[Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

[Obenchain, Valerie]

We've updated the release schedule and moved the deadline for errors to
next Friday, April 14.

Valerie


On 04/06/2017 10:29 AM, Stian Lågstad wrote:
> How does the error deadline tomorrow (http://www.bioconductor.org/
> developers/release-schedule/) affect packages that are still red because of
> this change? I don't know what else to do other than to wait for changes in
> Gviz (which my package is dependent on).
>
> Thanks.
>
> On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence <lawrence.michael at gene.com
>> wrote:
>> Sorry I have been traveling. Will get to it soon.
>>
>> On Apr 4, 2017 12:58 PM, "Rainer Johannes" <Johannes.Rainer at eurac.edu>
>> wrote:
>>
>>> Hi Herve,
>>>
>>> sorry for all the reds - actually I provided the patches to biovizBase
>> and
>>> ggbio, but it did not work out that smoothly that I hoped. For the other
>>> packages that depend on ensembldb there's no problem or only small
>> changes
>>> required (did contact the developers).
>>> Fingers crossed that Michael can patch biovizBase and ggbio soon.
>>>
>>> cheers, jo
>>>
>>>> On 4 Apr 2017, at 21:34, Hervé Pagès <hpages at fredhutch.org> wrote:
>>>>
>>>> Hi Johannes,
>>>>
>>>> This move is generating a lot of red today on the build report.
>>>> Hopefully biovizBase and ggbio can be fixed quickly. Note that
>>>> maybe a smoother path would have been to notify the maintainers
>>>> of these packages first and wait that they make the required
>>>> changes (i.e. to import the filters from AnnotationFilter)
>>>> before modifying ensembldb. Maybe for next time ;-)
>>>>
>>>> Cheers,
>>>> H.
>>>>
>>>> On 04/04/2017 04:02 AM, Rainer Johannes wrote:
>>>>>
>>>>> On 4 Apr 2017, at 10:59, Stian Lågstad <stianlagstad at gmail.com<mailto
>> :
>>> stianlagstad at gmail.com>> wrote:
>>>>> Hi,
>>>>>
>>>>> Thanks again for notifying me about the changes needed in chimeraviz.
>>> Right now I'm having problems installing Gviz - I get these errors:
>>>>> """
>>>>> No methods found in "GenomicAlignments" for requests:
>>> pmapFromTranscripts
>>>>> Error : object 'GRangesFilter' is not exported by
>> 'namespace:ensembldb'
>>>>> ERROR: lazy loading failed for package 'Gviz'
>>>>> """
>>>>>
>>>>> Are these errors caused by the change in ensembldb? If so: Do you know
>>> how I can keep developing without having to wait for Gviz?
>>>>>
>>>>> These come from biovizBase which Gviz imports. I've sent Micheal the
>>> fixes for biovizBase and ggbio that should fix this.
>>>>> We need to wait for the changes to be propagated, since also for
>>> ensembldb I get today still version 1.99.12 but not the new 1.99.13.
>>>>> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
>>> Johannes.Rainer at eurac.edu<mailto:Johannes.Rainer at eurac.edu>> wrote:
>>>>> Dear all,
>>>>>
>>>>> I've just committed a change in ensembldb (version 1.99.13) that
>>> removes all filter classes from it and imports them from the
>>> AnnotationFilter package. This change will break biovizBase and ggbio
>> (and
>>> all packages downstream of them, e.g. Gviz). I've already sent Michael
>>> Lawrence patches to fix both packages, but  there might still be some
>>> problems in the upcoming build reports I guess.
>>>>> I've also contacted the developers of the TVTB and chimeraviz packages
>>> and made them aware of the change. Could be that there are other packages
>>> out there possibly affected by the change. If so, let me know and I'll
>>> assist fixing the problems (if needed).
>>>>> cheers, jo
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing
>> list
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
>>> ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAf
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>>>>>
>>>>>
>>>>> --
>>>>> Stian Lågstad
>>>>> +47 41 80 80 25
>>>>>
>>>>>
>>>>>      [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
>>> ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAf
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>>> PpkQJQ6twQd8-on8IrI&s=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY&e=
>>>> --
>>>> Hervé Pagès
>>>>
>>>> Program in Computational Biology
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N, M1-B514
>>>> P.O. Box 19024
>>>> Seattle, WA 98109-1024
>>>>
>>>> E-mail: hpages at fredhutch.org
>>>> Phone:  (206) 667-5791
>>>> Fax:    (206) 667-1319
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>



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