[Bioc-devel] Missed change in S4Vectors

[Peter Hickey]

Sorry, that should say once I made the proposed change to "S4Vectors", not
"IRanges".

On Tue, 11 Aug 2015 8:51 am Peter Hickey <peter.hickey at gmail.com> wrote:

> Hi Hervé,
>
>
> Hmm, sorry I may have misdiagnosed my problem. I was having problems with
> some code in the bsseq vignette.
>
>
> The following demonstrates what was happening:
>
>
> > suppressPackageStartupMessages(library(bsseq))
>
> Warning message:
>
> In .recacheSubclasses(def at className, def, doSubclasses, env) :
>
>   undefined subclass "externalRefMethod" of class "expressionORfunction";
> definition not updated
>
> > data(BS.chr22)
>
> > head(seqnames(BS.chr22), n = 4)
>
> factor-Rle of length 4 with 1 run
>
> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>
>   object 'labeledLine' not found
>
> > sessionInfo()
>
> R version 3.2.1 (2015-06-18)
>
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>
> Running under: OS X 10.10.4 (Yosemite)
>
>
> locale:
>
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
>
> attached base packages:
>
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>
> [8] methods   base
>
>
> other attached packages:
>
> [1] bsseq_1.5.5                SummarizedExperiment_0.3.3
>
> [3] Biobase_2.29.1             GenomicRanges_1.21.18
>
> [5] GenomeInfoDb_1.5.10        IRanges_2.3.18
>
> [7] S4Vectors_0.7.12           matrixStats_0.14.2
>
> [9] BiocGenerics_0.15.6
>
>
> loaded via a namespace (and not attached):
>
>  [1] locfit_1.5-9.1   Rcpp_0.12.0      lattice_0.20-33  gtools_3.5.0
>
>  [5] chron_2.3-47     plyr_1.8.3       grid_3.2.1       magrittr_1.5
>
>  [9] scales_0.2.5     stringi_0.5-5    reshape2_1.4.1   XVector_0.9.1
>
> [13] data.table_1.9.4 tools_3.2.1      stringr_1.0.0    munsell_0.4.2
>
> [17] colorspace_1.2-6
>
>
> Once I made that proposed change to IRanges (locally) and re-install then
> it works as expected.
>
>
> Any ideas what I'm doing wrong?
>
>
> Thanks,
>
> Pete
>
>
>
> 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
>
>
> ______________________________________________________________________
>
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>
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>
> ______________________________________________________________________
>
>
>
> --
>
> Hervé Pagès
>
>
> Program in Computational Biology
>
> Division of Public Health Sciences
>
> Fred Hutchinson Cancer Research Center
>
> 1100 Fairview Ave. N, M1-B514
>
> P.O. Box 19024
>
> Seattle, WA 98109-1024
>
>
> E-mail: hpages at fredhutch.org
>
> Phone:  (206) 667-5791
>
> Fax:    (206) 667-1319
>

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