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

[Michael Lawrence]

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
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> >>
> >>
> >>
> >> --
> >> Stian Lågstad
> >> +47 41 80 80 25
> >>
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >>
> >
> > --
> > 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
>
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