the newest "rtracklayer" and "IRanges" packages are not compatible, is it because class "ANYTHING" is not defined in package "IRanges" since version 1.3.73 anymore? library(rtracklayer) Loading required package: RCurl Loading required package: bitops browserSession("UCSC")->inter range(inter) ###error! #Error in validObject(.Object) : # invalid class "ucscCart" object: superclass "ANYTHING" not defined in the #environment of the object's class rtracklayer:::ucscCart(inter) ###error! #Error in validObject(.Object) : # invalid class "ucscCart" object: superclass "ANYTHING" not defined in the #environment of the object's class getClass("ANYTHING",where=getNamespace("IRanges")) ##error! "ANYTHING" is not defined in package "IRanges" since version 1.3.75 #anymore #Error in getClass("ANYTHING", where = getNamespace("IRanges")) : # "ANYTHING" is not a defined class sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-14 r49685) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.5.13 RCurl_1.2-0 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.5.6 Biostrings_2.13.39 BSgenome_1.13.11 IRanges_1.3.75 Rcompression_0.6-0 XML_2.6-0

Have you tried reinstalling rtracklayer? Michael On Wed, Sep 16, 2009 at 8:14 PM, LiGang <luzifer.li@gmail.com> wrote: > > the newest "rtracklayer" and "IRanges" packages are not compatible, is it > because class "ANYTHING" is not defined in package "IRanges" since version > 1.3.73 anymore? > > library(rtracklayer) > > Loading required package: RCurl > Loading required package: bitops > > browserSession("UCSC")->inter > range(inter) > > > ###error! > #Error in validObject(.Object) : > # invalid class "ucscCart" object: superclass "ANYTHING" not defined in > the > #environment of the object's class > > rtracklayer:::ucscCart(inter) > > ###error! > #Error in validObject(.Object) : > # invalid class "ucscCart" object: superclass "ANYTHING" not defined in > the > #environment of the object's class > > getClass("ANYTHING",where=getNamespace("IRanges")) > > ##error! "ANYTHING" is not defined in package "IRanges" since version > 1.3.75 > #anymore > > #Error in getClass("ANYTHING", where = getNamespace("IRanges")) : > # "ANYTHING" is not a defined class > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-14 r49685) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.5.13 RCurl_1.2-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.5.6 Biostrings_2.13.39 BSgenome_1.13.11 IRanges_1.3.75 > Rcompression_0.6-0 XML_2.6-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]