[R-pkg-devel] Question about Clang 17 Error

[Reed A. Cartwright]

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.urbanek using 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 <racartwright using 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.gabor using 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
> >> <racartwright using 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$
> >>>
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