[R-pkg-devel] Question about Clang 17 Error
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 at 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/ [[alternative HTML version deleted]]
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