[Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method

Marcin Cieślik marcin.cieslik at gmail.com
Fri Sep 12 16:14:37 CEST 2014

Hi All,

I am developing a package for Bioconductor 3.0. I "import" on a number of

methods GenomicRanges rtracklayer BiocParallel GenomicFiles GenomicFeatures

I noticed that depending on the order by which these packages are
library'ed the code

summary(someBigWigFileViewObject, type="mean")

will silently fail (i.e. it returns) a summaryDefault object
         Length           Class            Mode
              1 BigWigFileViews              S4

Trying to pin-down the reason it appears that if AnnotatioDbi is loaded
after Biostrings (not a direct dependency but loaded) the summary function
changes from "s4" "generic" to "s3" "generic" which breaks GenomicFiles and
probably others stuff.


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