[R-pkg-devel] Question about Clang 17 Error

[Gábor Csárdi]

You might be able to reproduce it with the clang17 container here:
https://r-hub.github.io/containers/
You can either run it directly or with the rhub2 package:
https://github.com/r-hub/rhub2#readme

Gabor

On Wed, Sep 27, 2023 at 8:29 PM Reed A. Cartwright
<racartwright using gmail.com> wrote:
>
> My package, RBedrock, is now throwing an error when compiled against
> Clang17. The error log is here:
>
> https://www.stats.ox.ac.uk/pub/bdr/clang17/rbedrock.log
>
> The important part is
> """
> Error: package or namespace load failed for ‘rbedrock’ in dyn.load(file,
> DLLpath = DLLpath, ...):
>  unable to load shared object
> '/data/gannet/ripley/R/packages/tests-clang-trunk/rbedrock.Rcheck/00LOCK-rbedrock/00new/rbedrock/libs/rbedrock.so':
>
> /data/gannet/ripley/R/packages/tests-clang-trunk/rbedrock.Rcheck/00LOCK-rbedrock/00new/rbedrock/libs/rbedrock.so:
> undefined symbol: _ZNSt3__122__libcpp_verbose_abortEPKcz
> Error: loading failed
> """
>
> From what I can gather through googling, this error can be caused by using
> the C linker when one of the dependent libraries is a C++ library.
>
> I cannot tell if this is an issue with my package (likely) or CRAN's
> clang17 setup (less likely).
>
> Background about the package: rbedrock is written in C but links against a
> C++ library (Mojang's leveldb fork)  via the library's C-API functions. I
> use a dummy .cpp file in the source directory to trigger R into using the
> C++ linker. That does still seem to be happening according to the log.
>
> Has anyone seen this before and know where I should start looking to fix it?
>
> Thanks.
>
> --
> Reed A. Cartwright, PhD
> Associate Professor of Genomics, Evolution, and Bioinformatics
> School of Life Sciences and The Biodesign Institute
> Arizona State University
> ==================
> Address: The Biodesign Institute, PO Box 876401, Tempe, AZ 85287-6401 USA
> Packages: The Biodesign Institute, 1001 S. McAllister Ave, Tempe, AZ
> 85287-6401 USA
> Office: Biodesign B-220C, 1-480-965-9949
> Website: http://cartwrig.ht/
>
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