Not really sure how this package got into Bioconductor without properly
importing symbols into its namespace. NAMESPACE should have
import(BiocGenerics). Otherwise, you're seeing base::as.vector before the
search path. Think hard about whether you really need all those packages in
Depends, which end up on the search path. Like RColorBrewer, VennDiagram
and plyr. They can go into Imports. But make sure to import() them in your
NAMESPACE.
On Tue, Oct 29, 2013 at 2:10 AM, Johannes Waage <johannes.wa...@gmail.com>wrote:
> Dear devel-list,
>
> A package of mine was recently inducted into BioC, spliceR. A few users
> have written me, reporting that the annotatePTC function fails with:
>
> *Error in
>
> transcriptData[["exon_features"]][match(as.vector(GenomicRanges::strand(transcriptData[["exon_features"]])),
> : *
> * error in evaluating the argument 'i' in selecting a method for function
> '[': Error in
> as.vector(GenomicRanges::strand(transcriptData[["exon_features"]])) : *
> * no method for coercing this S4 class to a vector*
> *
> *
> at the line
>
> transcriptData[["exon_features"]] <-
>
> transcriptData[["exon_features"]][match(as.vector(GenomicRanges::strand(transcriptData[["exon_features"]])),c("+",
> "-"), nomatch = 0)
>
> Somehow, the casting of the output of strand() to a vector fails.
>
> This only happens for some users; repasting the function code into the R
> solves the problem, so I suspect the problem is in function masking, or
> perhaps the order of package dependencies.
>
> The relevant part of the DESCRIPTION file is as follows:
>
> Depends: R (>= 2.15.0), methods, cummeRbund, rtracklayer, GenomicRanges,
> VennDiagram, RColorBrewer, plyr
> Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome
> biocViews: Bioinformatics, DifferentialExpression,
> HighThroughputSequencing, HighThroughputSequencingData, RNAseq, RNAseqData,
> software, visualization
>
> Any help is much appreciated,
>
> All the best,
> Johannes W
>
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>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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