[Bioc-devel] Question about a package submission

[Kevin RUE]

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
>>>>>
>>>>>
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>>>>
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>>>>
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