jianhong/ChIPpeakAnno

disjointExons removed in Bioconductor 3.17

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yeyuan98 commented

Hi Jianhong,

Thanks so much for your great package. I noticed that in the bioconductor development version 3.17, disjointExons method is removed from ensembldb and GenomicFeatures packages, causing your ChIPpeakAnno package to fail during build.

Would it be possible to fix this issue simply by changing your code like the following?

from R/privateUtil.R, line 616-618

disjointExons(ranges,
                                      aggregateGenes=FALSE,
                                      includeTranscripts=TRUE)

to

GenomicFeatures::exonicParts(ranges,
                                      linked.to.single.gene.only=TRUE)

Commits related to the removal of disjointExons:
ensembldb
GenomicFeatures

Thanks a lot for your time!

jianhong commented