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: Bug#991919: Bioconductor API Bump to 3.13
Hi, On Thu, Aug 26, 2021 at 11:01:13AM +0200, Dylan Aïssi wrote: > > If this question is to the release team, than the following question we > > asked earlier requires an answer: > > > What's the status wrt. to the reverse dependencies. Do those that are > > > binNMU-able build against the new version? > > No, all these reverse dependencies need a manual upgrade with the new > upstream releases, they are not binNMU-able. > The Debian R Packages team will upgrade to the new upstream releases > all of the reverse dependencies. Actually most of the Bioc dependencies will need a version upgrade anyway. So we need manual intervention in any case and the r-pkg team will do so. Kind regards Andreas. -- http://fam-tille.de
Re: Bug#991919: Bioconductor API Bump to 3.13
Hi, Le jeu. 26 août 2021 à 09:49, Paul Gevers a écrit : > > If this question is to the release team, than the following question we > asked earlier requires an answer: > > What's the status wrt. to the reverse dependencies. Do those that are > > binNMU-able build against the new version? > No, all these reverse dependencies need a manual upgrade with the new upstream releases, they are not binNMU-able. The Debian R Packages team will upgrade to the new upstream releases all of the reverse dependencies. Best, Dylan
Re: Bug#991919: Bioconductor API Bump to 3.13
Hi Andreas, On 26-08-2021 07:45, Andreas Tille wrote: > 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? If this question is to the release team, than the following question we asked earlier requires an answer: > What's the status wrt. to the reverse dependencies. Do those that are > binNMU-able build against the new version? Paul OpenPGP_signature Description: OpenPGP digital signature
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
Bioconductor API Bump to 3.13
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 ...". 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? Best, Steffen
