Thanks, fixed in 1.9.35/1.8.11.


On Wed, Feb 5, 2014 at 12:35 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi,
>
> I just stumbled over the fact that 'writeVcf' for a 'VRanges' fails if
> 'sampleNames' is a factor with unused levels.  Here a small example:
>
> #+BEGIN_SRC R
>
> library(VariantAnnotation)
> example(VRanges)
> writeVcf(vr, "out.vcf") ## works
>
> f = sampleNames(vr)
> f ## levels: a, b
> levels(f) = c("a", "b", "c") ## c in unused
> f ## levels: a, b, c
> sampleNames(vr) = f
> writeVcf(vr, "out.vcf")  ## fails
>
> #+END_SRC
>
> Error in writeVcf(as(obj, "VCF"), filename, ...) :
>   error in evaluating the argument 'obj' in selecting a method for
> function 'writeVcf': Error in ans[sampleToUniq] <- as.vector(v) :
> replacement has length zero
>
> This occurs both with the latest bioc-release and bioc-devel.  I don't
> know what exactly is causing this, but please let me know if I can be of
> any help.
>
> Best wishes
> Julian
>
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>

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