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

[Henrik Bengtsson]

Seems to be solved by updating Biostrings (and/or IRanges).
library("Biostrings") gave the same error before updating.  Now:

> 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)'.

Welcome to oligoClasses version 1.9.22
> 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] oligoClasses_1.9.22 Biobase_2.5.8

loaded via a namespace (and not attached):
[1] affyio_1.15.1      Biostrings_2.15.11 IRanges_1.5.22

/Henrik

On Sat, Jan 2, 2010 at 3:50 PM, Henrik Bengtsson <hb at stat.berkeley.edu> wrote:
> 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
>