Is there any way to submit packages directly to the CRAN's clang17 setup? I can enable verbose output for CMake and compare the output, but I'd rather not clog up the CRAN incoming queue just to debug a linker error?
On Wed, Sep 27, 2023 at 2:43 PM Simon Urbanek <simon.urba...@r-project.org> wrote: > It looks like a C++ run-time mismatch between what cmake is using to build > the static library and what is used by R. Unfortunately, cmake hides the > actual compiler calls so it's hard to tell the difference, but that setup > relies on the correct sequence of library paths. > > The rhub manually forces -stdlib=libc++ to all its CXX flags > > https://urldefense.com/v3/__https://github.com/r-hub/rhub-linux-builders/blob/master/fedora-clang-devel/Makevars__;!!IKRxdwAv5BmarQ!bAZgiOQaK4hd5BTk_Ldx9IEHgzHKVbC-uMkvYv5GOVkZDvbedcGwS8dQ4MWXRjukFfds7UpiR9NDZfEoUCWeoVnCfrDa$ > so it is quite different from the gannet tests-clang-trunk setup (also > note the different library paths), but that's not something you can do > universally in the package, because it strongly depends on the toolchain > setup. > > Cheers, > Simon > > > > On 28/09/2023, at 9:37 AM, Reed A. Cartwright <racartwri...@gmail.com> > wrote: > > > > 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://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-package-devel__;!!IKRxdwAv5BmarQ!bAZgiOQaK4hd5BTk_Ldx9IEHgzHKVbC-uMkvYv5GOVkZDvbedcGwS8dQ4MWXRjukFfds7UpiR9NDZfEoUCWeoZEUmVSQ$ > > > > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
