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

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, Herv? Pag?s <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 L?gstad <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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