Dear Martin, Sorry for slightly diverting the thread solely based on the error message:
> Error in .Primitive("c")(<S4 object of class "Rle">, <S4 object of class > "Rle">) : > could not find symbol "recursive" in environment of the generic function > I can somewhat picture the issue from your explanation. > 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, ... > However, I cannot figure out how to avoid this issue on AppVeyor ( https://ci.appveyor.com/project/kevinrue/tvtb/build/job/srkobac85uksgcht). I have tried quite about 20 different combinations of settings in my YAML file (https://github.com/kevinrue/TVTB/commits/master) without success. I am not not sure how I may "manually reinstall" said packages, or somehow make sure the generic is define before all the relevant packages are installed. I'll admit that setting up a second Continuous Integration system is not the most pressing issue in my life, but I'm so close to succeeding that it is fairly frustrating to leave it at that :) Kind regards, Kevin On Thu, Oct 27, 2016 at 1:28 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > 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 generic >>>> >>> function >>> >>>> >>>> I 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 confidential > information. 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