[BioC] [ggbio+GenomicRanges] auto-plotting GRanges in R-devel fails

[Martin Morgan]

On 11/29/2012 10:17 AM, Tengfei Yin wrote:
> 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

I'm not exactly sure what's going on, but I notice that 'range' is actually a 
member of the group generic 'Summary', so I think that ggbio should 
importMethodsFrom(GenomicRanges, Summary) (and maybe similarly for IRanges, 
Summary?). I'd be interested in knowing how this gets fixed.

Martin

> 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 at 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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>
>
>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109