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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