hi, it happens only with "[", that's why i'm puzzled.
it behaves as if you load a GRanges object 'x' and try to subset it x[1] without loading 'GenomicRanges' first. robert. On 10/07/2014 05:05 PM, Michael Lawrence wrote:
Does that happen with the other methods or just "["? As a last resort, you could just drop the import (because "[" is a primitive, it should just work). On Tue, Oct 7, 2014 at 3:08 AM, Robert Castelo <robert.cast...@upf.edu <mailto:robert.cast...@upf.edu>> wrote: hi Martin, On 10/06/2014 07:24 PM, Martin Morgan wrote: [...] There are two 'as.vector' generics, one defined in Matrix and one in BiocGenerics (and made available via IRanges). These generics have different methods > showMethods(Matrix::as.vector) Function: as.vector (package base) x="abIndex", mode="ANY" x="abIndex", mode="character" x="ANY", mode="ANY" x="dgCMatrix", mode="missing" x="dgeMatrix", mode="missing" x="diagonalMatrix", mode="missing" x="dsCMatrix", mode="missing" x="ldenseMatrix", mode="missing" x="Matrix", mode="missing" x="ndenseMatrix", mode="missing" x="sparseVector", mode="character" x="sparseVector", mode="missing" > showMethods(BiocGenerics::as.__vector) Function: as.vector (package BiocGenerics) x="ANY" x="AtomicList" x="Rle" x="XDouble" x="XInteger" x="XRaw" x="XString" x="XStringSet" so it's important that your code clearly distinguish between generics. One possibility is to remove importMethodsFrom(IRanges, as.vector) from the NAMESPACE, and explicitly use IRanges::as.vector(...) in your code. ok, i've done this as it is the easiest at the moment to meet the release schedule. i guess that in the future i should try to avoid using the '::' operator by importing exclusively what is needed from each package. codetoolsBioC::__writeNamespaceImports("__qpgraph") might provide you with some guidance (it's not 100% reliable; available via svn at https://hedgehog.fhcrc.org/__bioconductor/trunk/madman/__Rpacks/codetoolsBioC <https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC>) about what functionality is being imported. thanks for the heads up about codetoolsBioC, i've tried it out and seen that some of the suggested imports are not necessary but some others i was really missing them (which makes me wonder how was it possible that he package did not break at those points). one further question related to NAMESPACE. i subset GRanges objects in the package via the '[' operator, i've included this into the NAMESPACE file as: importMethodsFrom(__GenomicRanges, c, cbind, rbind, "mcols<-", start, end, strand, sort, "[", "[<-", "[[", "[[<-", "$", "$<-") however, when the package reaches a subset operation x[i] with x being a GRanges object, an entire package loading sequence starts: Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ [... etc ...] which may look a bit odd to the user. for every other imported method the package uses them silently without loading the corresponding package, am i importing '[' for GRanges objects from the wrong package? is there a way to import '[' so that my package can use it without triggering that package loading sequence? thanks again! robert. _________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
-- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
