same error message. I think that I'm following the right formatting from the seqinr manual, which is located here: https://www.rdocumentation.org/packages/seqinr/versions/1.0-1/topics/choosebank.

I may be misunderstanding how to do this as I am a new R user trying to follow the tutorial from 'A Little Book of R for Bioinformatics, Release 0.1'. I am working on the 'Retrieving genome sequence data using SeqinR' section from page 15 (PDF page 19). The tutorial PDF can be found here: http://www.cs.ukzn.ac.za/~hughm/bio/docs/a-little-book-of-r-for-bioinformatics.pdf.

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