[Bioc-devel] Missed change in S4Vectors

Peter Hickey peter.hickey at gmail.com
Thu Aug 13 01:07:43 CEST 2015


Thanks, Hervé, that has indeed fixed my problem.
Pete

On Wed, 12 Aug 2015 at 02:12 Hervé Pagès <hpages at fredhutch.org> wrote:

> 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 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 <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
> >
> >
> >
>  ______________________________________________________________________
> >
> >     The information in this email is confidential and intended solely
> >     for the addressee.
> >
> >     You must not disclose, forward, print or use it without the
> >     permission of the sender.
> >
> >
>  ______________________________________________________________________
> >
> >
> >
> >     --
> >
> >     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 <mailto:hpages at fredhutch.org>
> >
> >     Phone:  (206) 667-5791
> >
> >     Fax:    (206) 667-1319
> >
>
> --
> 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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