[BioC] GenomicRanges functions unlist(GRangesList(x)) throw an error when used from an installed package

[Vincent Carey]

You are not getting the desired unlist() method.  You can put
importFrom(IRanges, unlist) in your NAMESPACE
if that's the unlist you intend to use throughout your package.  Or
you can disambiguate in line, with IRanges::unlist
in the function code.  (A hint is that the error message is precisely
the one issued by base::unlist, but this might not
be probative.)

On Mon, Jan 16, 2012 at 7:41 PM, Simon Coetzee <scoetzee at gmail.com> wrote:
> When I install a package of my own creation that uses the
> GenomicRanges package, I get an error:
>
> Error in unlist(x) : argument not a list
>
> the example function that throws this error is:
>
> TestFunction <- function (z)
> {
>     x <- GRangesList(z)
>     y <- unlist(x)
>     return(list(x, y))
> }
>
> I have created a package that contains this function, and an example
> dataset where this occurs.  It resides at
> http://dl.dropbox.com/u/1196228/TestingGRangesListUnlist_1.0.tar.gz
>
> There is no  problem when I enter the above commands, outside of the
> context of the function, or if I load the function into R through the
> source() command.  It only occurs if I install the package, and load
> it in via the library() command.
>
> example steps to recreate the issue:
> 1. Install package:
> R CMD INSTALL TestingGRangesListUnlist_1.0.tar.gz
> 2. Start R
> 3. library(TestingGRangesListUnlist)
> 4. data(test.data)
> 5. TestFunction(test.data)
> Error in unlist(x) : argument not a list
>
> output of traceback():
> 2: unlist(x)
> 1: TestFunction(test.data)
>
> output of sessionInfo():
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> LC_MONETARY=en_US.UTF-8
>  [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C
>               LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] TestingGRangesListUnlist_1.0 GenomicRanges_1.6.4
> IRanges_1.12.5               setwidth_0.9-4
> colorout_0.9-9
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.0
>
> Thanks for reading.
>
> Simon Coetzee
> --
>
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