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

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Apr 9 16:00:40 CEST 2019

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


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?


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