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

Awesome, thanks for the quick fix! > On Nov 3, 2016, at 14:50, Hervé Pagès 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

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

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

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

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

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

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

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

> 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

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

sessionInfo()? On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante 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

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

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