Re: Bioconductor API Bump to 3.13
Hi, On Sun, Aug 15, 2021 at 10:01:21AM +0200, Dylan Aïssi wrote: > > The transition tracker is on at > https://release.debian.org/transitions/html/r-api-bioc-3.13.html > > We are now waiting for the green-light from the release team (at > https://bugs.debian.org/991919) to start the transition of > bioconductor packages. All packages but one of the transition are now uploaded. The missing one is r-bioc-destiny where we are discussing a removal from the archive[1]. I wonder whether we should file an RC bug against r-bioc-destiny to trigger testing removal. I think we should now focus on autopkgtests of the r-bioc-* packages since some test were depending from packages in a higher transition level. Kind regards Andreas. [1] https://lists.debian.org/debian-r/2021/09/msg00067.html -- http://fam-tille.de
Re: Bioconductor API Bump to 3.13
Hi Nilesh, Le mar. 31 août 2021 à 09:07, Nilesh Patra a écrit : > > I just happened to see this commit[1]. Has the transition begun? > If so, can I do anything to help? > Yep :-) See https://bugs.debian.org/991919#44 I don't have too much free time. So, Feel free to upload all packages you can with routine-update. You can follow the order of this list > https://release.debian.org/transitions/html/r-api-bioc-3.13.html But, remember some bioc packages are not present in this list. In this case, this diagram can help you > https://salsa.debian.org/r-pkg-team/maintenance-utilities/-/blob/master/BioC_dependency-tree.ditaa Best, Dylan
Re: Bioconductor API Bump to 3.13
Hi Dylan, On 15 August 2021 1:31:21 pm IST, "Dylan Aïssi" wrote: >Hi Steffen, hi Andreas, > >Le jeu. 5 août 2021 à 06:18, Andreas Tille a écrit : >> Sure. We need a transition. Dylan (in CC) was kind enough to trigger >> this in the past and we should do so right after the release (I'm >> announcing here pseudo-VAC due to personal reasons on one hand as well >> as DebConf business - so please do not trust too much on my contribution >> on this transition. >> >> We do not habe better automatism than routne-update and the transition >> coordination webpage listing a sensible sequence to do this, thought. > >The transition tracker is on at >https://release.debian.org/transitions/html/r-api-bioc-3.13.html > >We are now waiting for the green-light from the release team (at >https://bugs.debian.org/991919) to start the transition of >bioconductor packages. I just happened to see this commit[1]. Has the transition begun? If so, can I do anything to help? [1]: https://salsa.debian.org/release-team/transition-data/-/commit/bdfbab308eff19bcd346a1829e7feb3d98da0444 Nilesh -- Sent from my Android device with K-9 Mail. Please excuse my brevity.
Re: Bioconductor API Bump to 3.13
Hi Dylan, On Sun, Aug 15, 2021 at 01:17:29PM +0200, Andreas Tille wrote: > Hi, > > On Sun, Aug 15, 2021 at 10:01:21AM +0200, Dylan Aïssi wrote: > > > > The transition tracker is on at > > https://release.debian.org/transitions/html/r-api-bioc-3.13.html > > > > We are now waiting for the green-light from the release team (at > > https://bugs.debian.org/991919) to start the transition of > > bioconductor packages. > > Thanks for triggering this. Meanwhile I'm starting upgrading > r-cran-packages from the end of the alphabeth (as traveling > connection permits). The transition page seems to be setup by the release team. When do you plan to start the transition? Kind regards Andreas. -- http://fam-tille.de
Re: Bioconductor API Bump to 3.13
Hi, On Sun, Aug 15, 2021 at 10:01:21AM +0200, Dylan Aïssi wrote: > > The transition tracker is on at > https://release.debian.org/transitions/html/r-api-bioc-3.13.html > > We are now waiting for the green-light from the release team (at > https://bugs.debian.org/991919) to start the transition of > bioconductor packages. Thanks for triggering this. Meanwhile I'm starting upgrading r-cran-packages from the end of the alphabeth (as traveling connection permits). Kind regards Andreas. -- http://fam-tille.de
Re: Bioconductor API Bump to 3.13
Hi Steffen, hi Andreas, Le jeu. 5 août 2021 à 06:18, Andreas Tille a écrit : > Sure. We need a transition. Dylan (in CC) was kind enough to trigger > this in the past and we should do so right after the release (I'm > announcing here pseudo-VAC due to personal reasons on one hand as well > as DebConf business - so please do not trust too much on my contribution > on this transition. > > We do not habe better automatism than routne-update and the transition > coordination webpage listing a sensible sequence to do this, thought. The transition tracker is on at https://release.debian.org/transitions/html/r-api-bioc-3.13.html We are now waiting for the green-light from the release team (at https://bugs.debian.org/991919) to start the transition of bioconductor packages. Best, Dylan
Re: Bioconductor API Bump to 3.13
Hi Steffen, On Wed, Aug 04, 2021 at 11:32:13AM +0200, Steffen Möller wrote: > Hello, > > Our distro currently holds > > $ apt-cache show r-bioc-biocgenerics| grep ^Provides > Provides: r-api-bioc-3.12 > > but about all of BioConductor now needs 3.13. The new > r-bioc-biocgenerics package providing 3.13 can be installed without > problems, but the then missing 3.12 of that API means that all other > reverse dependencies are considered invalid and are uninstalled with an > "apt --fix ...". Sure. We need a transition. Dylan (in CC) was kind enough to trigger this in the past and we should do so right after the release (I'm announcing here pseudo-VAC due to personal reasons on one hand as well as DebConf business - so please do not trust too much on my contribution on this transition. > In our videoconference I had suggested to have some fun events like the > bulk updating of qiime packages but we should give some extra thoughts > on how to deal with the BioConductor updates. Should this possibly be > automated? We do not habe better automatism than routne-update and the transition coordination webpage listing a sensible sequence to do this, thought. The connection to qiime is the question whether we need a qiime API version or not. Kind regards Andreas. -- http://fam-tille.de
