[Bioc-devel] Question about a package submission

Kevin RUE kevinrue67 at gmail.com
Fri Oct 28 16:08:44 CEST 2016 

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 <kevinrue67 at 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 <kevinrue67 at 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.vardaxis at 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 <kevinrue67 at gmail.com>
>>> Date: Friday 28 October 2016 at 12:38
>>> To: Martin Morgan <martin.morgan at roswellpark.org>
>>> Cc: Vincent Carey <stvjc at channing.harvard.edu>, Ioannis Vardaxis <
>>> ioannis.vardaxis at math.ntnu.no>, "bioc-devel at r-project.org" <
>>> bioc-devel at 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.morgan at 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 <
>>>>> stvjc at 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.vardaxis at 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 at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>>
>>>>>>         [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
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>>>>>
>>>>>
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