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

[Simon Urbanek]

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://github.com/r-hub/rhub-linux-builders/blob/master/fedora-clang-devel/Makevars
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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>>> 
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>> 
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