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.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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=m6HdfwMZhlzMOUf37A7tCI7r0js2hvbf_UxPDs8JfJ0&e= >> >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=m6HdfwMZhlzMOUf37A7tCI7r0js2hvbf_UxPDs8JfJ0&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
