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.mich...@gene.com > wrote: > Sorry I have been traveling. Will get to it soon. > > On Apr 4, 2017 12:58 PM, "Rainer Johannes" <johannes.rai...@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 <hpa...@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 <stianlags...@gmail.com<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: > > 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.rai...@eurac.edu<mailto:johannes.rai...@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@r-project.org<mailto:Bioc-devel@r-project.org> mailing > list > > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. > > ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAf > qt84VtBcfhQ&r= > > BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iJ2N4NzAka_Lu8P0_h6XWIy- > > PpkQJQ6twQd8-on8IrI&s=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY&e= > > >> > > >> > > >> > > >> -- > > >> Stian Lågstad > > >> +47 41 80 80 25 > > >> > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> _______________________________________________ > > >> Bioc-devel@r-project.org mailing list > > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. > > ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAf > qt84VtBcfhQ&r= > > BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iJ2N4NzAka_Lu8P0_h6XWIy- > > PpkQJQ6twQd8-on8IrI&s=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY&e= > > >> > > > > > > -- > > > Hervé Pagès > > > > > > Program in Computational Biology > > > Division of Public Health Sciences > > > Fred Hutchinson Cancer Research Center > > > 1100 Fairview Ave. N, M1-B514 > > > P.O. Box 19024 > > > Seattle, WA 98109-1024 > > > > > > E-mail: hpa...@fredhutch.org > > > Phone: (206) 667-5791 > > > Fax: (206) 667-1319 > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel