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jianhong / ChIPpeakAnno

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disjointExons removed in Bioconductor 3.17 #21

Closed yeyuan98 closed 1 year ago

yeyuan98 commented 1 year ago

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 1 year ago

Hi Ye Yuan,

Thank you for reporting. I just pushed the patch. It will take several days for updating.

Jianhong.

From: Ye Yuan @.> Date: Saturday, November 12, 2022 at 12:47 PM To: jianhong/ChIPpeakAnno @.> Cc: Subscribed @.***> Subject: [jianhong/ChIPpeakAnno] disjointExons removed in Bioconductor 3.17 (Issue #21)

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: ensembldbhttps://github.com/jorainer/ensembldb/commit/4bd6ababfc909e979dcb6f7cb5f8cc9a9ddde1ea GenomicFeatureshttps://github.com/Bioconductor/GenomicFeatures/commit/df02299383965c99c5abf592596ccc22c08a9bfa

Thanks a lot for your time!

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