Re: Bioconductor 3.19 transition
Hi Michael,
Am Sun, Jul 14, 2024 at 05:09:51PM +0200 schrieb Michael R. Crusoe:
> > Am Sat, Jul 13, 2024 at 02:04:52PM +0200 schrieb Michael R. Crusoe:
> Done with the local builds!
Cool.
> > > Then I'll cycle through the architecture dependent packages, doing a `ssh mirror.ftp-master.debian.org "dak rm --rdep-check --no-action r-bioc-$NAME"` check and adding the `architecture-is-64-bit` build-dep only when there are no no-bioc packages that would be affected.
>
> Luckily I thought about this a little bit and realized I can do a single query about the removals.
>
> ssh mirror.ftp-master.debian.org "dak rm --architecture=armel,armhf,i386 --no-arch-all-rdeps --binary-only --partial --rdep-check --no-action $(tr '\n' ' ' < ~/debian/bioc-3.19/packaged-any)"
> # where ~/debian/bioc-3.19/packaged-any is a list of packages I made that contain "Architecture: any" in their debian/control files
>
> The following non-bioc-3.19 packages would also need their 32-bit builds removed:
>
> r-bioc-deseq # not part of bioconductor since 3.13
> r-cran-nmf # build-dep on r-bioc-biobase
> r-cran-restfulr # build-dep on r-bioc-s4vectors
> r-cran-samr # build-dep on r-bioc-impute
> r-cran-wgcna # build-dep on r-bioc-impute, r-bioc-preprocesscore, r-bioc-go.db, r-bioc-annotationdbi
>
> Adding the 5 packages above to the `dak rm` query doesn't reveal any other issues, BUT removing 32-bit builds of any r-cran-* packages is not yet part of the agreement.
This sounds all very sensible! If I was not yet convinced that it was a
good idea to run for DPL I think this is a good outcome to deal with
those tasks automatically. ;-P
> Redoing my "dak rm" query without r-bioc-{biobase,s4vectors,impute,preprocesscore} shows no more issues.
Nice.
> So I'll add the build-dep on "architecture-is-64-bit" to these 76 packages and "extra_restrictions=skip-not-installable" to debian/tests/autopkgtest-pkg-r.conf in all the r-bioc-* packages.
ACK.
> > That looks great (and a lot of effort - thanks a lot!)
>
> You are welcome!
:-)
> > In case you might need some helping hand in the transition phase I might
> > see what I can do.
>
> Thanks!
It might be a bit short timing but I guess while beeing in DebCamp I
will probably find some time for it (but not at DebConf).
Thanks again
Andreas.
--
https://fam-tille.de
Reply to: