Compiling error of "fatal error: 'limits' file not found" when creating a custom kernel

[snowbugxs]

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Problem description

I am following the the tutorial example, [getting_started->tutorial01_app_development-> step05_kernel_object].
It is about creating a custom kernel class to solve the Darcy Pressure problem.
I get the compiling error when i do the "make -j4" step,
I am on Macos of darwin20.0.0 with Apple M1 chip.
By the way, why do source files have an extension of '.c' instead of '.cpp'?

Bellow is the last section of the compiling message,

In file included from /Users/xuesong/moose-dir/moose/framework/build/header_symlinks/ResidualObject.h:12:
In file included from /Users/xuesong/moose-dir/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/xuesong/moose-dir/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/xuesong/moose-dir/moose/framework/build/header_symlinks/MooseTypes.h:12:
In file included from /Users/xuesong/moose-dir/moose/framework/build/header_symlinks/Moose.h:12:
In file included from /Users/xuesong/moose-dir/moose/framework/build/header_symlinks/libMeshReducedNamespace.h:16:
In file included from /Users/xuesong/miniforge/envs/moose/libmesh/include/libmesh/libmesh.h:25:
In file included from /Users/xuesong/miniforge/envs/moose/libmesh/include/libmesh/libmesh_base.h:23:
/Users/xuesong/miniforge/envs/moose/libmesh/include/libmesh/id_types.h:23:10: fatal error: 'limits' file not found
#include <limits>
         ^~~~~~~~
1 error generated.
make: *** [/Users/xuesong/moose-dir/moose/framework/build.mk:180: /Users/xuesong/moose-dir/babbler/src/kernels/DarcyPressure.aarch64-apple-darwin20.0.0.opt.lo] Error 1
make: *** Waiting for unfinished jobs....

Output of the diagnostics.sh

(moose) xuesong@Xuesongs-MacBook-Air moose-dir % moose/scripts/diagnostics.sh
####################################################################################################
Influential Environment Variables

CC=mpicc
CC_FOR_BUILD=/Users/xuesong/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-clang
CFLAGS= -fPIC -fstack-protector-strong  -pipe -isystem /Users/xuesong/miniforge/envs/moose/include 
CONDA_CHANNEL=https://conda.software.inl.gov/public
CONDA_DEFAULT_ENV=moose
CONDA_EXE=/Users/xuesong/miniforge/bin/conda
CONDA_PREFIX=/Users/xuesong/miniforge/envs/moose
CONDA_PREFIX_1=/Users/xuesong/miniforge
CONDA_PROMPT_MODIFIER=(moose) 
CONDA_PYTHON_EXE=/Users/xuesong/miniforge/bin/python
CONDA_SHLVL=2
CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0
CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0
CPPFLAGS= -isystem /Users/xuesong/miniforge/envs/moose/include -mmacosx-version-min=11.3 
CURL_CA_BUNDLE=
CXX=mpicxx
CXXFLAGS= -fPIC -fstack-protector-strong  -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/xuesong/miniforge/envs/moose/include  -std=c++17
CXX_FOR_BUILD=/Users/xuesong/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-clang++
F77=mpif77
F90=mpif90
F95=/Users/xuesong/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-gfortran
FC=mpif90
FC_FOR_BUILD=/Users/xuesong/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-gfortran
FFLAGS=  -fPIC   -pipe -isystem /Users/xuesong/miniforge/envs/moose/include 
FI_PROVIDER=tcp
HDF5_DIR=/Users/xuesong/miniforge/envs/moose
LD=arm64-apple-darwin20.0.0-ld
LDFLAGS=-Wl,-headerpad_max_install_names  -Wl,-rpath,/Users/xuesong/miniforge/envs/moose/lib -L/Users/xuesong/miniforge/envs/moose/lib  -Wl,-ld_classic -Wl,-commons,use_dylibs
LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath /Users/xuesong/miniforge/envs/moose/lib -L/Users/xuesong/miniforge/envs/moose/lib
LIBMESH_DIR=/Users/xuesong/miniforge/envs/moose/libmesh
MOOSE_JOBS=6
MOOSE_NO_CODESIGN=true
PATH=/Applications/ParaView-5.13.0.app/Contents/MacOS:/Users/xuesong/miniforge/envs/moose/bin:/opt/homebrew/Cellar/mpich/4.2.3/bin:/Applications/Visual Studio Code.app/Contents/Resources/app/bin:/opt/homebrew/bin:/Applications/CMake.app/Contents/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Applications/ParaView-5.13.0.app/Contents/MacOS:/Users/xuesong/miniforge/bin:/opt/homebrew/Cellar/mpich/4.2.3/bin:/Applications/Visual Studio Code.app/Contents/Resources/app/bin:/Applications/CMake.app/Contents/bin:/Users/xuesong/miniforge/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/Apple/usr/bin:/Users/xuesong/miniforge/envs/moose/wasp/bin
PETSC_DIR=/Users/xuesong/miniforge/envs/moose/petsc
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
WASP_DIR=/Users/xuesong/miniforge/envs/moose/wasp
####################################################################################################
Compiler(s) (CC CXX FC F77 F90):

