[Bioc-devel] Missed change in S4Vectors

Peter Hickey peter.hickey at gmail.com
Tue Aug 11 00:51:46 CEST 2015

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)


[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?



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?



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.





--- 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



The information in this email is confidential and intended solely for the

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

Phone:  (206) 667-5791

Fax:    (206) 667-1319

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