FYI I've temporarily disabled the makeTxDbFromBiomart() examples in GenomicFeatures that have been responsible for this 'R CMD check' TIMEOUT for 2-3 days in a row:
https://bioconductor.org/checkResults/3.8/bioc-LATEST/GenomicFeatures/malbec1-checksrc.html Hopefully GenomicFeatures will pass CHECK on Linux tomorrow (it does on my laptop) and become available. Thanks for your patience and sorry for the inconvenience. H. On 11/2/18 09:15, Obenchain, Valerie wrote: > Historically we used to flush the repos before a release. At some point > we stopped and I could not remember why. The situation you describe > below is probably it. > > When preparing for 3.8, we ran into the case where we had quite a few > stale packages in the repos. Their 'staleness' was due to being renamed, > deprecated, etc. These left around old landing pages and appeared in > biocViews inappropriately. At the time it seemed like a good idea to > flush the repo (release only) for a clean start. This would result in no > products (landing page, tarball, ...) for packages that did not build in > the new release. (We also had a hiccup with generating landing pages > with stale links that we're working on. Should be fixed soon.) > > While no landing page / nonavailability is motivation for maintainers to > fix broken packages it's also an inconvenience for users and this is not > good. For the next release we'll probably do some combination of the two > - flush only packages not in the manifest. > > Sorry for this inconvenience - my fault entirely. > > Valerie > > PS/BTW I've fixed GenomicFeatures and if it doesn't have an internet > burp during the builds it should be available tomorrow. > > > > On 11/2/18 8:36 AM, Kasper Daniel Hansen wrote: >> 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 It is not flagging GenomicFeatures as out of date, presumably because it 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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_release_bioc_html_GenomicFeatures.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FmT-0xoyyS7SkXohUPZa3dftKzXkcDp0GhY-NytdV3Y&s=sl7JqHUHipgtjNOGSG-V5ILOiVoxXzIToIKGZKfOHRw&e= >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FmT-0xoyyS7SkXohUPZa3dftKzXkcDp0GhY-NytdV3Y&s=MBsI-xXM9KdhmmZQBexjPWmCtH1aeHPs6EPc03rVALI&e= >>> >>> >> [[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=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FmT-0xoyyS7SkXohUPZa3dftKzXkcDp0GhY-NytdV3Y&s=MBsI-xXM9KdhmmZQBexjPWmCtH1aeHPs6EPc03rVALI&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. > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FmT-0xoyyS7SkXohUPZa3dftKzXkcDp0GhY-NytdV3Y&s=MBsI-xXM9KdhmmZQBexjPWmCtH1aeHPs6EPc03rVALI&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. 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