On 5 Dec 2022, at 17:34, Martyn Plummer <martyn.plummer at gmail.com> wrote:
I have good news and bad news.
I found the source of the error. In your wrapper function
logsumexp <- function(x, a = NULL)
{
x <- as.matrix(x)
a <- if(is.null(a)) rep(double(0), ncol(x)) else as.vector(a)
logsumexp_Rcpp(x,a)
}
the expression rep(double(0), ncol(x)) is not doing what you think it is doing. It returns a numeric vector of length 0, whereas you actually want a vector of zeros of length ncol(x). Note that the same issue affects your softmax function.
I don't know what Rcpp does when you try add a numeric vector of length 0, but at R level it is quite a destructive operation
numeric(0)
This is not the behaviour you want. Here is a modified wrapper that makes the ASAN error message go away and adds some checks that the arguments are conforming.
logsumexp <- function(x, a = NULL)
{
x <- as.matrix(x)
a <- if(is.null(a)) rep(0.0, ncol(x)) else as.vector(a)
if (length(a) != ncol(x)) {
stop("Non-conforming arguments in logsumexp")
}
logsumexp_Rcpp(x,a)
}
That's the good news. The bad news is that you have a lot of memory leaks, so this is still not going to pass R CMD check with ASAN. You're going to need Dirk's container.
Martyn
On Mon, 5 Dec 2022 at 09:07, Luca Scrucca <luca.scrucca at unipg.it> wrote:
Dear all,
the "mclustAddons" R package contains some C++ functions included via Rcpp.
It's not the first time I've done this and, although I'm not a C++ expert, I've been able to get it right thanks to the wonderful Rcpp facilities.
Before submitting to CRAN the new version, I tested the package both locally (on MacOS - Intel machine) and via rhub on many platforms (debian, fedora, ubuntu, windows) with different versions of R (release, develop), including memory sanitizers/valgrind.
The "mclustAddons" package gives me no problems on any tested platform/version.
Unfortunately when I submit it to CRAN the problems start to arise. Below are the links to the log files:
- clang-ASAN <https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-ASAN/mclustAddons>
- gcc-ASAN <https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-ASAN/mclustAddons>
After several e-mails with CRAN maintainers they suggest me to set up an environment to safely reproduce the ASAN reports:
See https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt
This of course would be the next thing to do, and I have already asked for help to colleagues at the Physics Dept.
The code causing the problem is reported below and the offending line is the one with "xa = x.row(i) + a;".
Since I can't replicate the issue and test it, I can't resubmit the package to CRAN.
Perhaps a C++ expert will spot the problem at first sight...
However, the main problem I have (with CRAN) is that, despite all the efforts that one can reasonably made, it is impossible for a maintainer of a package to be sure that the package will be tested correctly on CRAN.
Thanks in advance for your help.
Luca
--
--------------------------------------
Luca Scrucca, PhD
Associate Professor of Statistics
Department of Economics
University of Perugia
Via A. Pascoli, 20
06123 Perugia (Italy)
Tel +39-075-5855231
Fax +39-075-5855950
E-mail luca.scrucca at unipg.it
Web page http://www.stat.unipg.it/luca
--------------------------------------
-- logsumexp.cpp ------------------------------------------------------
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericVector logsumexp_Rcpp(NumericMatrix x, NumericVector a)
{
// Efficiently computes log-sum-exp(x+a)
// x = matrix (n x d)
// a = vector (d)
double n = x.nrow();
double d = x.ncol();
NumericVector lse(n);
NumericVector xa(d);
double m = 0.0;
//
for (int i = 0; i < n; i++)
{
xa = x.row(i) + a;
m = max(xa);
lse[i] = m + log(sum(exp(xa-m)));
}
return lse;
}
/*** R
x = structure(c(-4.19768936334846, -23.3334911845962, -5.36851445858848,
-15.2896460085004, -3.06018772423303, -13.2857737610833, -3.69968442181734,
-5.33468420156765, -22.954092839643, -3.03420360101199, -23.3405056884397,
-2.6395810621981, -16.4338853853632, -3.23305725595493, -50.7400647615373,
-7.76487486677727, -57.9522847161203, -26.7659048640944, -2.41249310267583,
-44.9591733534474), dim = c(10L, 2L))
pro = c(0.644072589572232, 0.355927410427768)
logsumexp_Rcpp(x, log(pro))
*/
-----------------------------------------------------------------------