>>>>> Reed A Cartwright >>>>> on Wed, 11 Oct 2023 22:25:35 -0700 writes:
> Okay, I'll reach out to the CRAN team shortly. > I wanted to run it by the group here first because my interactions with the > CRAN team haven't always been positive and I need to make sure that I'm not > missing something "obvious". well.. one thing not enough obvious: Simon Urbanek _is_ part of the CRAN team (*). So at least you had a positive interaction with "them", now ! ;-) --- *) https://cran.r-project.org/CRAN_team.htm (which is the *first* hit when I web search "CRAN team" {with DuckDuckGo, a reasonable non-prying Google-alternative I}) Best, Martin > On Wed, Oct 11, 2023, 22:22 Simon Urbanek <simon.urba...@r-project.org> > wrote: >> Reed, >> >> please contact CRAN - this list can only help with general developer's >> questions, not specific issues with a particular CRAN setup - only the >> corresponding member of CRAN running the setup can help. I don't see >> anything obvious - we can see that it's a mismatch of run-times between the >> cmake build and the R linking, but from the package alone it's not clear to >> me why. >> >> Cheers, >> Simon >> >> >> On Oct 12, 2023, at 3:51 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 The package has now been archived and I do not have access to the 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 >> <https://urldefense.com/v3/__https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/rbedrock-00install.html__;!!IKRxdwAv5BmarQ!bn6F_bNAOxSfAFbevyOMVGtmTQT-u-wuccyvwupscx__4Spd0Z8C0FoUWbCPQ8QfDC_9g64_bzdKRZTTqo2U99WvIfoR$> >> >> If anyone can help me resolve this, I'd appreciate it. >> >> >> On Wed, Sep 27, 2023 at 2:54 PM Reed A. Cartwright <racartwri...@gmail.com> >> wrote: >> >>> Is there any way to submit packages directly to the CRAN's clang17 setup? >>> I can enable verbose output for CMake and compare the output, but I'd >>> rather not clog up the CRAN incoming queue just to debug a linker error? >>> >>> On Wed, Sep 27, 2023 at 2:43 PM Simon Urbanek < >>> simon.urba...@r-project.org> wrote: >>> >>>> It looks like a C++ run-time mismatch between what cmake is using to >>>> build the static library and what is used by R. Unfortunately, cmake hides >>>> the actual compiler calls so it's hard to tell the difference, but that >>>> setup relies on the correct sequence of library paths. >>>> >>>> The rhub manually forces -stdlib=libc++ to all its CXX flags >>>> >>>> https://urldefense.com/v3/__https://github.com/r-hub/rhub-linux-builders/blob/master/fedora-clang-devel/Makevars__;!!IKRxdwAv5BmarQ!bAZgiOQaK4hd5BTk_Ldx9IEHgzHKVbC-uMkvYv5GOVkZDvbedcGwS8dQ4MWXRjukFfds7UpiR9NDZfEoUCWeoVnCfrDa$ >>>> 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 ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel