> GenomeInfoDb::Seqinfo(genome='hg19') Error in file(file, "rt") : cannot open the connection > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin15.5.0 (64-bit) Running under: OS X 10.12.1 (Sierra)
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomeInfoDb_1.10.0 IRanges_2.8.0 S4Vectors_0.12.0 [4] BiocGenerics_0.20.0 > On Nov 3, 2016, at 08:19, Vincent Carey <st...@channing.harvard.edu> wrote: > > sessionInfo()? > > On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante <rcava...@umich.edu > <mailto: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> > <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 <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
