[Bioc-devel] Question about a package submission

[Kevin RUE]

(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
>>>>>
>>>>>
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>>>>
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>>>>
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