Sorry, this is fixed now in 2.6.

Michael

On Tue, Feb 2, 2010 at 3:04 AM, Robert Castelo <robert.castelo@upf.edu>wrote:

> dear list, and particularly the IRanges developers,
>
> i'm porting from BioC 2.4 to BioC 2.6 a script which is doing rbind on
> two RangedData objects and have noticed that this operation (rbind) now
> doesn't work when the ranges have names.
>
> i'm reproducing below the situation with BioC 2.4, 2.5 and 2.6 where for
> the latter two versions of BioC this functionality fails.
>
> *** BioC 2.4
>
> library(IRanges, warn.conflicts=FALSE)
>
> rd1 <- RangedData(IRanges(start=1:3,
>                          end=4:6))
> rd2 <- RangedData(IRanges(start=1:3,
>                          end=4:6))
> rbind(rd1, rd2)
> RangedData: 6 ranges by 0 columns
> columns(0):
> sequences(0):
> rd1 <- RangedData(IRanges(start=1:3,
>                          end=4:6,
>                          name=letters[1:3]))
> rd2 <- RangedData(IRanges(start=1:3,
>                          end=4:6,
>                          name=letters[4:6]))
> rbind(rd1, rd2)
> RangedData: 6 ranges by 0 columns
> columns(0):
> sequences(0):
> sessionInfo()
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] IRanges_1.2.3
>
>
> ** BioC 2.5
>
> library(IRanges, warn.conflicts=FALSE)
>
> rd1 <- RangedData(IRanges(start=1:3,
>                          end=4:6))
> rd2 <- RangedData(IRanges(start=1:3,
>                          end=4:6))
> rbind(rd1, rd2)
> RangedData with 6 rows and 0 value columns across 1 space
>        space    ranges |
>  <character> <IRanges> |
> 1           1    [1, 4] |
> 2           1    [2, 5] |
> 3           1    [3, 6] |
> 4           1    [1, 4] |
> 5           1    [2, 5] |
> 6           1    [3, 6] |
> rd1 <- RangedData(IRanges(start=1:3,
>                          end=4:6,
>                          name=letters[1:3]))
> rd2 <- RangedData(IRanges(start=1:3,
>                          end=4:6,
>                          name=letters[4:6]))
> rbind(rd1, rd2)
> Error in validObject(.Object) :
>  invalid class "RangedData" object: the names of the ranges must equal
> the rownames
> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] IRanges_1.4.10
>
> ** BioC 2.6
>
> library(IRanges, warn.conflicts=FALSE)
>
> rd1 <- RangedData(IRanges(start=1:3,
>                          end=4:6))
> rd2 <- RangedData(IRanges(start=1:3,
>                          end=4:6))
> rbind(rd1, rd2)
> RangedData with 6 rows and 0 value columns across 1 space
>        space    ranges |
>  <character> <IRanges> |
> 1           1    [1, 4] |
> 2           1    [2, 5] |
> 3           1    [3, 6] |
> 4           1    [1, 4] |
> 5           1    [2, 5] |
> 6           1    [3, 6] |
> rd1 <- RangedData(IRanges(start=1:3,
>                          end=4:6,
>                          name=letters[1:3]))
> rd2 <- RangedData(IRanges(start=1:3,
>                          end=4:6,
>                          name=letters[4:6]))
> rbind(rd1, rd2)
> Error in validObject(.Object) :
>  invalid class "RangedData" object: the names of the ranges must equal
> the rownames
> sessionInfo()
> R version 2.11.0 Under development (unstable) (2009-10-06 r49948)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] IRanges_1.5.37
>
>
> thanks!
> robert.
>
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