Hi Marcin, ----- Original Message ----- > From: "Marcin Cieślik" <marcin.cies...@gmail.com> > To: bioc-devel@r-project.org > Sent: Friday, September 12, 2014 7:14:37 AM > Subject: [Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles > summary method > > Hi All, > > I am developing a package for Bioconductor 3.0. I "import" on a > number of > packages: > > 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. >
I might be misunderstanding you but you shouldn't need to have library(x) in package code where x is any package that you Import. Be sure you have the package both in the Imports field of DESCRIPTION and in NAMESPACE as well; unless there are specific reasons not to, import the whole package in NAMESPACE. Does the problem still occur if you do this? Dan > Yours, > Marcin > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
