Fix build with gcc13

[iyanmv]

Submission Checklist

• [x] Run unit tests: ./runTests.py src/test/unit
• [x] Run cpplint: make cpplint
• [ ] Declare copyright holder and open-source license: see below

Summary

With GCC 13, some C++ Standard Library headers have been changed to no longer include other headers that were being used internally by the library (see, e.g. this). This has affected many other projects.

I noticed this when trying to run the tests with: python runTests.py -j$(nproc) src/test

The fix is simple, <cstdint> has to be included manually.

Intended Effect

Fix build with g++13

How to Verify

Run the tests

Side Effects

None?

Documentation

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[WardBrian]

@serban-nicusor-toptal any idea why this wouldn't have been caught by the bleeding-edge pipeline?

[WardBrian]

Oh, something else probably includes cstdint when we're doing complete CmdStan builds, which is why we missed it

[serban-nicusor-toptal]

Hey, I'm not sure. Just ran a fresh build, making sure everything is built with the latest, and checked versions afterward, looks fine there.

[iyanmv]

I'm using g++ (GCC) 13.2.1 20230801 with

#-- Compiler and Linker Flags
#CPPFLAGS=""
CFLAGS="-march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions \
        -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security \
        -fstack-clash-protection -fcf-protection"
CXXFLAGS="$CFLAGS -Wp,-D_GLIBCXX_ASSERTIONS"
LDFLAGS="-Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now"
LTOFLAGS="-flto=auto"

[iyanmv]

Oh, wait... I just realized that the python script is downloading from https://github.com/stan-dev/stanc3/releases/download/nightly/linux-stanc instead of using the compiled ones. So I cannot use that in my PKGBUILD.

Let me rerun the tests manually.

[iyanmv]

In any case, here is the error when I use the python script:

g++ -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes      -I lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I . -I lib/rapidjson_1.1.0/ -I lib/stan_math/ -I lib/stan_math/lib/eigen_3.4.0 -I lib/stan_math/lib/boost_1.81.0 -I lib/stan_math/lib/sundials_6.1.1/include -I lib/stan_math/lib/sundials_6.1.1/src/sundials -I lib/stan_math/lib/benchmark_1.5.1/googletest/googletest/include -I lib/stan_math/lib/benchmark_1.5.1/googletest/googletest -I lib/stan_math/lib/benchmark_1.5.1/googletest/googletest/include -I lib/stan_math/lib/benchmark_1.5.1/googletest/googletest      -DBOOST_DISABLE_ASSERTS         -DGTEST_HAS_PTHREAD=0 -DGTEST_HAS_PTHREAD=0  -c src/test/unit/io/json/json_data_handler_test.cpp -o test/unit/io/json/json_data_handler_test.o
In file included from src/stan/io/json/json_data_handler.hpp:5,
                 from src/stan/io/json/json_data.hpp:4,
                 from src/test/unit/io/json/json_data_handler_test.cpp:1:
src/stan/io/json/json_handler.hpp:97:38: error: ‘uint64_t’ has not been declared
   97 |   virtual void number_unsigned_int64(uint64_t n) {}
      |                                      ^~~~~~~~
make: *** [make/tests:64: test/unit/io/json/json_data_handler_test.o] Error 1
make: *** Waiting for unfinished jobs....

[iyanmv]

This is probably a different question/issue, but what is the right way of compiling CmdStan and run all tests (including stan and stan_math) with the binaries that were generated when compiling CmdStan (and not precompiled ones from Github). I think the issue is that the Makefile in (stan/make/tests) does not try to use the binaries in the parent folder (cmdstan/bin).

[andrjohns]

It looks like this is also an issue with clang++-17. I just had a CRAN submission fail with this error on Debian & Clang 17:

clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I"../inst/include" -D_REENTRANT -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0 -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/rapidjsonr/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c model_methods.cpp -o model_methods.o
In file included from model_methods.cpp:1:
In file included from ../inst/include/stan/io/json/json_data.hpp:4:
In file included from ../inst/include/stan/io/json/json_data_handler.hpp:5:
../inst/include/stan/io/json/json_handler.hpp:97:38: error: unknown type name 'uint64_t'
   97 |   virtual void number_unsigned_int64(uint64_t n) {}

[WardBrian]

@serban-nicusor-toptal how hard would it be to add the Stan unit tests to our bleeding-edge-compilers pipeline? So it would be Math unit (gcc/clang) -> Stan unit (gcc/clang) -> building a bunch of models (gcc/clang)

[serban-nicusor-toptal]

@serban-nicusor-toptal how hard would it be to add the Stan unit tests to our bleeding-edge-compilers pipeline? So it would be Math unit (gcc/clang) -> Stan unit (gcc/clang) -> building a bunch of models (gcc/clang)

Should be fairly simple I hope, will give it a try this weekend.