Awesome, thanks for the quick fix! > On Nov 3, 2016, at 14:50, Hervé Pagès <hpa...@fredhutch.org> wrote: > > Should now be fixed in release (GenomeInfoDb 1.10.1) and devel > (GenomeInfoDb 1.11.2). > > H. > > On 11/03/2016 11:12 AM, Hervé Pagès wrote: >> I'll look at this. I think Seqinfo(genome="hg19") needs to query >> NCBI to get some information (e.g. SequenceRole) that allows ordering >> the sequences in the returned Seqinfo in the "natural" order. >> >> H. >> >> On 11/03/2016 05:47 AM, Michael Lawrence wrote: >>> I think this is because the NCBI server switched to https (via a >>> redirect that I guess the R url() connection fails to follow). The >>> reason rtracklayer still works is that it's only querying UCSC. >>> GenomeInfoDb also queries NCBI to get the mappings to the NCBI >>> seqlevels. Does that really need to happen when only getting the >>> Seqinfo? >>> >>> >>> On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante >>> <rcava...@umich.edu> wrote: >>>> Hello, >>>> >>>> Sometime yesterday calls like GenomeInfoDb::Seqinfo(genome = 'hg19') >>>> stopped working with the error: >>>> >>>>> Error in file(file, "rt") : cannot open the connection >>>> >>>> From the documentation, that call relies on >>>> fetchExtendedChromInfoFromUCSC() and requires an internet connection, >>>> which I had and continue to have. I'm not really sure how to deal >>>> with this problem because the goldenPath link still works >>>> (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz >>>> <http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz>), >>>> so something else is broken... >>>> >>>> Oddly, calls to rtracklayer::import.bed() that specify a genome work. >>>> I don't have any BSgenome packages installed where I'm running it, >>>> and from the documentation for genome, "An attempt will be made to >>>> derive the ‘seqinfo’ on the return value using either an installed >>>> BSgenome package or UCSC, if network access is available." So I would >>>> guess that rtracklayer::import.bed() would use the same >>>> fetchExtendedChromInfoFromUCSC()...? >>>> >>>> On a related note, is there a non-BSgenome package that has the >>>> chromosome length / seqinfo information that doesn't require an >>>> internet connection (other than to download the package)? BSgenome is >>>> too large to require of users just for chromosome lengths. The org.db >>>> packages have chromosome lengths, but only with respect to one genome >>>> version for that organism, and from the documentation it isn't clear >>>> which version. >>>> >>>> Thanks, >>>> Raymond Cavalcante >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319
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