[Bioc-devel] GenomicFeatures

Obenchain, Valerie V@lerie@Obench@in @ending from Ro@wellP@rk@org
Fri Nov 2 17:15:58 CET 2018

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.


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 It is not flagging GenomicFeatures as out of date, presumably because it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://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
>>          [[alternative HTML version deleted]]
>>      _______________________________________________
>>      Bioc-devel using r-project.org mailing list
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