I was unable to reproduce the error on the rhub's clang17 docker image. I notice that the linking command is slightly different between systems. And this suggests that I need to find some way to get CRAN to pass -stdlib flag at the linking stage.
CRAN: /usr/local/clang17/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang17/lib -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o rbedrock.so actors.o bedrock_leveldb.o dummy.o init.o key_conv.o nbt.o random.o subchunk.o support.o -L./leveldb-mcpe/build -pthread -lleveldb -lz RHUB: clang++-17 -stdlib=libc++ -std=gnu++14 -shared -L/opt/R/devel/lib/R/lib -L/usr/local/lib -o rbedrock.so actors.o bedrock_leveldb.o dummy.o init.o key_conv.o nbt.o random.o subchunk.o support.o -L./leveldb-mcpe/build -pthread -lleveldb -lz -L/opt/R/devel/lib/R/lib -lR On Wed, Sep 27, 2023 at 11:36 AM Gábor Csárdi <csardi.ga...@gmail.com> wrote: > You might be able to reproduce it with the clang17 container here: > > https://urldefense.com/v3/__https://r-hub.github.io/containers/__;!!IKRxdwAv5BmarQ!a5vkX68B5unua6_Zsh92b99AXfbJiewU7Mp0nqAKE0JDT8v3g2d08JZ8Yq_0ubp0j4GeTWWLjLVAN-FoLqhhk9c$ > You can either run it directly or with the rhub2 package: > > https://urldefense.com/v3/__https://github.com/r-hub/rhub2*readme__;Iw!!IKRxdwAv5BmarQ!a5vkX68B5unua6_Zsh92b99AXfbJiewU7Mp0nqAKE0JDT8v3g2d08JZ8Yq_0ubp0j4GeTWWLjLVAN-FoxPbUQlE$ > > Gabor > > On Wed, Sep 27, 2023 at 8:29 PM Reed A. Cartwright > <racartwri...@gmail.com> wrote: > > > > My package, RBedrock, is now throwing an error when compiled against > > Clang17. The error log is here: > > > > > https://urldefense.com/v3/__https://www.stats.ox.ac.uk/pub/bdr/clang17/rbedrock.log__;!!IKRxdwAv5BmarQ!a5vkX68B5unua6_Zsh92b99AXfbJiewU7Mp0nqAKE0JDT8v3g2d08JZ8Yq_0ubp0j4GeTWWLjLVAN-FoNhThuZA$ > > > > 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: > https://urldefense.com/v3/__http://cartwrig.ht/__;!!IKRxdwAv5BmarQ!a5vkX68B5unua6_Zsh92b99AXfbJiewU7Mp0nqAKE0JDT8v3g2d08JZ8Yq_0ubp0j4GeTWWLjLVAN-Fo7waq1VI$ > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-package-devel@r-project.org mailing list > > > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-package-devel__;!!IKRxdwAv5BmarQ!a5vkX68B5unua6_Zsh92b99AXfbJiewU7Mp0nqAKE0JDT8v3g2d08JZ8Yq_0ubp0j4GeTWWLjLVAN-FocAOfF7A$ > ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
