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

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 The package has now been archived and I do not have access to the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 at 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 at 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 at 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 G?bor Cs?rdi <csardi.gabor at 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 at 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
==================
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