[Bioc-devel] Windows-specific build error of 'seqCAT' package

Valerie Obenchain obench@|n@v@|er|e @end|ng |rom gene@com
Fri Mar 15 19:10:17 CET 2019

Hi Erik,
I think the problem was introduced in a contributed patch applied to
VariantAnnotation in devel. I've reverted the patch and expect
VariantAnnotation (and downstream packages) to clear up on Windows with
tomorrow's builds.

On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius <erik.fasterius using outlook.com>

> Hi,
> My seqCAT package recently broke building on the Windows platform, which I
> assume has to do with changes to the VariantAnnotation package (upon which
> seqCAT depends). The error (which comes during the creation of the
> vignette) looks like this:
> Quitting from lines 102-112 (seqCAT.Rmd)
> Error: processing vignette 'seqCAT.Rmd' failed with diagnostics:
> invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column
> DataFrame with names Number, Type, Description
> invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column
> DataFrame with names Number, Type, Description
> --- failed re-building 'seqCAT.Rmd'
> It builds and completes all checks successfully on all other platforms,
> though. I have no experience with Windows, so I don’t really know how to
> even start debugging this issue (I’m working on OS X). Given that other
> platforms are working fine I’m thinking (hoping) that this is some
> incompatibility with recent changes to VariantAnnotation (or its
> dependencies) and the Windows platform, but I have no clue if this is the
> case.
> Does anybody have any idea as to what is the issue here, or have any tips
> regarding to be debug something on a different platform than the one you
> are using yourself?
> Erik
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