Hi Kevin,
The easiest way for me to reproduce the issue on Linux was to upload the zip
file containing the R package folder plus the .Rproj file onto my Rstudio
Server. This zip file can be found here:
http://singmann.org/download/teaching/r/mptmin.zip
There I opened a new R script, and entered the following lines to crash R:
require(devtools)
load_all(recompile = TRUE)
no_trigger()
trigger()
I just retried it and reliably crashed my RStudio Server.
Thanks a lot,
Henrik
Am 15.10.2014 um 23:53 schrieb Kevin Ushey:
Hi Henrik,
Thanks for putting this together. FWIW, I cannot reproduce this error
(either with `trigger()` or `no_trigger()`) on OS X, nor when building
from source on a Windows VM (while inside RStudio).
I also tried running the address and undefined behavior sanitizers
when executing the code and nothing was picked up.
Can you post the compiler output you get when using
`devtools::load_all()` vs. a regular `R CMD INSTALL` ? I wonder if the
compile flags are somehow different and if that could lead to a
problem.
Can you also elaborate on how you can reproduce this on Linux? This is
the environment we're most familiar with and so if we can reproduce
there then we can most easily discover a solution. I wonder if using
`gctorture(TRUE)` before running `trigger()` would make the assertion
failure more likely.
Thanks,
Kevin
On Wed, Oct 15, 2014 at 2:15 PM, Henrik Singmann
<henrik.singm...@psychologie.uni-freiburg.de> wrote:
Hi Dirk and list,
I have now managed to isolate the problem. The cpp file posted below can on
both Windows and Linux crash R if (a) compiled by winbuilder (windows only)
or if build via devtools::load_all() or from within Rstudio ("Build &
Reload") and (b) when using the appropriate input.
The following input crashes R:
S <- 3
Ineq <- structure(0, .Dim = c(1L, 1L))
But this input is okay:
S <- 3
Ineq <- structure(c(-1, 1, 0), .Dim = c(1L, 3L))
The c++ function producing the problem is (where SS = S and ineq = Ineq):
#### code follows ######
SEXP determinant2( SEXP SS, SEXP ineq){
BEGIN_RCPP
using namespace Rcpp;
using Eigen::Map;
using Eigen::VectorXd;
using Eigen::RowVectorXd;
using Eigen::MatrixXd;
const int S = Rcpp::as<int>(SS);
const Map<MatrixXd> Ineq(as<Map<MatrixXd> >(ineq));
RNGScope scope;
VectorXd thetaTMP;
RowVectorXd theta;
VectorXd IneqT;
thetaTMP = Rcpp::as<VectorXd>(rbeta(S, 0.5, 0.5));
theta = thetaTMP.transpose();
IneqT = (theta*Ineq.transpose());
return wrap(0);
END_RCPP
}
#### code ends ######
I have build a package which contains nothing but this code and two
functions trigger() and no_trigger() the former of which crashes R and the
latter does not crash R. The package can be found here:
http://singmann.org/download/teaching/r/MPTbug_1.0.0.tar.gz
But as I said, when installing from source, the two functions work. Only
when using the binary from winbuilder or building via devtools or RStudio
does trigger() crash R. The winbuilder version can be found here
(temporarily): http://win-builder.r-project.org/M4yLs8R7tFR1/
The problem obviously seems to be (theta*Ineq.transpose()) if Ineq is a
scalar 0. But why it works given one compilation and not the other is
outside of my knowledge space. Any help would obviously be really
appreciated.
Cheers,
Henrik
Am 15.10.2014 um 21:13 schrieb Dirk Eddelbuettel:
Hi Henrik,
On 15 October 2014 at 20:59, Henrik Singmann wrote:
| Dear list,
|
| I have the following weird problem and would be really glad for any
input:
|
| The windows binary from CRAN for my package MPTinR, which uses
RcppEigen, leads to an "Assertion failed" error which crashes R with a
simple example given below (which unfortunately is not part of the examples
and henceforth not tested by CRAN).
|
| Interestingly enough, the problem disappears when installing the package
on Windows from source or when using Linux (Ubuntu). But it also appears
when using a binary version of MPTinR from winbuilder (temporarily available
here: http://win-builder.r-project.org/h18PJ7B55VAq), R-devel and
corresponding binary from CRAN, and I could replicate the error on a range
of different Windows machines. The error also always disappears when
installing from source. I am also extremely confident that this problem
didn't exist in the past, I and others have used this functionality
regularly with the CRAN windows binary.
|
| ###### code starts #######
| require(MPTinR)
| data(d.broeder)
| m.2htm <- system.file("extdata", "5points.2htm.model", package =
"MPTinR")
| get.mpt.fia(d.broeder, m.2htm)
| ###### code ends #######
|
| The complete error message is:
|
| ###### error message starts #######
| Assertion failed!
|
| Program: C:\Program Files\RStudio\bin\x64\rsession.exe
| File:
d:/RCompile/CRANpkg/lib/3.1/RcppEigen/include/Eigen/src/Core/ProductBase.h,
Line 95
|
| Expression: a_lhs.cols() == a_rhs.rows() && "invalid matrix product" &&
"if you wanted a coeff-wise or a dot product use the respective explicit
functions"
|
| This application has requested the Runtime to terminate it in an unusual
way.
| Please contact the application's support team for more information.
| ###### error message ends #######
|
| When adding such an example to the code and resubmitting it to
winbuilder it now also crashes, see
http://win-builder.r-project.org/0ei38q0t48h2/00check.log
| But again, when installing the same package on my machine from source it
works.
It would help us if you could create a minimally reproducible example
exhibit
this behaviour.
About 24 CRAN packages use RcppEigen. The error could be yours, or ours.
But
given the information provided so far it is hard to say more.
You could also try R along with valgrind on Linux to see if that tickles
it.
Dirk
| Best,
| Henrik
|
| PS: A session info (without attaching MPTinR) is given below:
|
| R version 3.1.1 (2014-07-10)
| Platform: x86_64-w64-mingw32/x64 (64-bit)
|
| locale:
| [1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252
LC_MONETARY=German_Switzerland.1252
| [4] LC_NUMERIC=C LC_TIME=German_Switzerland.1252
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| other attached packages:
| [1] devtools_1.6
|
| loaded via a namespace (and not attached):
| [1] fortunes_1.5-2 tools_3.1.1
|
|
|
| --
| Dr. Henrik Singmann
| Universität Zürich, Schweiz
| http://singmann.org
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel-Z+qqJ2/841ddxcdgmxqagq2ug9vpuwmkqh7oeaqu...@public.gmane.org
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
--
Dr. Henrik Singmann
Universität Zürich, Schweiz
http://singmann.org
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--
Dr. Henrik Singmann
PostDoc
Universität Zürich, Schweiz
http://singmann.org
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