Le Thu, Apr 27, 2017 at 01:16:11PM -0500, Dirk Eddelbuettel a écrit : > Could you fill me in about what broke with BioC and what caused it?
As far as I understand, something changed with the c() generic, which broke packages providing a S4 method for it. The breakage and the solution were reported on <https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010559.html>. There was somewhere a better explanation on why it happens, but I could not find it anymore. In brief, it has to do with the fact that upon installation, some S4 functions capture part of their environment, and the c() declarations in R 3.3.2 are not compatible with the c() function (or method, etc., sorry for the imprecise vocabulary) in R 3.3.3, and therefore packages need to be reinstalled. And since our Debian packages (and R Win/Mac pacakges) are essentially a copy of installed packages, we need to rebuild the affected ones. Thus, while BioC was more affected since it heavily uses S4, I would expect that some CRAN packages were broken as well. Continuous integration of Debian's packages did not pinpoint problems in the r-cran-* namespace, but as exemplified by r-bioc-xvector, some regression tests have only partial coverage. > I am not sure I understand why people would want to do partial upgrades. > Debian stable is support. Debian testing is supported. Hybrid mixes of the > two are risque. I do agree and would not recommend mixes, especially since the CRAN and Debian backports are available. But Debian officially supports partial upgrades, in the sense that if the dependency graph allows for it, then it should work. In that sense, preventing partial upgrades through the use of r-api-4 would be an acceptable solution. Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
