[Rd] difficulty with sanitizer using bigmemory

[Henrik Bengtsson]

The https://builder.r-hub.io/advanced provides an 'R CMD check
--as-cran' for 'Debian Linux, R-devel, GCC ASAN/UBSAN'.  You can
either upload it there or launch it from you local R prompt;

> rhub::check()
── Choose build platform
...
10: Debian Linux, R-devel, GCC ASAN/UBSAN (linux-x86_64-rocker-gcc-san)
...
20: Windows Server 2008 R2 SP1, R-release, 32/64 bit (windows-x86_64-release)

With some luck, you might be able to reproduce those CRAN sanity checks there.

/Henrik

On Wed, Jul 24, 2019 at 9:21 AM pete mohanty <pete.mohanty using gmail.com> wrote:
>
> Dear all,
>
> bigKRLS, which has been on CRAN for a couple of years, had to be pulled
> recently due to what seems to be a sanitizer issue stemming from its use of
> bigmemory. bigKRLS works fine (we’ve used it ourselves on many different
> platforms and have had over 15,000 downloads without an end user reporting
> difficulties because of this issue). Unfortunately, we have been unable to
> reproduce the UndefinedBehaviorSanitizer error locally, and are unsure how
> to proceed. We corresponded with Michael Kane, author of bigmemory, who
> seems to think the issue may be on the CRAN side. At his suggestion, we
> switched to filebacked big matrices, which didn’t resolve the issue. We
> also tried adding MAIN_LDFLAGS = -fsanitize=undefined,address to the
> MAKEVARS, which didn’t do the trick either.
>
> Here are some links:
>
>
>    1.
>
>    bigKRLS repo: https://github.com/rdrr1990/bigKRLS
>    2.
>
>    bigKRLS file backs all big matrices with a helper function called
>    ‘to.big.matrix’ found starting on line 116 of
>    bigKRLS/bigKRLS_Rcpp_functions.R:
>    https://github.com/rdrr1990/bigKRLS/blob/master/R/bigKRLS_Rcpp_functions.R
>    3.
>
>    Discussion with Michael Kane:
>    https://github.com/kaneplusplus/bigmemory/issues/73#issuecomment-330543207
>
>
>
> And here is the main error itself:
>
> package bigKRLS_3.0.5.tar.gz has been auto-processed.
>
> The auto-check found additional issues for the *last* version released on
> CRAN:
>
>   clang-UBSAN <
> https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-UBSAN/bigKRLS>
>
>   gcc-UBSAN <https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/bigKRLS>
>
> Clicking through, you find that
>
> > test_check("bigKRLS")
>
> gauss_kernel.cpp:38:40: runtime error: member call on address
> 0x6120001f2c40 which does not point to an object of type 'BigMatrix'
>
> 0x6120001f2c40: note: object is of type 'FileBackedBigMatrix'
>
> [details omitted]
>
> SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior
> gauss_kernel.cpp:38:40 in
>
> /data/gannet/ripley/R/test-clang/bigmemory/include/bigmemory/BigMatrix.h:41:28:
> runtime error: member access within address 0x6120001f2c40 which does not
> point to an object of type 'BigMatrix'
>
> 0x6120001f2c40: note: object is of type 'FileBackedBigMatrix'
>
> But FileBackedBigMatrix are BigMatrix objects and earlier versions of the
> package which did not file back generated similar errors. (R CMD check
> --as-cran does not yield these errors on Ubuntu 16.04 or MacOS Sierra,
> which has made it particularly tricky to work on.)
>
> Any and all help would be greatly appreciated!!
>
> Best,
>
> Pete Mohanty and Robert Shaffer
>
>
> --
> Pete Mohanty, PhD
> Science, Engineering & Education Fellow
> Stanford University
> Department of Statistics
> https://sites.google.com/site/petemohanty/
>
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>
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