[Bioc-devel] oligoClasses v1.9.22 broken [using R v2.11.0 devel (2010-01-02 r50883)]

[Henrik Bengtsson]

FYI:

% R --vanilla

> library(oligoClasses)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Error in sub("([^-]+)_.*", "\\1", info$pkgname) :
  could not find symbol "extended" in environment of the generic function
Error : unable to load R code in package 'Biostrings'
Error: package/namespace load failed for 'oligoClasses'


This is probably related to:

DEPRECATED & DEFUNCT

    o	Basic regular expressions are defunct, and strsplit(), grep(),
	grepl(), sub(), gsub(), regexpr() and gregexpr() no longer
	have an 'extended' argument.

Source: http://cran.r-project.org/bin/windows/base/NEWS.R-2.11.0dev


> packageDescription("oligoClasses")
Package: oligoClasses
Version: 1.9.22
Title: Classes for high-throughput arrays supported by oligo
Author: Benilton Carvalho <bcarvalh at jhsph.edu> and Robert Scharpf
        <rscharpf at jhsph.edu>
Maintainer: Benilton Carvalho <bcarvalh at jhsph.edu>
Depends: Biobase, methods
Suggests: pd.genomewidesnp.6, pd.genomewidesnp.5,
        pd.mapping50k.hind240, pd.mapping50k.xba240,
        pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm,
        genomewidesnp5Crlmm
Imports: graphics, Biostrings (>= 2.13.9), Biobase (>= 2.7.0), affyio
Description: This package contains class definitions, validity checks,
        and initialization methods for classes used by the oligo
        package and friends.
License: GPL (>= 2)
LazyLoad: yes
Collate: AllClasses.R AllGenerics.R functions.R initialize-methods.R
        methods-AlleleSet.R methods-FeatureSet.R methods-oligoSnpSet.R
        methods-CNSet.R methods-PDInfo.R methods-SnpSet.R
        show-methods.R zzz.R
biocViews: Infrastructure
Packaged: 2009-12-30 22:29:47 UTC; biocbuild
Built: R 2.11.0; ; 2009-12-31 03:25:58 UTC; windows

-- File: C:\Users\hb/R/win-library/2.11/oligoClasses/Meta/package.rds



> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-01-02 r50883)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biobase_2.5.8

loaded via a namespace (and not attached):
[1] affyio_1.15.1  IRanges_1.3.93


/Henrik