[Bioc-devel] GenomeInfoDB SeqInfo function error

Hervé Pagès hp@ge@ @ending from fredhutch@org
Thu Sep 27 18:34:38 CEST 2018

Hi Dario,

On 09/13/2018 09:18 AM, Dario Righelli wrote:
> Hello everyone,
> I'm using in DEScan2 package the GenomeInfoDb::Seqinfo function with genome="mm10".
> And sometimes it appens to retrieve this error message
> "cannot open the connection to 'https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_635_GCF-5F000001635.20-5FGRCm38_GCF-5F000001635.20-5FGRCm38-5Fassembly-5Freport.txt&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-DK9eRRfECV1yPP6ZtcqI5wTDmAcAznmepaSA1e4lRE&s=lJUG8lKk4WIQQWiOaXjM3CYfr-ksMFhs5svvIk6kUyY&e='"
> Even if the the file is reachable.

I cannot reproduce this, not too surprisingly...

This kind of intermittent internet access problem is not uncommon
and typically hard to reproduce. GenomeInfoDb::Seqinfo() was trying
to download a file from ftp.ncbi.nlm.nih.gov and failed for some
reason. It could be because NCBI's FTP site was temporarily unavailable
or because of any other network problem between NCBI and the machine
where GenomeInfoDb::Seqinfo() was called. Unfortunately there is not
much we can do about these transient connectivity issues in general.

However we can mitigate them:

- One way to mitigate them though would be to use a caching mechanism
   e.g. to use BiocFileCache to store the data downloaded by
   GenomeInfoDb::Seqinfo(genoe="some_genome") locally the 1st time
   it's downloaded for a particular genome.

- Another way would be to have this data already included in
   GenomeInfoDb (or GenomeInfoDbData) for the most frequently used
   genomes. In addition, the caching mechanism could still be used
   for the other genomes.

- Another way to mitigate this maybe would be to have
   GenomeInfoDb::Seqinfo(genoe="some_genome") re-try the download
   a couple of times (after waiting 1 or 2 sec before re-trying)
   before giving up. This could be done in combination with the
   above features. The re-try feature could even be integrated to

Although for now my feeling is that this issue is maybe not so much
of an annoyance to justify putting these new developments high on
the TODO list.

Just throwing some random thoughts here. Don't know what others
think about this.

> I noticed it because I received an ERROR report from the bioconductor test bot.
> I have a unit test for my package that doesn't pass on linux, but it works on other machines.
> Looking on the Internet, this seems like an old (solved) problem.

Would you mind sharing a link to this information? Thanks!


> What do you suggest to do?
> thanks,
> dario
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

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