browserView does not work in 'rtracklayer' [failure to coerce "CompressedIntegerList"] library(rtracklayer) browserSession("UCSC")->session browserView(session, GenomicRanges(start=10000,end=100000, chrom="1",genome="hg18")) ### Error in as.character.default(<s4 object="" of="" class="" "compressedintegerlist"="">) : ### no method for coercing this S4 class to a vector #================================== 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_1.5.14 RCurl_1.2-0 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.5.6 Biostrings_2.13.40 BSgenome_1.13.12 IRanges_1.3.77 Rcompression_0.6-0 XML_2.6-0

Thanks for bringing this IRanges change to my attention. Fixed in 1.5.15. On Tue, Sep 22, 2009 at 12:11 AM, LiGang <luzifer.li@gmail.com> wrote: > > browserView does not work in 'rtracklayer' [failure to > coerce "CompressedIntegerList"] > > > library(rtracklayer) > browserSession("UCSC")->session > browserView(session, GenomicRanges(start=10000,end=100000, > chrom="1",genome="hg18")) > > ### Error in as.character.default(<s4 object="" of=""> class "CompressedIntegerList">) : > ### no method for coercing this S4 class to a vector > > #================================== > 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_1.5.14 RCurl_1.2-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.5.6 Biostrings_2.13.40 BSgenome_1.13.12 > IRanges_1.3.77 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]]