Conversion to VRanges Error

Bioconductor / VariantAnnotation

Annotation of Genetic Variants

https://bioconductor.org/packages/VariantAnnotation

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Conversion to VRanges Error #44

Closed DarioS closed 3 years ago

DarioS commented 3 years ago

I think that this worked in the past. I recently began working with Bioconductor 3.12.

fl <- system.file("extdata", "ex2.vcf", package = "VariantAnnotation")
vcf <- readVcf(fl, genome = "hg19")
as(vcf, "VRanges") # Error in ans[] <- x : replacement has length zero

mtmorgan commented 3 years ago

I don't see this; is your installation valid? BiocManager::valid() should return TRUE, and BiocManager::version() should return 3.12.

DarioS commented 3 years ago

Indeed, it seems like the recent upgrade failed for a small number of packages. I should have checked first.