Hi,

I'm a R and Bioconductor beginner currently trying to get myself familiar with the Gviz package,
thus "playing" around with the examples provided in the package manual. I'm using
Bioconductor version 2.12 and this is what is happening:

> library(GenomicRanges)
> library(Gviz)
> data(cpgIslands)
> chr <- as.character(unique(seqnames(cpgIslands)))
> gen <- genome(cpgIslands)
> AnnotationTrack(cpgIslands, name = "CpG") -> atrack
> GenomeAxisTrack() -> gtrack
> plotTracks(atrack, gtrack)

Fehler in rep(no, length.out = length(ans)) :
  attempt to replicate an object of type 'S4'

Further information:

--------------------------------------------
> traceback()
8: ifelse(is.null(from), -Inf, from)
7: ifelse(is.null(from), -Inf, from)
6: .local(x, ...)
5: FUN(X[[1L]], ...)
4: FUN(X[[1L]], ...)
3: lapply(trackList, subset, from = from, to = to, chromosome = chromosome,
       sort = FALSE, stacks = FALSE, use.defaults = FALSE)
2: lapply(trackList, subset, from = from, to = to, chromosome = chromosome,
       sort = FALSE, stacks = FALSE, use.defaults = FALSE)
1: plotTracks(atrack, gtrack)

-----------------------------------------------------

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GenomicRanges_1.12.5 IRanges_1.18.3       BiocGenerics_0.6.0   Gviz_1.4.5           BiocInstaller_1.10.3

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.22.6   Biobase_2.20.1         biomaRt_2.16.0         Biostrings_2.28.0      biovizBase_1.8.1
 [6] bitops_1.0-6           BSgenome_1.28.0        cluster_1.14.4         colorspace_1.2-2       DBI_0.2-7
[11] dichromat_2.0-0        GenomicFeatures_1.12.3 Hmisc_3.12-2           labeling_0.2           lattice_0.20-23
[16] munsell_0.4.2          plyr_1.8               RColorBrewer_1.0-5     RCurl_1.95-4.1         rpart_4.1-3
[21] Rsamtools_1.12.4       RSQLite_0.11.4         rtracklayer_1.20.4     scales_0.2.3           stats4_3.0.1
[26] stringr_0.6.2          tools_3.0.1            XML_3.98-1.1           zlibbioc_1.6.0
------------------------------------------------

Thanks for you help!

Dominik


[The Ohio State University]
Dr. Dominik Jäger
Biological Sciences Department of Microbiology
405 Biological Science Building | 484 West 12th Avenue Columbus, OH 43210
(614)-682-6890 Office
jager.9@osu.edu<mailto:jager.9@osu.edu> osu.edu<http://osu.edu>

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