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

[Dan Tenenbaum]

Hi Marcin,

----- Original Message -----
> From: "Marcin Cieślik" <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
> 
> 	[[alternative HTML version deleted]]
> 
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