[Bioc-devel] BUG: conversion of IRanges DataFrame to data.frame raises error IFF AnnotationDbi loaded

[Steve Lianoglou]

Hi Malcolm,,,,,

On Tue, Oct 2, 2012 at 1:21 PM, Cook, Malcolm <MEC at stowers.org> wrote:
> H'lo,
>
> I get this error:
>
> Error in as.data.frame(DataFrame(a = 1)) :
>   could not find function "injectIntoScope"
>
> when coercing a DataFrame to a data.frame, but only when preceeded by:
>
> library(AnnotationDbi)
>
> The following transcript demos in more detail.
>
> Is there a workaround for me pending a fix?

Strangely, it all actually works for me even after I load the
AnnotationDbi package.

I see that your mixing devel (AnnotationDbi) and release versions
(IRanges) of some packages, could this be the problem?

Perhaps you could try `IRanges::as.data.frame(DataFrame(a = 1))` might work?

-steve

>
> Thanks!
>
> Malcolm
>
>
>> library(IRanges)
> Loading required package: BiocGenerics
> Attaching package: 'BiocGenerics'
> ...
>> as.data.frame(DataFrame(a=1))
>   a
> 1 1
>> showMethods("as.data.frame")
> Function: as.data.frame (package base)
> x="ANY"
> x="AtomicList"
> x="DataFrame"
> x="DataFrameList"
> x="GappedRanges"
> x="GroupedIRanges"
> x="Hits"
> x="OverlapEncodings"
> x="RangedData"
> x="Ranges"
> x="RangesList"
> x="Rle"
> x="Vector"
> x="numeric"
>     (inherited from: x="ANY")
>
>> library(AnnotationDbi)
> ...
>> as.data.frame(DataFrame(a=1))
> Error in as.data.frame(DataFrame(a = 1)) :
>   could not find function "injectIntoScope"
>> showMethods("as.data.frame")
> Function: as.data.frame (package base)
> x="ANY"
> x="AtomicList"
> x="Bimap"
> x="DataFrame"
> x="DataFrameList"
> x="GappedRanges"
> x="GroupedIRanges"
> x="Hits"
> x="OverlapEncodings"
> x="RangedData"
> x="Ranges"
> x="RangesList"
> x="Rle"
> x="Vector"
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] AnnotationDbi_1.19.31 Biobase_2.17.7        IRanges_1.14.4        BiocGenerics_0.3.1
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5       RSQLite_0.11.2  compiler_2.15.0 stats4_2.15.0   tools_2.15.0
>>
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact