Thanks for the quick check, Hervé.
R-3.0 is shaping up to be a good one ... I mean, I was excited for the
64-bit integer support, but now ... this is already fixed? yes!
:-)
Cheers,
-steve
On Wed, Mar 6, 2013 at 12:42 PM, Hervé Pagès <hpa...@fhcrc.org> wrote:
> Hi Steve,
>
>
> On 03/06/2013 09:10 AM, Steve Lianoglou wrote:
>>
>> I don't think I've seen this one discussed before .. consider:
>>
>> ========= Reproduce me ===========
>> library(IRanges)
>> df1 <- data.frame(a=rnorm(10), b=head(letters, 10))
>> df2 <- transform(df1, b=factor(b))
>> df3 <- transform(df1, b=factor(b, sample(b), ordered=TRUE))
>>
>> DF1 <- DataFrame(df1)
>> DF2 <- DataFrame(df2)
>> DF3 <- DataFrame(df3)
>>
>> ## Now let's take a look at them
>> DF1 ## looks purty
>>
>> DF2 ## looks nice
>>
>> DF3 ## woops!
>>
>> DataFrame with 10 rows and 2 columns
>> Error in matrix(unlist(lapply(object, function(x) paste("<", class(x), :
>> length of 'dimnames' [2] not equal to array extent
>> ===================================
>
>
> This problem seems to be gone in BioC devel:
>
> > DF3
>
> DataFrame with 10 rows and 2 columns
> a b
> <numeric> <ordered>
> 1 -0.98455768 a
> 2 0.35134835 b
> 3 0.04657733 c
> 4 1.86833121 d
> 5 0.54396927 e
> 6 -0.64201201 f
> 7 0.45709514 g
> 8 0.47964197 h
> 9 -1.37778026 i
> 10 0.07408252 j
>
> > sessionInfo()
> R Under development (unstable) (2013-02-19 r62008)
> 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] IRanges_1.17.35 BiocGenerics_0.5.6
>
> loaded via a namespace (and not attached):
> [1] stats4_3.0.0 tools_3.0.0
>
> H.
>
>
>>
>> Here it only looks like it's messing w/ the `show` method, but it will
>> bite you in other places where you expect DataFrame's to function "as
>> normal."
>>
>> I'll take a deeper look at this after I get through a deadline for
>> next week, but if someone has some time between now and then ...
>>
>> Relevant info:
>>
>> R version 2.15.2 Patched (2012-11-12 r61105)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> ....
>> other attached packages:
>> [1] IRanges_1.16.6 BiocGenerics_0.4.0 devtools_1.1
>>
>>
>> -steve
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
--
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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
