[Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

Raymond Cavalcante rcavalca at umich.edu
Thu Nov 3 13:46:46 CET 2016

> 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)

[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 <stvjc at channing.harvard.edu> wrote:
> sessionInfo()?
> On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante <rcavalca at umich.edu <mailto:rcavalca at 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
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