[Bioc-devel] Question about a package submission

[Ioannis Vardaxis]

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<mailto:kevinrue67 at gmail.com>>
Date: Friday 28 October 2016 at 12:38
To: Martin Morgan <martin.morgan at roswellpark.org<mailto:martin.morgan at roswellpark.org>>
Cc: Vincent Carey <stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>>, Ioannis Vardaxis <ioannis.vardaxis at math.ntnu.no<mailto:ioannis.vardaxis at math.ntnu.no>>, "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto: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<mailto: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<mailto: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<mailto: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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