Re: Conflict between R 4.5 and some (mostly r-bioc 3.20) R packages
r-bioc-pwalign / r-bioc-shortread: this appears to be
https://github.com/Bioconductor/pwalign/issues/11 ; I have pushed the
upstream fix.
r-cran-rlang: I have pushed a version with an r-base-core (>= 4.5.0~)
Depends.
r-bioc-bioccheck: the explicit version check is actually in
r-cran-biocmanager (at
https://sources.debian.org/src/r-cran-biocmanager/1.30.25+dfsg-1/R/version.R/?hl=329#L329
), which is used by BiocCheck:::checkSingleColon and
BiocCheck:::checkIsPackageNameAlreadyInUse. I have pushed a version
removing the tests of those functions. (I also tried the override
mechanism described at
https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#unsupported-r-bioconductor-versions
+
https://sources.debian.org/src/dh-r/20241218/scripts/pkg-r-autopkgtest/?hl=32#L32
, but it didn't work.)
This version check will also fail BiocManager::install(),
BiocManager::available(), BiocManager::repositories(),
BiocCheck:::checkSingleColon, BiocCheck:::checkIsPackageNameAlreadyInUse
if actual users try to use them, which raises the question of whether we
should change the check message to say that this is expected in Debian,
and that users can uninstall r-bioc-* and run
BiocManager::install(version = "3.21") if they want an
upstream-supported version.
(I *don't* think we should disable the check entirely: we *are* doing
something upstream don't recommend, and the fact that I've done so much
of the work is *not* intended to be an opinion on whether it was ever a
good idea.)
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