[Rcpp-devel] [RcppParallel] Segfault but only on TravisCI

Kevin Ushey kevinushey at gmail.com
Wed Jan 17 17:41:56 CET 2018

In your RcppParallel worker, it looks like you're trying to write to
an Rcpp matrix; e.g. you have:

    distmat_(i,j) = local_calculator->calculate(i,j);

where distmat_ is a matrix. You should avoid using Rcpp classes within
RcppParallel workers, as there's no guarantee that the methods
available on Rcpp classes are thread-safe (and this could lead to
these kinds of segfaults).

I'll echo Dirk and say that without a minimally reproducible example
(or access to the package source code) there's not much else we can

You could try running your code with `gctorture(TRUE)` to see if that
triggers your segfault more reliably -- if that's the case, then you
almost surely have an protection issue somewhere (most likely the
result of using non-threadsafe APIs within an RcppParallel worker, but
without full context it's impossible to be sure)

On Wed, Jan 17, 2018 at 4:32 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
> On 16 January 2018 at 21:02, Alexis Sarda wrote:
> | Hello,
> |
> | I am integrating RcppParallel into my R package and I'm running into
> | strange problems with segmentation faults, but only during the continuous
> | integration checks. I have essentially variations of the following (I hope
> | GitHub gist links are ok):
> |
> | https://gist.github.com/asardaes/7d78af394f848a967997ff23e433c9cf
> |
> | On TravisCI, my Linux builds simply freeze, and the OSX builds show
> | messages like:
> |
> | *** caught segfault ***
> | address 0x100000001, cause 'memory not mapped'
> |
> | I would assume that my distance functions are trying to access memory they
> | shouldn't, but during interactive use everything works flawlessly, and I've
> | tested all of the following with no problems (which also test correctness,
> | i.e. numeric consistency with respect to past results):
> |
> | - Local Linux R CMD check
> | - Local Windows R CMD check
> | - CRAN's WinBuilder check
> | - AppVeyor (x32 and x64 Windows)
> | - Docker R CMD check using rocker's r-devel-san
> | - Local Linux R CMD check with valgrind (no leaks)
> |
> | It is worth mentioning that some of the examples ran during the OSX build
> | show incorrect results long before the segfault occurs: some results are
> | zero when they shouldn't be. I don't have access to a machine with OSX, but
> | the Linux builds in TravisCI also show problems (no segfaults explicitly,
> | just hangs).
> |
> | I am at my wit's end. Any input would be appreciated.
> Hard to tell for us, but maybe try the old and trusted route of smaller and
> smaller reproducible examples til you reproduce it?
> Or else if it _just_ Travis CI maybe it is a compiler version issue?  Travis
> is very conservative in its default setup but there are .travis.yaml scripts
> out there that turn on the PPA for compiler builds giving you gcc-5, gcc-6,
> ... amd different clang versions.
> Dirk
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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