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

[Pages, Herve]

Hi Daniel,

The 'invalid class "VCFHeader" object' error on Windows has been fixed 
in Rhtslib 1.15.6.

Cheers,

H.

On 4/11/19 04:04, Daniel Cameron wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1079&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=Q4Uek0PObHV1TC1upYL6ddQ6B1mJYdmnRWbZiu9Xk2M&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_StructuralVariantAnnotation-5Fbuildreport-5F20190411011937.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=-gAUBmCTCkhHFFtG8VTHK3TcNePZ2TpClbWqf25xkn8&e=
>
>
> 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
>>
>>          [[alternative HTML version deleted]]
>>
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-- 
Hervé Pagès

Program in Computational Biology
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