[BioC] IRanges glitch: error restoring saved RangedData object

[Martin Morgan]

Hi Michael --

I think this is a problem in the methods package; the 'show' method
found is for DataTable, instead of RangedData. I'll pursue this
elsewhere and let you know what comes of it.

Martin

On 08/13/2010 02:44 AM, Michael Dondrup wrote:
> Hi,
> I guess I found a little bug in IRanges. When loading a saved RangedData object before loading library(IRanges)
> before, then IRanges is loaded automatically but the RangeData object is rendered unusable. Only restarting R lets me access
> the object.
>  The following code reproduces this:
> $ R --vanilla
> version 2.11.1 (2010-05-31)...
>> library(IRanges)
>> rd = RangedData(IRanges(start=c(1:10), width=2, names=letters[1:10]), space="chr1", score=rnorm(10))
>> rd
> RangedData with 10 rows and 1 value column across 1 space
>         space    ranges |       score
>   <character> <IRanges> |   <numeric>
> a        chr1  [ 1,  2] | -0.79949926
> b        chr1  [ 2,  3] |  1.09152227
> c        chr1  [ 3,  4] |  0.19032854
> d        chr1  [ 4,  5] |  0.37248408
> e        chr1  [ 5,  6] |  0.68396618
> f        chr1  [ 6,  7] | -1.19804918
> g        chr1  [ 7,  8] |  0.01221636
> h        chr1  [ 8,  9] |  0.66203090
> i        chr1  [ 9, 10] |  0.39848133
> j        chr1  [10, 11] |  0.15233945
>> save(rd, file="rd.r")
>> q()
> # restart R
> $ R --vanilla
>> load("rd.r")
>> rd
> Loading required package: IRanges
> 
> Attaching package: 'IRanges'
> 
> The following object(s) are masked from 'package:base':
> 
>     cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
>     rbind, rep.int, table
> 
> RangedData with 10 rows and 1 column
> Error in dimnames(x) <- dn : 
>   length of 'dimnames' [1] not equal to array extent
>>
> 
> Note that this depends on presence of rownames. If you make an object
> rd = RangedData(IRanges(start=c(1:10), width=2), space="chr1", score=rnorm(10))
> without named IRanges, the result after loading is
>> rd
> Loading required package: IRanges
> 
> Attaching package: 'IRanges'
> 
> The following object(s) are masked from 'package:base':
> 
>     cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
>     rbind, rep.int, table
> 
> RangedData with 10 rows and 1 column
>           chr1
>   <RangedData>
> 1     ########
> 
>> sessionInfo()
> R version 2.11.1 (2010-05-31) 
> x86_64-unknown-linux-gnu 
> 
> 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=C              LC_MESSAGES=en_US.UTF-8   
>  [7] LC_PAPER=no_NO.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=no_NO.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] IRanges_1.6.11
>>
> 
>  
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


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

Location: Arnold Building M1 B861
Phone: (206) 667-2793