Hi Paul,

Thanks a lot for the feedback, looks like you are using the latest
bioc-devel branch, as you reported, I noticed ggbio has some issue with
latest GenomicRanges. Basically range,GenomicRanges works if you just load
'GenomicRanges' package, but after loading ggbio, range, GenomicRanges
doesn't work anymore. Even though it looks like they both calling the right
method at 'range' level, but could be some namespace issues, I am working
on this now, and will let you know when I figure it out what's going on and
submit a fix.

Thanks again.

Tengfei

On Thu, Nov 29, 2012 at 2:48 AM, Paul Theodor Pyl
<paul.theodor.pyl@embl.de>wrote:

> Hi all,
>
> I observe the following behaviour in my R-devel when I try to autoplot a
> GRanges with ggbio:
>
> > library(ggbio)
> > library(GenomicRanges)
> > autoplot( GRanges( Rle("10",1), ranges=IRanges( start = 1000, width=110
> ) ) )
> Error in start(range(object, ignore.strand = TRUE)) :
>   error in evaluating the argument 'x' in selecting a method for function
> 'start': Error in .local(o\
> bject, ...) :
>   could not find function "unsafe.update.GRanges"
> > sessionInfo()
> R Under development (unstable) (2012-11-28 r61176)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils datasets  methods
> [8] base
>
> other attached packages:
> [1] BiocInstaller_1.9.4   ggbio_1.7.6 ggplot2_0.9.2.1
> [4] GenomicRanges_1.11.15 IRanges_1.17.15 BiocGenerics_0.5.1
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.21.7     Biobase_2.19.1 biomaRt_2.15.0
>  [4] Biostrings_2.27.7        biovizBase_1.7.2 bitops_1.0-5
>  [7] BSgenome_1.27.1          cluster_1.14.3 colorspace_1.2-0
> [10] compiler_2.16.0          DBI_0.2-5 dichromat_1.2-4
> [13] digest_0.6.0             GenomicFeatures_1.11.5 grid_2.16.0
> [16] gridExtra_0.9.1          gtable_0.1.1 Hmisc_3.10-1
> [19] labeling_0.1             lattice_0.20-10 MASS_7.3-22
> [22] memoise_0.1              munsell_0.4 plyr_1.7.1
> [25] proto_0.3-9.2            RColorBrewer_1.0-5 RCurl_1.95-3
> [28] reshape2_1.2.1           Rsamtools_1.11.11 RSQLite_0.11.2
> [31] rtracklayer_1.19.6       scales_0.2.2 stats4_2.16.0
> [34] stringr_0.6.1            tools_2.16.0 VariantAnnotation_1.5.17
> [37] XML_3.95-0.1             zlibbioc_1.5.0
>
> Thanks,
> Paul
>
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>



-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274

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