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

Thu Apr 6 19:10:57 CEST 2017

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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> > >>
> > >
> > > --
> > > 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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-- 
Stian Lågstad
+47 41 80 80 25

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