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

[Rainer Johannes]

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
>> 
>> _______________________________________________
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>> 
>> 
>> --
>> Stian Lågstad
>> +47 41 80 80 25
>> 
>> 
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> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
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