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.sheph...@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-boun...@r-project.org> on behalf of Daniel > Cameron <dan...@danielcameron.com> > *Sent:* Tuesday, April 9, 2019 7:21:54 AM > *To:* bioc-devel@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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
