[BioC] IRanges: as.matrix.RangesMatching not found with NAMESPACE
Michael Dondrup
Michael.Dondrup at uni.no
Thu Mar 25 15:03:26 CET 2010
Hi,
I made a package depending on IRanges. When I try to use as.matrix on a RangesMatching object,
there is an error message, if I don't have a NAMESPACE or I just source the file it works. Am I doing something wrong?
I made a reproducible example, used package skeleton to build the package for this.
The whole test -package is available at:
http://www.bccs.uni.no/~mdo041/anRpackage/
#require (IRanges)
doit <- function() {
query <- IRanges(c(1, 4, 9), c(5, 7, 10))
subject <- IRanges(c(2, 2, 10), c(2, 3, 12))
tree <- IntervalTree(subject)
## check if it works?
ol = findOverlaps(query, tree, multiple = TRUE) # c(2, NA, 3)
print (ol)
print (typeof(ol))
as.matrix(ol)
}
NAMESPACE:
exportPattern("^[[:alpha:]]+")
Here is the output:
> library(anRpackage)
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
Map,
cbind,
mapply,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
> doit()
An object of class "RangesMatching"
Slot "matchMatrix":
query subject
[1,] 1 2
[2,] 1 1
[3,] 3 3
Slot "DIM":
[1] 3 3
[1] "S4"
Error in as.vector(data) :
no method for coercing this S4 class to a vector
And that is the output when there is no NAMESPACE
> library(anRpackage)
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
Map,
cbind,
mapply,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
> doit()
An object of class "RangesMatching"
Slot "matchMatrix":
query subject
[1,] 1 2
[2,] 1 1
[3,] 3 3
Slot "DIM":
[1] 3 3
[1] "S4"
query subject
[1,] 1 2
[2,] 1 1
[3,] 3 3
>
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] anRpackage_1.0 IRanges_1.4.16
loaded via a namespace (and not attached):
[1] tools_2.10.1
>
Best
Michael Dondrup
Post-doctoral researcher
Uni BCCS
Thormøhlensgate 55, N-5008 Bergen, Norway
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