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

Thu Oct 12 04:54:19 CEST 2023

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 <racartwright using 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 The package has now been archived and I do not have access to the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 <racartwright using 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.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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>>> >>>
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>>> >>
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