which $CC; /Users/xuesong/miniforge/envs/moose/bin/mpicc
$CC --version; clang version 16.0.6
$CC -show; arm64-apple-darwin20.0.0-clang -I/Users/xuesong/miniforge/envs/moose/include -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -Wl,-rpath,/Users/xuesong/miniforge/envs/moose/lib -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -lmpi -lpmpi

which $CXX; /Users/xuesong/miniforge/envs/moose/bin/mpicxx
$CXX --version; clang version 16.0.6
$CXX -show; arm64-apple-darwin20.0.0-clang++ -I/Users/xuesong/miniforge/envs/moose/include -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -Wl,-rpath,/Users/xuesong/miniforge/envs/moose/lib -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -lmpicxx -lmpi -lpmpi

which $FC; /Users/xuesong/miniforge/envs/moose/bin/mpif90
$FC --version; GNU Fortran (GCC) 12.3.0
$FC -show; arm64-apple-darwin20.0.0-gfortran -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -Wl,-rpath,/Users/xuesong/miniforge/envs/moose/lib -I/Users/xuesong/miniforge/envs/moose/include -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -lmpifort -lmpi -lpmpi

which $F77; /Users/xuesong/miniforge/envs/moose/bin/mpif77
$F77 --version; GNU Fortran (GCC) 12.3.0
$F77 -show; arm64-apple-darwin20.0.0-gfortran -I/Users/xuesong/miniforge/envs/moose/include -fallow-argument-mismatch -L/Users/xuesong/miniforge/envs/moose/lib -Wl,-rpath,/Users/xuesong/miniforge/envs/moose/lib -I/Users/xuesong/miniforge/envs/moose/include -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -lmpifort -lmpi -lpmpi

which $F90; /Users/xuesong/miniforge/envs/moose/bin/mpif90
$F90 --version; GNU Fortran (GCC) 12.3.0
$F90 -show; arm64-apple-darwin20.0.0-gfortran -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -Wl,-rpath,/Users/xuesong/miniforge/envs/moose/lib -I/Users/xuesong/miniforge/envs/moose/include -I/Users/xuesong/miniforge/envs/moose/include -L/Users/xuesong/miniforge/envs/moose/lib -lmpifort -lmpi -lpmpi

OK
####################################################################################################
Python Sanity Checks

/usr/bin/env python3 --version; (reporting as: Python 3.11.8) matches
which python3 python;

/Users/xuesong/miniforge/envs/moose/bin/python3 --version; == Python 3.11.8
/Users/xuesong/miniforge/envs/moose/bin/python --version; == Python 3.11.8

OK
####################################################################################################
Python Modules (TestHarness, run-ability)

OK
####################################################################################################
MOOSE Repository/Conda Version Checks

              Installed     Required

OK

checks PASSED

[GiudGiud]

You seem to be missing the C++ standard headers. Did you install the rest of the dependencies using conda and if so did you remember to activate the environment?

[snowbugxs]

Hi. I follow the installation instructions. i am using conda and activate the environment. I attached the output from the diagnostics.sh.

[GiudGiud]

oh there is your problem

By the way, why do source files have an extension of '.c' instead of '.cpp'?

it's not .c.
It should be .C

.c is for C code. .C for C++

[snowbugxs]

Thanks. It solves my problem. May I suggest to make a statement about the cpp file extention.