UBSAN issues: RcppParallel

[jlmelville]

Running rhub::check_with_sanitizers() has confirmed that the UBSAN issues reported for RcppAnnoy in #50 are fixed with RcppAnnoy 0.0.15. Unfortunately, there are lots of UBSAN complaints originating with RcppParallel. I don't think this is due to me using the package incorrectly, because the RcppParallel CRAN checks give the same messages (see https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/RcppParallel/RcppParallel-Ex.Rout).

They seem to originate with the Intel tbb library and are well known by the RcppParallel maintainers (see e.g. RcppCore/RcppParallel#36), but they can't do anything about it. The risk here is that the strategy of saying that the UBSAN issues are harmless and originate from a package uwot is using is exactly the strategy that stopped working with RcppAnnoy.

A possible alternative is to look at RcppThread which has a parallel for construct and is not currently showing any check problems.

[jlmelville]

I had hoped that setting -DRCPP_PARALLEL_USE_TBB=0 in the compiler flags would turn off the use of TBB and just use TinyThread++. Unfortunately, that doesn't seem to be the case. I have asked about this at RcppCore/RcppParallel#106.

At any rate, if I take the relevant bits of RcppParallel, add it to an inst directory and thoroughly scour it of any tbb-related material, then the sanitizer seems to pass (it claims there is a 'prep error', but I don't see any runtime errors in the output).

If there is any good news to doing things this way, it's that we don't need a Makevars.win, we don't need to go to RScript to get the linker path and we don't need to use the non-standard += in Makevars, which lets us avoid the NOTE in the check (maybe we never needed it though).

If I have to go down this road, perhaps maintenance would be simpler (at the cost of more up-front work) by keeping only what is necessary for the parallel-for code, adapting it for std::thread, and dropping even tthread.

[jlmelville]

There's a new version of RcppParallel out that seems to fix these issues, but I have stuck with a std::thread-only version of the code I need which is less than 80 lines. It's in inst/include/RcppPerpendicular.h (renamed to avoid any clashing of namespaces but to indicate its origin) and remains GPL2.