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

2017-04-07 Thread Rainer Johannes
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

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

2017-04-06 Thread Hervé Pagès
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:

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

2017-04-06 Thread Hahne, Florian
ich...@gene.com>, "bioc-devel@r-project.org" <bioc-devel@r-project.org>, Florian Hahne <florian.ha...@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

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

2017-04-06 Thread Hahne, Florian
ael Lawrence <lawrence.mich...@gene.com>, "bioc-devel@r-project.org" <bioc-devel@r-project.org>, Florian Hahne <florian.ha...@novartis.com> Subject: Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter @Florian: nothing you have to change. I ch

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

2017-04-06 Thread Rainer Johannes
@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

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

2017-04-06 Thread Obenchain, Valerie
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

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

2017-04-06 Thread Hahne, Florian
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

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

2017-04-06 Thread Stian Lågstad
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

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

2017-04-04 Thread Michael Lawrence
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 >

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

2017-04-04 Thread Rainer Johannes
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

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

2017-04-04 Thread Hervé Pagès
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

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

2017-04-04 Thread Rainer Johannes
On 4 Apr 2017, at 10:59, Stian Lågstad > 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

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

2017-04-03 Thread Rainer Johannes
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