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

Thu Apr 6 22:35:58 CEST 2017

And by Rainer I mean Johannes. It is late…

From: Rainer Johannes <Johannes.Rainer at eurac.edu>
Date: Thursday, 6 April 2017 at 22:07
To: "Obenchain, Valerie" <Valerie.Obenchain at RoswellPark.org>
Cc: Stian Lågstad <stianlagstad at gmail.com>, Michael Lawrence <lawrence.michael at gene.com>, "bioc-devel at r-project.org" <bioc-devel at r-project.org>, Florian Hahne <florian.hahne at novartis.com>
Subject: Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

@Florian: nothing you have to change. I checked all packages and 70 of them have problems related to the relocation of the filters. For 63 of them everything should be fine once the updated versions of biovizBase and ggbio are built. This fixes also Gviz and most of the packages with them.

For the remaining packages I either provided patches, pull requests or am in contact with the developers. I checked these packages and there is not very much more to do than importing filters from AnnotationFilter instead of ensembldb.

Fingers crossed - tomorrow everything could be OK again - and sorry again for all the havoc

cheers, jo

On 6 Apr 2017, at 21:27, Obenchain, Valerie <Valerie.Obenchain at RoswellPark.org<mailto:Valerie.Obenchain at RoswellPark.org>> wrote:

We've updated the release schedule and moved the deadline for errors to
next Friday, April 14.

Valerie

On 04/06/2017 10:29 AM, Stian Lågstad wrote:

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<mailto: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<mailto: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<mailto: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><mailto
:

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><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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