Thanks for sharing your solution Ioannis. Unfortunately, it did not solve my situation on AppVeyor: https://ci.appveyor.com/project/kevinrue/tvtb/build/1.0.29
I'll keep trying a few more things. Best Kevin On Fri, Oct 28, 2016 at 12:13 PM, Ioannis Vardaxis < ioannis.varda...@math.ntnu.no> wrote: > For me, running biocLite(c("rtracklayer", "S4Vectors", "XVector", > "IRanges", > "Biostrings", "GenomicRanges", "GenomicAlignments")) > Worked and solved the error. > > Ioannis > -- > Ioannis Vardaxis > Stipendiat IMF > NTNU > > From: Kevin RUE <kevinru...@gmail.com> > Date: Friday 28 October 2016 at 12:38 > To: Martin Morgan <martin.mor...@roswellpark.org> > Cc: Vincent Carey <st...@channing.harvard.edu>, Ioannis Vardaxis < > ioannis.varda...@math.ntnu.no>, "bioc-devel@r-project.org" < > bioc-devel@r-project.org> > Subject: Re: [Bioc-devel] Question about a package submission > > 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. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel