[Bioc-devel] Switch from GenomeInfoDb to new Seqinfo package

[Hervé Pagès]

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
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