Many packages have made the switch from GenomeInfoDb to Seqinfo but
there are still a number of packages that fail on the devel daily report
because of the new location of the Seqinfo class definition.
If your package is failing with an error that says "there is no package
called GenomeInfoDb" or "unable to load required package GenomeInfoDb",
them it is most likely because it contains some Seqinfo-holding
serialized objects. Here is an example of such package:
https://bioconductor.org/checkResults/3.22/bioc-LATEST/CellBench/
I've fixed 50 packages with Seqinfo-holding serialized objects this
morning. Here's the list:
aggregateBioVar
ASURAT
Banksy
blase
BUSseq
CellBench
CellMixS
CellTrails
Cepo
CHETAH
CiteFuse
clusterExperiment
clustSIGNAL
consensusSeekeR
cytomapper
dandelionR
dar
distinct
GloScope
Ibex
jazzPanda
lemur
MEB
MGnifyR
mia
miaTime
muscat
peco
POWSC
RegionalST
scDataviz
scDD
scDesign3
scds
scider
scMerge
scp
scReClassify
slalom
sosta
SpaNorm
spatialHeatmap
speckle
SPIAT
spicyR
SpotSweeper
Statial
SVP
tidySingleCellExperiment
tricycle
Note that I committed and pushed directly to git.bioconductor.org so if
you maintain any of the above packages please make sure to resync your
GitHub repo with the repo at git.bioconductor.org.
Don't hesitate to let me know if you have questions about this.
Best,
H.
On 22/06/2025 01:52, Hervé Pagès wrote:
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
[email protected]
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