Bug#991919: transition: r-api-bioc-3.13
Hi Nilesh, On Sat, Sep 11, 2021 at 11:24:44PM +0530, Nilesh Patra wrote: > > I did few uploads to get the transition moving forward. Current blocker is > for r-bioc-biocsingular which needs r-bioc-scaledmatrix and the latter is > still in NEW. > For scaledmatrix, I've asked already on the #-ftp IRC as well, hopefully it > gets proc soon. > > This is blocking a few packages, but I'm in the process of uploading the rest > which are not directly uploaded. > Will upload a few packages tomorrow as well. Before going offline again I quickly uploaded r-bioc-biocsingular so this can keep on moving now. > > There is one thing I would love to be solved soon: I just cheated > > with the test suite of biomformat in this patch: > > > > > > https://salsa.debian.org/r-pkg-team/r-bioc-biomformat/-/blob/master/debian/patches/fixme_disable_test_for_the_moment.patch > > Looking at the error, and also at the calls for those, they are called with > `suppressWarnings(read_biom(min_sparse_hdf5))` > So probably the file was not good already, since it explicitly tries to > suppress warnings. > _*Maybe*_ in this release, there were a few changes that rendered the file > unusable to for analysis. > To me, it does not appear high priority. I would love to see that settled anyway since it looks suspicious to me. > > I would love if somebody could find a fix - may be by discussing > > with upstream. > > No time, sorry :) It would be really cool if someone could take this task. Kind regards Andreas. -- http://fam-tille.de
Bug#991919: transition: r-api-bioc-3.13
On 9/11/21 12:27 PM, Andreas Tille wrote: > Hi, > > the blockers mentioned below are done now. Those who have some > spare time might like to continue with the transition. I will > not contribute relevant things until Tuesday. I did few uploads to get the transition moving forward. Current blocker is for r-bioc-biocsingular which needs r-bioc-scaledmatrix and the latter is still in NEW. For scaledmatrix, I've asked already on the #-ftp IRC as well, hopefully it gets proc soon. This is blocking a few packages, but I'm in the process of uploading the rest which are not directly uploaded. Will upload a few packages tomorrow as well. > There is one thing I would love to be solved soon: I just cheated > with the test suite of biomformat in this patch: > > > https://salsa.debian.org/r-pkg-team/r-bioc-biomformat/-/blob/master/debian/patches/fixme_disable_test_for_the_moment.patch Looking at the error, and also at the calls for those, they are called with `suppressWarnings(read_biom(min_sparse_hdf5))` So probably the file was not good already, since it explicitly tries to suppress warnings. _*Maybe*_ in this release, there were a few changes that rendered the file unusable to for analysis. To me, it does not appear high priority. > I would love if somebody could find a fix - may be by discussing > with upstream. No time, sorry :) Cheers, -- Nilesh Patra Debian Developer, Uploading ⢀⣴⠾⠻⢶⣦⠀ ⣾⠁⢠⠒⠀⣿⡁ ⢿⡄⠘⠷⠚⠋ nil...@debian.org / nileshpatra.info / tchncs.de ⠈⠳⣄ OpenPGP_signature Description: OpenPGP digital signature
Bug#991919: transition: r-api-bioc-3.13
Hi, the blockers mentioned below are done now. Those who have some spare time might like to continue with the transition. I will not contribute relevant things until Tuesday. There is one thing I would love to be solved soon: I just cheated with the test suite of biomformat in this patch: https://salsa.debian.org/r-pkg-team/r-bioc-biomformat/-/blob/master/debian/patches/fixme_disable_test_for_the_moment.patch I would love if somebody could find a fix - may be by discussing with upstream. Kind regards Andreas. On Wed, Sep 08, 2021 at 04:15:28PM +0200, Andreas Tille wrote: > Hi, > > I'd like to give a short status update here. > I have uploaded several r-bioc-* packages. Currently I'm facing two > blockers > > * libhdf5-dev needs an update which can be expected soon[1] > thanks to Gilles Filippini > + r-bioc-rtracklayer needs r-bioc-biocio and r-cran-restfulr > which are both in new. I've pinged #debian-ftp on IRC about > this > > Most (probably all) packages listed in the transition tracker > are affected. I added the actual issue to d/changelog of those > packages I touched. > > I'll be unable to do anything about this from 11.-13. September. > > Kind regards > >Andreas. > > > [1] https://lists.debian.org/debian-r/2021/09/msg00037.html > > -- > http://fam-tille.de > > -- http://fam-tille.de
Bug#991919: transition: r-api-bioc-3.13
Hi, I'd like to give a short status update here. I have uploaded several r-bioc-* packages. Currently I'm facing two blockers * libhdf5-dev needs an update which can be expected soon[1] thanks to Gilles Filippini + r-bioc-rtracklayer needs r-bioc-biocio and r-cran-restfulr which are both in new. I've pinged #debian-ftp on IRC about this Most (probably all) packages listed in the transition tracker are affected. I added the actual issue to d/changelog of those packages I touched. I'll be unable to do anything about this from 11.-13. September. Kind regards Andreas. [1] https://lists.debian.org/debian-r/2021/09/msg00037.html -- http://fam-tille.de
Bug#991919: transition: r-api-bioc-3.13
Control: tags -1 moreinfo On 2021-08-05 15:03:24 +0200, Dylan Aïssi wrote: > Package: release.debian.org > Severity: normal > User: release.debian@packages.debian.org > Usertags: transition > X-Debbugs-CC: debia...@lists.debian.org, debian-...@lists.debian.org > > > Hi, > Bioconductor 3.13 was released in May [1]. All r-bioc-* packages need > a manual upgrade (after the release of bullseye). > > [1] https://bioconductor.org/news/bioc_3_13_release/ > > Please set up a tracker manually, since this is a transition of a > virtual package name. What's the status wrt. to the reverse dependencies. Do those that are binNMU-able build against the new version? Cheers > > Ben file: > - > title = "r-api-bioc-3.13"; > is_affected = .depends ~ /r-api-bioc/; > is_good = .depends ~ "r-api-bioc-3.13"; > is_bad = .depends ~ "r-api-bioc-3.12"; > - > > Best, > Dylan > -- Sebastian Ramacher signature.asc Description: PGP signature
Bug#991919: transition: r-api-bioc-3.13
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition X-Debbugs-CC: debia...@lists.debian.org, debian-...@lists.debian.org Hi, Bioconductor 3.13 was released in May [1]. All r-bioc-* packages need a manual upgrade (after the release of bullseye). [1] https://bioconductor.org/news/bioc_3_13_release/ Please set up a tracker manually, since this is a transition of a virtual package name. Ben file: - title = "r-api-bioc-3.13"; is_affected = .depends ~ /r-api-bioc/; is_good = .depends ~ "r-api-bioc-3.13"; is_bad = .depends ~ "r-api-bioc-3.12"; - Best, Dylan
