[Bioc-devel] isDisjoint Function Broken

[Pages, Herve]

Hi Dario,

Please try again with the latest GenomicRanges. Yours is lagging several versions behind.

Cheers,
H.

----- Original Message -----
From: "Dario Strbenac" <D.Strbenac at garvan.org.au>
To: bioc-devel at r-project.org
Sent: Sunday, August 21, 2011 6:00:31 PM
Subject: [Bioc-devel] isDisjoint Function Broken

Hello,

I'm testing out the development version of GenomicRanges and the function isDisjoint appears to depend on a no longer present function, orderTwoIntegers, in IRanges.

> summary(gene.exons)
     Length       Class        Mode 
      22482 GRangesList          S4 
> exons.disjoint <- isDisjoint(gene.exons)
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'orderTwoIntegers' not found
> sessionInfo()
R Under development (unstable) (2011-07-31 r56569)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252    

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

other attached packages:
[1] Rsamtools_1.5.51       GenomicFeatures_1.5.16 BSgenome_1.21.3        Biostrings_2.21.9     
[5] GenomicRanges_1.5.22   IRanges_1.11.24       

loaded via a namespace (and not attached):
[1] Biobase_2.13.7      biomaRt_2.6.0       DBI_0.2-5           RCurl_1.5-0.1       RSQLite_0.9-4      
[6] rtracklayer_1.13.11 tools_2.14.0        XML_3.2-0.2         zlibbioc_0.1.7     



--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia

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