(What puzzles me most is that it builds fine on Travis CI <https://travis-ci.org/kevinrue/TVTB>, just not on AppVeyor <https://ci.appveyor.com/project/kevinrue/tvtb>).
MS Windows issue? Best, Kevin On Fri, Oct 28, 2016 at 12:30 PM, Kevin RUE <kevinru...@gmail.com> wrote: > 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