[Bioc-devel] GenomicFeatures

[Kasper Daniel Hansen]

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It is not flagging GenomicFeatures as out of date, presumably because it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  I was just surprised to not see it flagged as being out of
date.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.bioc using 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 is no way to flag it as out-of-date, sort of like a package you'd installed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 using r-project.org on behalf of kasperdanielhansen using 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     it doesn't report GenomicFeatures as out of date, despite the fact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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