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

Valerie Obenchain obench@|n@v@|er|e @end|ng |rom gene@com
Sat Mar 16 22:51:39 CET 2019

It doesn't look like it was the patch - the error is still there. I'll look
in to this some more.

On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain <obenchav using gene.com>

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