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

Hi Marcin,

----- Original Message -----
From: "Marcin Cie?lik" <marcin.cieslik at gmail.com>
To: bioc-devel at 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

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