[Bioc-devel] Missed change in S4Vectors
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>
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
______________________________________________________________________
The information in this email is confidential and intended solely for the
addressee.
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______________________________________________________________________
Herv? Pag?s 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 [[alternative HTML version deleted]]