[Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
United States
[keeping the list in the loop] ----- Original Message ----- > From: "Marcin Cie?lik" <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 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 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > >
GO Biostrings rtracklayer GenomicRanges BiocParallel GenomicFiles • 730 views
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