[Bioc-devel] New package submission failing only in devel due to dependent package errors

[Daniel Cameron]

The package adds structural variant functionality on top of
VariantAnnotation. It's been pretty stable for the last 18 months and
getting more users so I thought it was time to bit the bullet and get it
into BioConductor. install_github() isn't the ideal distribution mechanism
for a package with so many BioConductor dependencies.

https://github.com/Bioconductor/Contributions/issues/1079
http://bioconductor.org/spb_reports/StructuralVariantAnnotation_buildreport_20190411011937.html


No errors in the linux/mac builds although I did just add a warning from a
commit addressing review feedback.

On Wed, Apr 10, 2019 at 12:00 AM Shepherd, Lori <
Lori.Shepherd using roswellpark.org> wrote:

> We are aware of the issue in VariantAnnotation and hopefully will have a
> fix soon.  We have been seeing this ERROR on tokay2 (windows)  but not on
> the other two platforms.  Is this the case for your package?  What is the
> name/package issue number of the submitted package?    If so,  we would
> accept your package conditionally since the ERROR is not with your package
> directly as long as it is building on the other two platforms without
> ERROR.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Daniel
> Cameron <daniel using danielcameron.com>
> *Sent:* Tuesday, April 9, 2019 7:21:54 AM
> *To:* bioc-devel using r-project.org
> *Subject:* [Bioc-devel] New package submission failing only in devel due
> to dependent package errors
>
> Hello,
>
> I am attempting to submit a new package, and everything builds correctly
> against R 3.5 and release bioconductor, but the package build is failing in
> devel due to a dependent package. The build error is:
>
> Quitting from lines 52-56 (vignettes.Rmd)
> Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
> invalid class "VCFHeader" object: 'info(VCFHeader)' must be a 3 column
> DataFrame with names Number, Type, Description
> --- failed re-building 'vignettes.Rmd'
>
> Which I can reproduce locally when building against devel but I'm not sure
> what do you as the offending line is:
> vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")The VCF itself is valid
> (in that it complies with the VCF specifications), and has been parsing
> just fine in my unit tests since May 2016, it's just failing in devel.
>
> Presumably this is a blocker for package acceptance but I'm not sure
> exactly how to proceed given the change is not in my package. Should I be
> raising an issue against VariantAnnotation and hoping it gets resolved fast
> enough for my package to go in this round, or should I also be doing
> something else?
>
> Thanks
> Daniel
>
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>
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