Lates BiocManager It is not flagging GenomicFeatures as out of date, presumably because it doesn't exists in the repos. So in some sense it is all internally consistent. I was just surprised to not see it flagged as being out of date.
I guess I am also confused about what happens at release. Is the repos wiped? Because at some time pre-release GenomicFeatures existed in the Bioc 3.8 repos, and (usually) that would mean it would fall back to this previous version (seemingly 1.33.6 based on https://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html yet this package does not seem to exists (despite the URL)). Ok, this is all a rather unfortunate and special case which I am not sure how should be handled. I was just surprised at what I am seeing, but I am also quite confident that when the package is fixed, it'll all work fine. Best, Kasper On Fri, Nov 2, 2018 at 10:05 AM Martin Morgan <mtmorgan.b...@gmail.com> wrote: > For which BiocManager::version() is this? BiocManager::valid() checks > within versions, and if there's no GenomicFeatures to reference, then there > is no way to flag it as out-of-date, sort of like a package you'd installed > that was in neither CRAN nor Bioconductor. > > Though of course we'd like GenomicFeatures to be available in 3.8 > > Martin > > On 11/2/18, 1:05 PM, "Bioc-devel on behalf of Kasper Daniel Hansen" < > bioc-devel-boun...@r-project.org on behalf of kasperdanielhan...@gmail.com> > wrote: > > Seem broken in release. > > And btw., because it is broken, when I run > BiocManager::valid() > it doesn't report GenomicFeatures as out of date, despite the fact > that I > have version 1.33.2 installed, and there are newer versions in the > 1.33.x > hierarchy and the "right" (but broken) version in Bioc 3.8 is 1.34.0. > > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel