Also the most recent source code tested by CRAN is here: https://github.com/reedacartwright/rbedrock/tree/v0.3.1
On Wed, Oct 11, 2023 at 7:51 PM Reed A. Cartwright <racartwri...@gmail.com> wrote: > 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 The package has now been archived and I do not have access to the 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
