[R-pkg-devel] R CMD check crash for Ubuntu 14.04 R-3.2.1 only

[Charles Geyer]

The diff for bar.Rout is OK.  The solution is the same (the two matrices
have the same rows and so determine the same convex polyhedron).  Why it
picks different orders of rows on different machines, I have no idea.

I also saw the pages of warnings from gcc -W -Wall -Wextra but they are all
about unused variables and unused arguments of functions.  AFAIK these are
not real problems.

I should say that I did not write most of the code.  This package is an R
interface to the computational geometry provided by cddlib, which is not
something linux distributions package.  So in order to avoid hassle, I just
included the cddlib code (which is GPL) in the src directory and added its
author Komei Fukuda to the authors of the package.

AFAIK this code is very high quality from a numerical analysis standpoint,
however much it may fall below the coding standards of most C coders.
Anyway it is the only free software computational geometry code I know
about, so it is the only game in town unless statisticians want to just say
"we cannot deal with problems like that".

This code may actually segfault somewhere, but we haven't seen it in
practice unless this is its fault (rather than the 32 bit R-3.2.1 build for
Ubuntu 14.04).  We still don't have a way to tell which to blame.

I am trying to follow the debugging rules (http://debuggingrules.com/) the
most important here being "divide and conquer".  Until we know where the
crash occurs, we are just clueless.

On Sat, Jul 4, 2015 at 3:35 AM, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> Charles,
>
> I took a look based on your tar ball.  When I use the normal 'loud'
> setting I
> default to for g++ (ie -pedantic -Wall) or clang++ I get more than a page
> full of errors.  I just tried it using the UBSAN-via-clang instrumented R I
> provide via a docker container (and for which I showed usage during the
> 'rocker: Docker on R' tutorial preceding useR! -- slides now on my
> presentation page).  It also does not segfault, but it shows a test
> difference:
>
>   Running ‘bar.R’
>     Comparing ‘bar.Rout’ to ‘bar.Rout.save’ ...8d7
>     <
>     51,54c50,53
>     < [1,]    0    1    0    1    0    0
>     < [2,]    0    1    1    0    0    0
>     < [3,]    0    1    0    0    1    0
>     < [4,]    0    1    0    0    0    1
>     ---
>     > [1,]    0    1    0    0    0    1
>     > [2,]    0    1    0    0    1    0
>     > [3,]    0    1    0    1    0    0
>     > [4,]    0    1    1    0    0    0
>       Running ‘bug2.R’
>         Comparing ‘bug2.Rout’ to ‘bug2.Rout.save’ ...8d7
>         <
>
> (You also seem to consistently differ in one newline which is just a
> nuisance
> and not an error,)
>
> So no free lunch yet.  I fear you may have to minimize the package somewhat
> to hopefully arrive at minimally reproducible example.  So far you seem to
> have a Heisenbug (https://en.wikipedia.org/wiki/Heisenbug)
>
> Sorry I cannot offer more help.
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>



-- 
Charles Geyer
Professor, School of Statistics
University of Minnesota
charlie at stat.umn.edu

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