[Bioc-devel] GenomicFeatures

[Pages, Herve]

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 It is not flagging GenomicFeatures as out of date, presumably because it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.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]]
>>>
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>>>
>>>
>> 	[[alternative HTML version deleted]]
>>
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>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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