[Bioc-devel] Question about a package submission

[Martin Morgan]

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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>>>
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>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
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