[Bioc-devel] Missed change in S4Vectors

Hi Peter,

Yesterday I realized that I didn't bump S4Vectors version properly
after I moved selectSome() from BiocGenerics to S4Vectors so this
could explain the problem you're seeing. I think that if you just
re-install S4Vectors locally (without making the change you proposed)
the issue will go away. Hopefully...

H.

On 08/10/2015 06:46 PM, Peter Hickey wrote:

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
<mailto:peter.hickey at gmail.com>> wrote:

    Hi Herv?,


    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 Herv?,


    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 <mailto: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 <mailto:hickey at wehi.edu.au>

    http://www.wehi.edu.au