clang16 warnings

[Quentin62]

Message from Brian:

clang 16 is being prepared for release in early March, so it is time to
start reporting its issues. See
https://www.stats.ox.ac.uk/pub/bdr/clang16/

Shortly these logs will appear as 'clang16' additional issues.

Please correct before 2023-02-16 to safely retain your package on CRAN.
(Some have much closer deadlines for other issues.)

README.txt

Tests as for fedora-clang but using clang 16.0.0git rather than 15.0.7.
This is scheduled for release on Mar 7th.

Currently using C23 as the default C standard (but C23 issues are
reported elsewhare).

Other details as
https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-clang

References for Rf_length in system headers come from includeing R headers
before system headers rather than after: see 'Writing R Extnesions'.

The [-Wenum-constexpr-conversion] errors seen in

RSQLite

are from the old Boost headers.

std:unary_function was deprecated in C+11 and removed in C++17, and finally
in clang 16 in C++17 mode. Boost 1.80 was still using it.

RMixtCompIO.out

• using log directory ‘/data/gannet/ripley/R/packages/tests-clang-trunk/RMixtCompIO.Rcheck’
• using R Under development (unstable) (2023-01-20 r83646)
• using platform: x86_64-pc-linux-gnu (64-bit)
• R was compiled by
  clang version 16.0.0 (https://github.com/llvm/llvm-project.git 2133e8b9f942f91ec54e28c580fccf6d6b26c62e)
  GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘RMixtCompIO/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘RMixtCompIO’ version ‘4.0.8’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘RMixtCompIO’ can be installed ... [454s/374s] ERROR
  Installation failed.
  See ‘/data/gannet/ripley/R/packages/tests-clang-trunk/RMixtCompIO.Rcheck/00install.out’ for details.
• DONE

Status: 1 ERROR
See
‘/data/gannet/ripley/R/packages/tests-clang-trunk/RMixtCompIO.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:16.95, 436.39 + 19.82

RMixtCompIO.log

[Quentin62]

the error seems to come from the sort overload for custom matrix
https://github.com/modal-inria/MixtComp/blob/master/MixtComp/src/lib/LinAlg/EigenMatrixBaseAddons.h#L237-L240

In file included from lib/Mixture/Functional/FunctionCS.cpp:23:
In file included from lib/Mixture/Functional/FuncCSClass.h:26:
In file included from lib/LinAlg/LinAlg.h:26:
In file included from lib/LinAlg/Typedef.h:27:
In file included from /usr/local/clang-trunk/bin/../include/c++/v1/string:576:
In file included from /usr/local/clang-trunk/bin/../include/c++/v1/string_view:1025:
In file included from /usr/local/clang-trunk/bin/../include/c++/v1/algorithm:1771:
In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__algorithm/nth_element.h:15:
/usr/local/clang-trunk/bin/../include/c++/v1/__algorithm/sort.h:656:11: error: no viable overloaded '-='
__lm1 -= (__right_bitset == 0) ? difference_type(__detail::__block_size) : difference_type(0);
~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/clang-trunk/bin/../include/c++/v1/__algorithm/sort.h:859:20: note: in instantiation of function template specialization 'std::__bitset_partition<std::_ClassicAlgPolicy, Eigen::MatrixBase<Eigen::Matrix<double, -1, 1, 0>>::Iterator, std::__less &>' requested here
? std::__bitset_partition<_AlgPolicy, _RandomAccessIterator, _Compare>(__first, __last, __comp)
^
/usr/local/clang-trunk/bin/../include/c++/v1/__algorithm/sort.h:919:8: note: in instantiation of function template specialization 'std::__introsort<std::_ClassicAlgPolicy, std::__less &, Eigen::MatrixBase<Eigen::Matrix<double, -1, 1, 0>>::Iterator, false>' requested here
std::__introsort<_AlgPolicy,
^
/usr/local/clang-trunk/bin/../include/c++/v1/__algorithm/sort.h:983:10: note: in instantiation of function template specialization 'std::__sort<std::__less &, Eigen::MatrixBase<Eigen::Matrix<double, -1, 1, 0>>::Iterator>' requested here
std::__sort<_WrappedComp>(std::__unwrap_iter(__first), std::__unwrap_iter(__last), __wrapped_comp);
^
/usr/local/clang-trunk/bin/../include/c++/v1/__algorithm/sort.h:990:8: note: in instantiation of function template specialization 'std::__sort_impl<std::_ClassicAlgPolicy, Eigen::MatrixBase<Eigen::Matrix<double, -1, 1, 0>>::Iterator, std::__less>' requested here
std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp);
^
/usr/local/clang-trunk/bin/../include/c++/v1/__algorithm/sort.h:996:8: note: in instantiation of function template specialization 'std::sort<Eigen::MatrixBase<Eigen::Matrix<double, -1, 1, 0>>::Iterator, std::__less>' requested here
std::sort(__first, __last, __less<typename iterator_traits<_RandomAccessIterator>::value_type>());
^
lib/LinAlg/EigenMatrixBaseAddons.h:239:7: note: in instantiation of function template specialization 'std::sort<Eigen::MatrixBase<Eigen::Matrix<double, -1, 1, 0>>::Iterator>' requested here
std::sort(derived().begin(), derived().end());
^
lib/Mixture/Functional/FunctionCS.cpp:237:10: note: in instantiation of member function 'Eigen::MatrixBase<Eigen::Matrix<double, -1, 1, 0>>::sort' requested here
sortedT.sort();

[Quentin62]

Dockerfile provided by Vincent Dorie

Hi all,

I managed to get clang16 and libc++ (which was the real culprit for my package) built using Docker, built R itself, and reproduced the errors on the check page. I've attached the Docker file. Unfortunately, I'm using Apple silicon so things will need to be modified x86. Since I wasn't familiar with Docker to start, the procedure for me was:

0. Install Docker, cd to folder with the Docker file
1. Execute docker build -t clang .
2. Execute docker run -i -t clang /bin/bash
3. Run bin/R to install dependencies or compile packages

I hope that helps! I'm happy to answer any questions, but I would not say that I'm any kind of expert.

Best,
Vince

[Quentin62]

R-hub now provides a docker container and a github actions: r-hub/rhub-linux-builders#67 (comment)