Question

seqinr package - choosebank() function not connecting

1

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jayanthisahithi ▴ 10

@jayanthisahithi-9946

Last seen 8.1 years ago

Hi, I've been looking at the "seqinr" package, for manipulation of sequence data. I can't connect to
the databases using the choosebank() function. I get the following error message:

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() : 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).

my computer is connected to the internet ,iam trying from 10 days but iam unable to execute this.can you please suggest a way to do it.

Thank you

seqinr choose bank error message • 3.2k views

ADD COMMENT • link updated 8.1 years ago by Martin Morgan 25k • written 8.1 years ago by jayanthisahithi ▴ 10

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hi,

i am now thinking to use that R package, actually seqinr is not a biocondcutor, even if it looks like Biocondcutor.

i also have same problem as above and sent an email to the package author ,but no response yet.

i think that problem is due to the Fire wall setting in the comapny security.

FireWall disrupts the access to database where seqinR use.

if you have already solved this problem, would you mind telling me the port number and address where I should describe in access control list ?

ADD REPLY • link 7.7 years ago maedakus ▴ 10

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The CRAN home page for seqinr says that bug reports should be filed at http://r-forge.r-project.org/mail/?group_id=220 . The seqinr-forum archive at that location has recent activity, so you are likely to get an answer there.

ADD REPLY • link 7.7 years ago Martin Morgan 25k

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Thank you so much !

ADD REPLY • link 7.7 years ago maedakus ▴ 10

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Did any of you ever figure this out? I'm experiencing the same problem ...

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?

ADD REPLY • link 5.7 years ago daviqd.halvorsen • 0

score 0 · Answer 1 · 2016-03-18

0

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 days ago

United States

seqinr isn't a Bioconductor package so you should contact maintainer('seqinr') for support.

ADD COMMENT • link 8.1 years ago Martin Morgan 25k

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It is showing like this Simon Penel <simon.penel@univ-lyon1.fr> ...sir,iam doing a project regarding dna sequencing.for that i need to execute some functions using "R" language..Iam unable to execute the functions..please suggest me a way to do it...

Thank you

ADD REPLY • link 8.1 years ago jayanthisahithi ▴ 10

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This site is used to support Bioconductor packages. seqinr is NOT a Bioconductor package. For help with seqinr and for your specific problem, send email to Simon Penel.

ADD REPLY • link 8.1 years ago Martin Morgan 25k