Re: [Bioc-devel] SSL connect error on package build machine

2016-09-27 Thread Tyler Smith
Great, thanks! On Tue, Sep 27, 2016, at 09:10 PM, Dan Tenenbaum wrote: > Seems like that was a transient error. I was able to kick off another > build that did not have this problem. > > https://github.com/Bioconductor/Contributions/issues/155#issuecomment-250036650 > > Dan > > > -

Re: [Bioc-devel] SSL connect error on package build machine

2016-09-27 Thread Dan Tenenbaum
Seems like that was a transient error. I was able to kick off another build that did not have this problem. https://github.com/Bioconductor/Contributions/issues/155#issuecomment-250036650 Dan - Original Message - > From: "Tyler Smith" > To: "bioc-devel"

Re: [Bioc-devel] VCF Intersection Using readVcf Remarkably Slow

2016-09-27 Thread Michael Lawrence
I think the basic problem is that each range requires a separate query through tabix. BAM and tabix are designed to be fast for single queries, like what a genome browser might generate, but not for querying thousands of regions at once. At least that's the way it seems to me. The index is only at

[Bioc-devel] VCF Intersection Using readVcf Remarkably Slow

2016-09-27 Thread Dario Strbenac
Good day, file <- system.file("extdata", "chr22.vcf.gz", package = "VariantAnnotation") anotherFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", package = "VariantAnnotation") aSet <- readVcf(file, "hg19") system.time(commonMutations <- readVcf(anotherFile, "hg19", rowRanges(aSet)))

[Bioc-devel] SSL connect error on package build machine

2016-09-27 Thread Tyler Smith
Hi, I've just submitted a new package. The automated build generated an error which I think (?) is a problem on one of the build servers (SSL connect error in querying the bioc-devel list). I'm not sure if I'm far enough along in the process for my assigned human to be alerted to this, or if

[Bioc-devel] Warning when Reading Example VCF

2016-09-27 Thread Dario Strbenac
Good day, When importing a VCF file from VariantAnnotation's data directory into R, a warning is emitted. library(VariantAnnotation) aFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", package = "VariantAnnotation") aSet <- readVcf(aFile, "hg19") Warning message: In