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I'm using setdiff() with two GR objects and before updating R on my computer my code worked fine: 

library(GenomicFeatures)
library(data.table)
library("TxDb.Celegans.UCSC.ce6.ensGene")
txdb<-TxDb.Celegans.UCSC.ce6.ensGene
introns<-intronsByTranscript(txdb)
exons<-exons(txdb)
minimal_introns<-setdiff(unlist(introns),exons,ignore.strand=F)

but now I have this error:

Error in setdiff(unlist(introns), unlist(exons), ignore.strand = F) : unused argument (ignore.strand = F)

if I run setdiff() without ignore.strand= F I have this:

Error in as.vector(x) : no method for coercing this S4 class to a vector

I found a post that suggest some problem with the NAMESPACE file https://stat.ethz.ch/pipermail/bioconductor/2014-September/061440.html

But I don't know where to find that NAMESPACE file and how to fix it.

Mariela Cortés López
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  • Hi Mariela, what version of R/Bioconductor are you using? Can you post the output of `sessionInfo()`? I just tried this with R 3.3.2 and Bioconductor 3.4 and it worked fine for me. – Keith Hughitt Dec 06 '16 at 03:19
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    Is the version 3.3.2 and Bioconductor 3.4 I think that I just solved the problem starting a new session. – Mariela Cortés López Dec 06 '16 at 18:30

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