[Bioc-devel] Missed change in S4Vectors

[Hervé Pagès]

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