Update: I submitted a new version of the package, but it did not fix the issue. The package has now been archived and I do not have access to the error log output anymore from r-devel-linux-x86_64-fedora-clang.
I did reproduce CRAN's configuration in a VM using the information provided by CRAN for r-devel-linux-x86_64-fedora-clang. I still cannot reproduce the error and at this point I believe that there is a chance that CRAN's machine is misconfigured. The specific error happens after rbedrock has been compiled and linked successfully. The specific error is that the symbol _ZNSt3__122__libcpp_verbose_abortEPKcz cannot be found when rbedrock.so is loaded.This symbol was introduced into libc++ in Clang 15.0. What I believe to be happening to cause the error is that Clang++ 17 is adding a reference to this symbol when compiling and linking rbedrock.so but the dynamic linker is loading an older version of libc++.so when trying to load rbedrock.so and the symbol is not found. If this is the cause, then I think that the CRAN machine needs to configure the dynamic linker to use the Clang++ 17 libc++.so, or add the proper command line options to R's config variables. It's possible that the CRAN's r-devel-linux-x86_64-fedora-clang machine is fine and I've missed something, and I would be happy if someone could help me figure out what it is. Also, a new issue cropped up when 0.3.1 was tested on the r-oldrel-macos-x86_64 machine. /usr/bin/ar seems to have failed to produce an archive. The other Mac versions did fine, so I'm not sure if this is a random error or something related to my package. The error log is here: https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/rbedrock-00install.html If anyone can help me resolve this, I'd appreciate it. On Wed, Sep 27, 2023 at 2:54 PM Reed A. Cartwright <racartwri...@gmail.com> wrote: > 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
