[BioC] IRanges::rbind with names stopped working

[Robert Castelo]

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.