On Tue, Jul 27, 2010 at 4:46 PM, mattia pelizzola <
mattia.pelizzola@gmail.com> wrote:

> Hi,
>
> I am building a package and I have a strange issue that is even
> difficult to provide an example for.
>
> I have a method 'Join' in this package that I am working on that uses
> the union function from the IRanges library.
> Now, on a clean R startup, if I load my library and I use this method
> Join I get an error. I think that the union function from the library
> graph is called in place of the one from IRanges ..
>



You can also work around this issue by specifying the exact method you want
to use in your Join method:
IRanges::union

rather than "union" by itself.  This will use the union method from IRanges.

In the long run, consider using Imports instead of depends for packages.
 Then, in your NAMESPACE file, use importFrom().  This way, you can import
methods specifically from packages.

In DESCRIPTION:
Imports: IRanges

in NAMESPACE:
importFrom(IRanges,union)

Sean

> Join(gel1, gel2, method='union')
> Error in as.vector(x) : no method for coercing this S4 class to a vector
> >
> > traceback()
> 5: as.vector(x)
> 4: unique(c(as.vector(x), as.vector(y)))
> 3: union(IR1, IR2)
> 2: Join(gel1, gel2, method = "union")
> 1: Join(gel1, gel2, method = "union")
>
> At the same time, if I execute on the console:
> > union(IRanges(), IRanges())
> IRanges of length 0
>
> it works perfectly.
>
> Finally, if I manually source the code containing my Join method, even
> the union function within this method now is working ..
> > source('./R/BSmetClasses_GElist.R')
> > a=Join(gel1, gel2, method='union')
>
> This is the same code of the library that is installed and running ..
> I know that now the method is on my GlobalEnv but I can't understand
> how this would change the result.
>
>
> > union
> standardGeneric for "union" defined from package "base"
>
> function (x, y)
> standardGeneric("union")
> <environment: 0x3a99228>
> Methods may be defined for arguments: x, y
> Use  showMethods("union")  for currently available ones.
>
> > showMethods('union')
> Function: union (package base)
> x="ANY", y="ANY"
> x="ANY", y="GeneSetCollection"
> x="CollectionIdType", y="CollectionIdType"
> x="CollectionType", y="CollectionType"
> x="GeneColorSet", y="GeneColorSet"
> x="GeneSetCollection", y="ANY"
> x="GeneSet", y="GeneSet"
> x="GRanges", y="GRanges"
> x="graphBAM", y="graphBAM"
> x="graph", y="graph"
> x="IRanges", y="IRanges"
> x="RangesList", y="RangesList"
> x="XStringSet", y="XStringSet"
>
>
>
> I am quite confused and sorry that I can't provide any more meaningful
> example,
>
> mattia
>
>
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> 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=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] methylPipe_1.0.0     RMySQL_0.7-4         BSgenome_1.16.1
>  [4] Biostrings_2.16.0    GenomicRanges_1.0.1  IRanges_1.6.1
>  [7] GOstats_2.14.0       RSQLite_0.9-0        DBI_0.2-5
> [10] graph_1.26.0         Category_2.14.0      AnnotationDbi_1.10.1
> [13] Biobase_2.8.0        rtracklayer_1.8.1    RCurl_1.4-2
> [16] nlme_3.1-96          snow_0.3-3           marray_1.26.0
> [19] limma_3.4.0          gplots_2.7.4         caTools_1.10
> [22] bitops_1.0-4.1       gdata_2.8.0          gtools_2.6.2
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.26.0   genefilter_1.30.0 GO.db_2.4.1       GSEABase_1.10.0
>  [5] lattice_0.18-5    RBGL_1.24.0       splines_2.11.0    survival_2.35-8
>  [9] tools_2.11.0      XML_3.1-0         xtable_1.5-6
> >
>
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>

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