[R-pkg-devel] how to change from -fsanitize=undefined to -fsanitize=address

[Youyi Fong]

Here is a solution worked out by the wonderful staff from our scientific
computing support team at the Fred Hutchinson Cancer Research Center. I
really don't know how Dan did it, but the way he explained to me was that
he came across this github repository by Dirk:
https://github.com/rocker-org/r-devel-san-clang. There was the Docker file
which built the clang-san image, but he did not find the image itself in
Docker Hub. So he built it himself and pushed it as
dtenenba/r-devel-san-clang.

The issue I encountered with r-debug was related to ulimit. It turns out
that it be specific to the machine I was working on. Dan used a different
machine and that went away.

Using the docker image dtenenba/r-devel-san-clang on that new machine, I
was able to install my package, and upon running the test code, to
reproduce the memory issue reported by the CRAN team.

I then tested whether r-debug might also work on that machine. It sort of
did as it returned a memory-related error when I tried

RDsan CMD INSTALL mypkg

But it is not as helpful as the behavior by  dtenenba/r-devel-san-clang.




On Fri, Nov 29, 2019 at 1:48 PM Youyi Fong <youyifong using gmail.com> wrote:

> Hi Dirk,
>
> Thanks very much. Following your suggestion, I tried r-debug, following
> the readme on https://github.com/wch/r-debug. After starting docker as
> recommended,
>
> docker run --rm -ti --security-opt seccomp=unconfined wch1/r-debug
>
> I was able to call RD. But calling RDsan or RDcsan resulted in errors:
>
> root using 258bfdfcce6c:/# RDsan
> ==17==ERROR: AddressSanitizer failed to allocate 0xdfff0001000
> (15392894357504) bytes at address 2008fff7000 (errno: 12)
> ==17==ReserveShadowMemoryRange failed while trying to map 0xdfff0001000
> bytes. Perhaps you're using ulimit -v
> Aborted (core dumped)
>
>
> I have also tried rhub before, following this article:
> https://cran.r-project.org/web/packages/rhub/vignettes/local-debugging.html As
> you indicated, it may have worked for others, but got the following error:
>
> >>>>>==================== Installing system requirements
> 3b3a65d751c026b7629d2038242c92290cf97853525978381b6e59f41c8500d3
>
> >>>>>==================== Starting Docker container
> 04d6065323ef732bf89c26df7d547efff40774206a0ac6a24b3d9cdb021cb08e
> ls: cannot access '/opt/R-*': No such file or directory
> > source('https://bioconductor.org/biocLite.R')
> Error: With R version 3.5 or greater, install Bioconductor packages using
> BiocManager; see https://bioconductor.org/install
> Execution halted
> Error in run(bash, c(file.path(wd, "rhub-linux.sh"), args), echo = TRUE,  :
>   System command error
>
>
>
> This is where I am stuck at right now.
>
> Thanks,
> Youyi
>
>
> On Fri, Nov 29, 2019 at 10:46 AM Dirk Eddelbuettel <edd using debian.org> wrote:
>
>>
>> Youyi,
>>
>> It looks like you are trying to debug a _current_ SAN / ASAN / UBSAN error
>> against your package by leaning on documentation I wrote five years ago
>> specifically for another package (called "sanitizers") used to validate
>> the
>> initial Docker container builds I made (and to ensure the error these
>> SAN/ASAN/UBSAN containers were supposed to trigger were triggered).
>>
>> Today, your quickest bet to launch a sanitizer run may be via the rhub
>> platforms.  Clearly the easiest to launch ("no download"), but at times a
>> little inconsistent.  An alternative is the suite of containers
>> maintained by
>> Winston described at their repo at https://github.com/wch/r-debug at
>> available from the Docker Hub.
>>
>> All that said, exact configurations matters and the fact remains that we
>> all
>> still haven't managed to automatically provide the configurations used by
>> CRAN. There are possible "gaps" between what CRAN uses and what may be
>> available pre-built: compiler versions, builds, sanitizer options, ... and
>> these can be enough to not replicate an issue.  I think I would try
>> Winston's
>> r-debug next.
>>
>> Hope this helps, Dirk
>>
>> --
>> http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>>
>

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