Dear fellow Bioconductor developers,
The Seqinfo class and its accessors were moved from the GenomeInfoDb
package to the new Seqinfo package in BioC 3.22. Packages that import
any of the accessors 'seqnames', 'seqlevels', 'seqlenghs', 'isCircular',
'genome', 'seqinfo', and/or the 'Seqinfo' constructor function from
GenomeInfoDb will now need to import them from the Seqinfo package. The
main remaining business of the GenomeInfoDb package is the
"seqlevelsStyle business" which has grown significantly in complexity in
the recent years. Having the "core Seqinfo business" (i.e. Seqinfo class
+ constructor + accessors) in its own lightweight package with a reduced
number of deps makes a lot of sense.
I've switched 40+ packages from GenomeInfoDb to Seqinfo already, but
many more packages will need to make that switch. Note that I committed
and pushed directly to git.bioconductor.org to expedite things, so
please make sure to resync your GitHub repo with the repo at
git.bioconductor.org if your package depends on GenomeInfoDb because
there's a chance that it has been switched.
A couple more things:
- The latest version of GenomeInfoDb (1.45.5) imports the new Seqinfo
package and re-exports the Seqinfo constructor and accessors. This is to
help with backward compatibility.
- Even with the re-export trick, some packages will still fail. I
actually expect a significant number of packages to fail on Monday when
the next daily build report for BioC 3.22 is out. I'll try to take care
of as many as I can but it might take a few days before I start doing
so. Depending on how many there are, I might also need help.
Sorry in advance for the inconvenience and thanks for your patience.
H.
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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