[Bioc-devel] Switch from GenomeInfoDb to new Seqinfo package
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, Herv? Pag?s 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.
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com