Hi Herve > On 7 Apr 2017, at 07:42, Hervé Pagès <hpa...@fredhutch.org> 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 for that). I did also fix wiggleplotr and made a pull request, but the developer did not yet react to that. cheers, jo > https://bioconductor.org/checkResults/3.5/bioc-LATEST/Pbase/malbec2-buildsrc.html > > H. > > > On 04/06/2017 01:07 PM, Rainer Johannes wrote: >> @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.obench...@roswellpark.org<mailto:valerie.obench...@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 >> (https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLQ9KUUm3u9dA66MERqNGNYccQtXR7ieDcLKZZMrSII&s=mdDgNHoW4wRbQFZFJ4a7r2gUE_n6XQspfZvlgjQ94c8&e= >> 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<mailto: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<mailto: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<mailto: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><mailto >> : >> 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><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><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<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= >> -- >> 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<mailto:hpa...@fredhutch.org> >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> _______________________________________________ >> 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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLQ9KUUm3u9dA66MERqNGNYccQtXR7ieDcLKZZMrSII&s=Vw_1NtWytQstePp1FRdu2QDh9haBBsacP3zFsPhs_Qo&e= >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLQ9KUUm3u9dA66MERqNGNYccQtXR7ieDcLKZZMrSII&s=Vw_1NtWytQstePp1FRdu2QDh9haBBsacP3zFsPhs_Qo&e= >> >> >> >> >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> _______________________________________________ >> 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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLQ9KUUm3u9dA66MERqNGNYccQtXR7ieDcLKZZMrSII&s=Vw_1NtWytQstePp1FRdu2QDh9haBBsacP3zFsPhs_Qo&e= >> >> >> [[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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLQ9KUUm3u9dA66MERqNGNYccQtXR7ieDcLKZZMrSII&s=Vw_1NtWytQstePp1FRdu2QDh9haBBsacP3zFsPhs_Qo&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
