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

Rainer Johannes Johannes.Rainer at eurac.edu
Tue Apr 4 13:02:13 CEST 2017

On 4 Apr 2017, at 10:59, Stian Lågstad <stianlagstad at gmail.com<mailto:stianlagstad at gmail.com>> wrote:


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

Stian Lågstad
+47 41 80 80 25

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