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

[Dan Tenenbaum]

[keeping the list in the loop]

----- Original Message -----
> From: "Marcin Cieślik" <marcin.cieslik at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Sent: Friday, September 12, 2014 10:15:55 AM
> Subject: Re: [Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method
> 
> 
> Dear Dan,
> 
> 
> Thank you, the problem went away when I moved everything to NAMESPACE
> like you suggested.
> 
> 
> Should packages needed only for tests be also put into NAMESPACE and
> DESCRIPTION?
> 

These packages can go into Suggests and don't need to be in NAMESPACE. You do need to library() these packages in your test code.
Dan

> 
> Yours,
> Marcin
> 
> 
> 
> 
> 
> 
> On Fri, Sep 12, 2014 at 12:47 PM, Dan Tenenbaum < dtenenba at fhcrc.org
> > wrote:
> 
> 
> 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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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
>