[Bioc-devel] Question about a package submission

[Kevin RUE]

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
>>>>
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>>>>
>>>> _______________________________________________
>>>> 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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>>
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>>
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