> On Sat, Apr 1, 2017 at 15:24:53 +0900, Charles Plessy wrote: > > > > as a follow-up to #858183, I looked at which other R Bioconductor > > packages were broken by R 3.3.3-1, and it seems that the previous round > > of binNMUs did not repair some of them. > > > > Can you make the followig binNMUs ? > > > > nmu r-bioc-rsamtools_1.26.1-2 . ANY . -m "Rebuild for R 3.3.3." > > nmu r-bioc-shortread_1.32.0-1 . ANY . -m "Rebuild for R 3.3.3." > > nmu r-bioc-variantannotation_1.20.2-1 . ANY . -m "Rebuild for R 3.3.3." > > nmu r-bioc-genomicalignments_1.10.0-1 . ANY . -m "Rebuild for R 3.3.3."
Le Sun, Apr 30, 2017 at 06:08:46PM +0200, Julien Cristau a écrit : > > > binNMUs are not an acceptable way to deal with silent breakage. If R > 3.3.3-1 breaks reverse dependencies, it needs to not be co-installable > with them. Hi Julien, I understand that Debian wants partial upgrades to be supported (even in the sense of preventing them with Breaks relationships), but with R we are not yet there. Please also note that I am not the maintainer of the r-base package. Jessie ships R 3.1.1 and Stretch will ship R 3.3.3. In the R ecosystem, users are expected to rebuild their packages when upgrading R to a new minor version (for instance from 3.1.x to 3.3.x). In practice, many packages keep working and backward incompatibilities are announced in advance. Unfortunately, in the case of 3.3.3, it even broke backwards incompatiblity with the previous patchlevel version 3.3.2, in an unexpected way. This is what I am trying to address now. You can of course open a bug on r-base asking for Breaks declarations to be added, but at the moment I can not tell if something would be missing, as I am focusing on the issue of making Stretch's r-base work with Stretch's R packages, and not with Jessie ones or some that can now only be found on snapshots.debian.org. For the next release cycle, we may be able to prevent Stretch's R packages to be used with Buster's r-base package, as our build scripts now insert a dependency on the virtual package 'r-api-3' that r-base provides; we are actually discussing about bumping it to r-api-4 in <https://bugs.debian.org/861333>. I hope it clarifies my efforts. Many thanks for the binNMUs, it helped me a lot. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan
