"makeTxDbFromGFF" error ?!

Question

[dina.hesham139]

Hey, I'm using deseq2 after kallisto to analyze rice data. I'm using an ensembl gtf and I want to create a txdb. I used this one:

txdb2 <- makeTxDbFromGFF(file="C:/Users/Dee/Desktop/Thesis_rice/Oryza_sativa.IRGSP-1.0.37.gtf", format=("gtf"), dataSource=paste("ftp://ftp.ensemblgenomes.org/pub/plants/release-37/gtf/oryza_sativa/",sep=""), organism="Oryza sativa")

and I got that error:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in c(x, value) : 
  could not find symbol "recursive" in environment of the generic function

I can't figure out what's wrong, any help?

[GenoMax]

See this thread for a solution.

[dina.hesham139]

I re-installed all the packages and the error is not yet resolved!

Answer 1

[Bastien Hervé]

What is the result of sessionInfo() to get informations about your running session ?

I presume you got R version 3.3.3 which has some trouble with some packages as mentionned in @genomax answer.

Try to update to R version 3.4.0 and reinstall Deseq2 :

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")