[BioC] IRanges glitch: error restoring saved RangedData object
Michael Dondrup
Michael.Dondrup at uni.no
Fri Aug 13 11:44:46 CEST 2010
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
>
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