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.hic...@gmail.com <mailto:peter.hic...@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@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 <maintai...@bioconductor.org <mailto:maintai...@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 hic...@wehi.edu.au <mailto:hic...@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: hpa...@fredhutch.org <mailto:hpa...@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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
