On 10/27/2016 08:22 AM, Kevin RUE wrote:
Hi Ioannis, Vincent,I'm in the middle of debugging a similar situation myself, which may provide a reproducible example at a package level. I am in the process of setting up AppVeyor CI for my package, and my R CMD check fails because of the same error. https://ci.appveyor.com/project/kevinrue/tvtb/build/1.0.11 To debug the issue, I am also currently updating my local installation to the latest devel packages (until biocValid() returns TRUE). Once that is done, I may be able to provide a more practical minimal working example for the issue (i.e. the code in one of my man pages).
I think that the generic was redefined in base R, but you have packages that were installed before the generic was redefined. The methods in the installed packages think that they are associated with the generic at the time of installation, rather than at runtime.
Unfortunately I think this means manually re-installing even up-to-date packages that define S4 "c" methods; likely this is a complicated stack of dependencies including rtracklayer, S4Vectors, XVector, IRanges, Biostrings, GenomicRanges, GenomicAlignments, ...
Marin
Best, Kevin On Thu, Oct 27, 2016 at 12:23 PM, Vincent Carey <st...@channing.harvard.edu> wrote:Please send a reproducible example with value of sessionInfo() at time of error. On Thu, Oct 27, 2016 at 7:06 AM, Ioannis Vardaxis < ioannis.varda...@math.ntnu.no> wrote:Hi, I am using the R-devel version for writing an R package. I tried to use the c(Granges,Granges) command to merge two Granges objects and I get the following error: Error in .Primitive("c")(<S4 object of class "Rle">, <S4 object of class "Rle">) : could not find symbol "recursive" in environment of the genericfunctionI also get the same error when I use InteractionSet::GInteractions(Granges,Granges). I downloaded IRanges, GenomicRanges and InteractionSet packages from the source. How can I solve this error? Best, Ioannis -- Ioannis Vardaxis Stipendiat IMF NTNU [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
