[Bioc-devel] GenomicFeatures

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It is not flagging GenomicFeatures as out of date, presumably because it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  I was just surprised to not see it flagged as being out of
date.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.bioc at 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-bounces at r-project.org on behalf of kasperdanielhansen at 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

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