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@loci) / x@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@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@.Data
function (x, ...)
nrow(x@loci)/x@ploidy
problem.method@.Data
function (x, ...)
nrow(x@loci)/x@ploidy
<environment: 0x101f85040>
# Swap the problem function for the one I created:
problem.method@.Data <- test.method@.Data
save(problem.method, file = "fixed.method.rdata")
# Here's the error (both with my method and the original):
as.vector(test.method@defined, "character")
Error: C stack usage 7970892 is too close to the limit
as.vector(problem.method@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@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
"
*The universe doesn't care what you believe. The wonderful thing about
science is that it doesn't ask for your faith, it just asks for your
eyes.*" - Randall Munroe
"*Lighthouses are more helpful than churches.*"
- Benjamin Franklin
"*...but I'll take a GPS over either one.*"
- John C. "Craig" George
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