[Bioc-devel] GenomicFeatures

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Fri Nov 2 16:36:11 CET 2018

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It is not flagging GenomicFeatures as out of date, presumably because it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

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
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.


On Fri, Nov 2, 2018 at 10:05 AM Martin Morgan <mtmorgan.bioc using gmail.com>

> 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 is no way to flag it as out-of-date, sort of like a package you'd installed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     it doesn't report GenomicFeatures as out of date, despite the fact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
>         [[alternative HTML version deleted]]
>     _______________________________________________
>     Bioc-devel using r-project.org mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list