[R-pkg-devel] R CMD check crash for Ubuntu 14.04 R-3.2.1 only
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 [[alternative HTML version deleted]]