[R] C stack error in as.vector() starting in R 3.3.0

[Eric Archer - NOAA Federal]

Apologies for the long post. This is an issue I have been struggling with
and I have tried to be as complete, to the point, and reproducible as
possible.

In documenting a package with roxygen2, I have come across an error that
does not occur in R 3.2.4 revised, but does occur in R 3.3.0 and 3.3.1.
Using traceback() and debug(), I've traced the error to a call made to
as.vector(x, "character") that seems to get stuck in a loop which
culminates in this error:

Error: C stack usage  7970892 is too close to the limit

The object that causes this error is of a signature type for a method. With
some playing around, I've been able to work out that the error is actually
associated with the method that roxygen2 creates when doing its magic.
Something happens when this method definition with its associated
environment is in the workspace that causes the error.

At this point, I should stress again that the error does NOT occur in R
3.2.4 revised or earlier, but does occur in R 3.3.0 and 3.3.1. I have also
tested this with several versions of roxygen2 and that does not make a
difference. Thus, my ultimate question is what has changed in R 3.3.0 that
would lead to this so that the roxygen2 maintainers can correct it?

As a test, I created a signature identical to the one that causes the error
and tried the as.vector() command that would generate the loop. I don't get
the error in my command line generated object, nor with the object that is
extracted from the method definition. However, when I load the method
definition into the workspace, the error will happen on either my command
line generated object, or the one extracted from the method definition and
will not stop happening until I restart R.

I have reported this error as an issue on the roxygen2 GitHub repository
and it has been crossposted by another user who had a similar experience
with a different package on the devtools repository. Those posts, which
contain more information are here:

https://github.com/klutometis/roxygen/issues/475
https://github.com/hadley/devtools/issues/1234

Below is the result of sessionInfo() and the output of a session
demonstrating the effect. The files used are in a zip file here:
https://github.com/klutometis/roxygen/files/335417/error.test.rdata.files.zip

 > sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_3.3.0

> rm(list = ls())
>
> # Create test class and method
> setClass(Class = "gtypes", slots = c(loci = "data.frame", ploidy =
"numeric"), package = "roxygen_devtest")
> setGeneric("nInd", function(x, ...) standardGeneric("nInd"), package =
"adegenet")
[1] "nInd"
> setMethod("nInd", "gtypes", function(x, ...) nrow(x at loci) / x at ploidy)
[1] "nInd"
>
> test.method <- getMethod("nInd", "gtypes")
> str(test.method)
Formal class 'MethodDefinition' [package "methods"] with 4 slots
  ..@ .Data  :function (x, ...)
  ..@ target :Formal class 'signature' [package "methods"] with 3 slots
  .. .. ..@ .Data  : chr "gtypes"
  .. .. ..@ names  : chr "x"
  .. .. ..@ package: chr "roxygen_devtest"
  ..@ defined:Formal class 'signature' [package "methods"] with 3 slots
  .. .. ..@ .Data  : chr "gtypes"
  .. .. ..@ names  : chr "x"
  .. .. ..@ package: chr "roxygen_devtest"
  ..@ generic: atomic [1:1] nInd
  .. ..- attr(*, "package")= chr "adegenet"
>
> # No error:
> as.vector(test.method at defined, "character")
[1] "gtypes"
>
> # This is the method that generates the error
> load("problem.method.rdata")
>
> # Notice the difference in the environments of the two functions:
> test.method at .Data
function (x, ...)
nrow(x at loci)/x at ploidy
> problem.method at .Data
function (x, ...)
nrow(x at loci)/x at ploidy
<environment: 0x101f85040>
>
> # Swap the problem function for the one I created:
> problem.method at .Data <- test.method at .Data
> save(problem.method, file = "fixed.method.rdata")
>
> # Here's the error (both with my method and the original):
> as.vector(test.method at defined, "character")
Error: C stack usage  7970892 is too close to the limit
> as.vector(problem.method at defined, "character")
Error: C stack usage  7970892 is too close to the limit

Restarting R session...

> # *** Restart R for this to work ***
> rm(list = ls())
>
> load("fixed.method.rdata")
> as.vector(problem.method at defined, "character")
[1] "gtypes"

----

*Eric Archer, Ph.D.*
Southwest Fisheries Science Center
NMFS, NOAA
8901 La Jolla Shores Drive
La Jolla, CA 92037 USA
858-546-7121 (work)
858-546-7003 (FAX)

Marine Mammal Genetics Group: swfsc.noaa.gov/mmtd-mmgenetics
ETP Cetacean Assessment Program: swfsc.noaa.gov/mmtd-etp
https://github/ericarcher

"


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