[Bioc-devel] Missed change in S4Vectors

[Hervé Pagès]

Hi Peter,

Starting with S4Vectors 0.7.12, labeledLine() belongs to S4Vectors so
using the triple colon should not be necessary (and doing so will
actually trigger a note from R CMD check). Can you provide more
details on why you need this?

Thanks,
H.


On 08/09/2015 09:16 PM, Peter Hickey wrote:
> Hi Hervé,
>
> I was having trouble with some devel code of mine and tracked it down to some recent updates moving the internal utility labeledLine() from BiocGenerics to S4Vectors. The labeledLine() internal function wasn’t being found when called in certain circumstances. Here’s an svn diff to fix the bug in the S4Vectors package.
>
> Cheers,
> Pete
>
> Index: DESCRIPTION
> ===================================================================
> --- DESCRIPTION	(revision 107278)
> +++ DESCRIPTION	(working copy)
> @@ -8,7 +8,7 @@
>   	interest (e.g. DataFrame, Rle, and Hits) are implemented in the
>   	S4Vectors package itself (many more are implemented in the IRanges
>   	package and in other Bioconductor infrastructure packages).
> -Version: 0.7.12
> +Version: 0.7.13
>   Author: H. Pages, M. Lawrence and P. Aboyoun
>   Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
>   biocViews: Infrastructure, DataRepresentation
> Index: R/List-class.R
> ===================================================================
> --- R/List-class.R	(revision 107278)
> +++ R/List-class.R	(working copy)
> @@ -86,7 +86,7 @@
>                 cat(classNameForDisplay(object), " of length ", lo,
>                     "\n", sep = "")
>                 if (!is.null(names(object)))
> -                cat(labeledLine("names", names(object)))
> +                cat(S4Vectors:::labeledLine("names", names(object)))
>             })
>
>
> --------------------------------
> Peter Hickey,
> PhD Student/Research Assistant,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> Ph: +613 9345 2324
>
> hickey at wehi.edu.au
> http://www.wehi.edu.au
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:19}}