sessionInfo()? 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
