[Rcpp-devel] Help with R CMD CHECK for rtree package

Kent Johnson kjohnson at akoyabio.com
Thu May 6 21:05:53 CEST 2021

From: Dirk Eddelbuettel <edd at debian.org>
Sent: Thursday, May 6, 2021 8:42 AM

On 6 May 2021 at 10:45, Iñaki Ucar wrote:
| > The full output is here: https://github.com/akoyabio/rtree/runs/2502841486?check_suite_focus=true
| > The message says "See below..." but there is nothing below?
| Below I see this:
| * checking whether package 'rtree' can be installed ... WARNING
| Found the following significant warnings:
|   D:/a/_temp/Library/BH/include/boost/geometry/index/detail/varray_detail.hpp:544:13:
| warning: 'void* memcpy(void*, const void*, size_t)' writing to an
| object of type 'struct std::pair<boost::geometry::model::point<double,
| 2, boost::geometry::cs::cartesian>, unsigned int>' with no trivial
| copy-assignment; use copy-assignment or copy-initialization instead
| [-Wclass-memaccess]
| And even more details if you download the artifacts of your build and
| review that file. So it's a Boost thing, and there's probably nothing
| you can do about it beyond talking to CRAN. There are packages on CRAN
| with these warnings.

Thank you Iñaki for pointing me to the actual warning. With some digging I have found the cause but not the solution.

This warning is disabled via #pragma in boost/container/detail/copy_move_algo.hpp; the changeset (from Sept 2018) is here:

In the BH package, these #pragmas have been commented out here:
which then causes my code to emit the warnings.

I'm not sure how to proceed. I can try submitting to CRAN with an explanation of the warnings. ISTM it would be better for {BH} to be submitted with the #pragmas in place; then there is just one fix and one exception, rather than the possibility of multiple packages having this issue. Dirk, do you have any recommendation?

But for me it actually failed to build at
 - RHub
 - win-builder r-release
 - win-builder r-devel
when I submitted an unchanged tarball (with me as maintainer to get the result).

When I submit to RHub and build on "Windows Server 2008 R2 SP1, R-release, 32/64 bit" I get the same errors as I see on GitHub and local builds. I did not try win-builder.

So there may be more going on.  Could just be a setup issue which happens at
RHub and win-builder.  But Boost Geometry may be a more dicey part of Boost.

I think the commented-out #pragmas explain these warnings.

| > Running on my local Windows 10 PC I get this warning and a note:
| >
| > -- R CMD check results ---------------------------------------- rtree 0.2.0 ----
| > Duration: 1m 2.2s
| >
| > > checking whether package 'rtree' can be installed ... WARNING
| >   See below...
| >
| > > checking compiled code ... NOTE
| >   Note: information on .o files for x64 is not available
| >   File 'C:/Research/rtree.Rcheck/rtree/libs/x64/rtree.dll':
| >     Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| >     Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
| >     Found 'printf', possibly from 'printf' (C)
| This is problably a false positive.

Maybe. Maybe not. It does not seem to reproduce on Linux.

I think this is a false positive, there are other reports of this on Stack Overflow.

Thank you both for your help, any suggestions on the best way to proceed are very welcome.

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