Seems to be a MS Windows thing indeed. I have installed R-devel from scratch on a Window machine, then a fresh installation of BioC (biocLite()), then installed my package, and I get the error: > c(GRanges(), GRanges()) Error in c(GRanges(), GRanges()) : could not find symbol "recursive" in environment of the generic function
I have also run the following, but then I got the above error message again: biocLite(c("rtracklayer", "S4Vectors", "XVector", "IRanges", "Biostrings", "GenomicRanges", "GenomicAlignments")) I'll keep digging... :) Kevin On Fri, Oct 28, 2016 at 1:48 PM, Kevin RUE <kevinru...@gmail.com> wrote: > (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. 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