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

[Charles Geyer]

I should add a more direct question.  When a crash occurs ONLY when running
R CMD check, how does one debug that?  Usually one would say that R CMD
check --use-valgrind
is the answer.  But it only segfaults when --use-vagrind is not used.  So
somehow we have to debug R CMD check itself.  How?

On Sat, Jul 4, 2015 at 10:15 AM, Charles Geyer <charlie at stat.umn.edu> wrote:

> 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
>



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

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