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 patc
On 4 Apr 2017, at 10:59, Stian Lågstad
mailto:stianlags...@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: pmapFromTransc
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 filt
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 Mi
Sorry I have been traveling. Will get to it soon.
On Apr 4, 2017 12:58 PM, "Rainer Johannes"
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 ense
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
I thought that this all originates in biovizBase? So there’s nothing to change
in Gviz unless I miss a crucial point here.
Florian
On 06.04.17, 19:10, "Bioc-devel on behalf of Stian Lågstad"
wrote:
How does the error deadline tomorrow (http://www.bioconductor.org/
developers/release-sc
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
>
@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
Thanks, Rainer. Always happy if I don’t have to fix anything ☺
From: Rainer Johannes
Date: Thursday, 6 April 2017 at 22:07
To: "Obenchain, Valerie"
Cc: Stian Lågstad , Michael Lawrence
, "bioc-devel@r-project.org"
, Florian Hahne
Subject: Re: [Bioc-devel] Filter classes
And by Rainer I mean Johannes. It is late…
From: Rainer Johannes
Date: Thursday, 6 April 2017 at 22:07
To: "Obenchain, Valerie"
Cc: Stian Lågstad , Michael Lawrence
, "bioc-devel@r-project.org"
, Florian Hahne
Subject: Re: [Bioc-devel] Filter classes moved from ensembldb
Hi Johannes,
Thanks for contacting the developers of the packages affected by this
change. FWIW Pbase is also affected (didn't see it in your list):
https://bioconductor.org/checkResults/3.5/bioc-LATEST/Pbase/malbec2-buildsrc.html
H.
On 04/06/2017 01:07 PM, Rainer Johannes wrote:
@Florian:
Hi Herve
> On 7 Apr 2017, at 07:42, Hervé Pagès wrote:
>
> Hi Johannes,
>
> Thanks for contacting the developers of the packages affected by this
> change. FWIW Pbase is also affected (didn't see it in your list):
>
I fixed Pbase - changes have not been committed to Bioc yet (asked Laurent fo
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