sagelib-10.4.beta6 FTBFS on conda (graphic_matroid)

[bagasme]

Environment

- **OS**: Arch Linux
- **Sage Version**: 10.4.beta6

Steps To Reproduce

To reproduce:

• Setup new conda environment (with Python 3.11):

$ ./bootstrap-conda
$ conda env create --file environment-optional-3.11.prod.yml --name sagemath

• Set up environment variables and configure:

$ export CFLAGS="-O2 -march=haswell -mtune=haswell"
$ export CXXFLAGS="$CFLAGS"
$ export FCFLAGS="$CFLAGS"
$ export MAKE="make -j2"
$ ./bootstrap
$ ./configure --prefix=$CONDA_PREFIX --with-python=$CONDA_PREFIX/bin/python --enable-fricas=yes --with-system-eclib=no

• Build:

$ make

Config log

config.log

Package logs

sagelib-10.4.beta6.log

Additional Information

I'm trying to build sage 10.4.beta6 on conda environment (using environment-optional-3.11.yml to create the env). The build erred out on sagelib-10.4.beta6 spkg (especially on sage.tests.stl_vector extension).

Error messages with compiler warnings:

[spkg-install]     building 'sage.tests.stl_vector' extension
[spkg-install]     /home/bagas/miniconda3/envs/sagemath/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -fPIC -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bagas/miniconda3/envs/sagemath/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -fPIC -Isage/cpython -I/home/bagas/miniconda3/envs/sagemath/lib/python3.11/site-packages/cysignals -I/home/bagas/repo/sagemath/src -I/home/bagas/miniconda3/envs/sagemath/lib/python3.11/site-packages/numpy/core/include -I/home/bagas/miniconda3/envs/sagemath/include/python3.11 -I/home/bagas/miniconda3/envs/sagemath/include/python3.11 -c sage/tests/stl_vector.cpp -o build/temp.linux-x86_64-cpython-311/sage/tests/stl_vector.o
[spkg-install]     sage/tests/stl_vector.cpp: In function 'PyObject* __pyx_pf_4sage_5tests_10stl_vector_14stl_int_vector_4__getitem__(__pyx_obj_4sage_5tests_10stl_vector_stl_int_vector*, int)':
[spkg-install]     sage/tests/stl_vector.cpp:6870:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
[spkg-install]      6870 |       __pyx_t_1 = (__pyx_v_i < __pyx_v_self->data->size());
[spkg-install]           |                    ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp: At global scope:
[spkg-install]     sage/tests/stl_vector.cpp:6493:18: warning: 'PyObject* __pyx_pw_4sage_7cpython_6string_3str_to_bytes(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      6493 | static PyObject *__pyx_pw_4sage_7cpython_6string_3str_to_bytes(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:6240:18: warning: 'PyObject* __pyx_pw_4sage_7cpython_6string_1bytes_to_str(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      6240 | static PyObject *__pyx_pw_4sage_7cpython_6string_1bytes_to_str(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:5888:18: warning: 'PyObject* __pyx_pw_4sage_9structure_7richcmp_9revop(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      5888 | static PyObject *__pyx_pw_4sage_9structure_7richcmp_9revop(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:5712:18: warning: 'PyObject* __pyx_pw_4sage_9structure_7richcmp_7rich_to_bool_sgn(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      5712 | static PyObject *__pyx_pw_4sage_9structure_7richcmp_7rich_to_bool_sgn(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:5534:18: warning: 'PyObject* __pyx_pw_4sage_9structure_7richcmp_5rich_to_bool(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      5534 | static PyObject *__pyx_pw_4sage_9structure_7richcmp_5rich_to_bool(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:5291:18: warning: 'PyObject* __pyx_pw_4sage_9structure_7richcmp_3richcmp_not_equal(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      5291 | static PyObject *__pyx_pw_4sage_9structure_7richcmp_3richcmp_not_equal(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:5019:18: warning: 'PyObject* __pyx_pw_4sage_9structure_7richcmp_1richcmp(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      5019 | static PyObject *__pyx_pw_4sage_9structure_7richcmp_1richcmp(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:4756:18: warning: 'PyObject* __pyx_pw_4sage_9structure_7element_3have_same_parent(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      4756 | static PyObject *__pyx_pw_4sage_9structure_7element_3have_same_parent(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     sage/tests/stl_vector.cpp:4338:18: warning: 'PyObject* __pyx_pw_4sage_9structure_7element_1parent(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' defined but not used [-Wunused-function]
[spkg-install]      4338 | static PyObject *__pyx_pw_4sage_9structure_7element_1parent(PyObject *__pyx_self,
[spkg-install]           |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[spkg-install]     /home/bagas/miniconda3/envs/sagemath/bin/x86_64-conda-linux-gnu-c++ -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/bagas/miniconda3/envs/sagemath/lib -Wl,-rpath-link,/home/bagas/miniconda3/envs/sagemath/lib -L/home/bagas/miniconda3/envs/sagemath/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/bagas/miniconda3/envs/sagemath/lib -Wl,-rpath-link,/home/bagas/miniconda3/envs/sagemath/lib -L/home/bagas/miniconda3/envs/sagemath/lib -Wl,-rpath-link,/home/bagas/miniconda3/envs/sagemath/lib -L/home/bagas/miniconda3/envs/sagemath/lib -Wl,-rpath,/home/bagas/miniconda3/envs/sagemath/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/bagas/miniconda3/envs/sagemath/lib -Wl,-rpath-link,/home/bagas/miniconda3/envs/sagemath/lib -L/home/bagas/miniconda3/envs/sagemath/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bagas/miniconda3/envs/sagemath/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include build/temp.linux-x86_64-cpython-311/sage/tests/stl_vector.o -lgmp -o build/lib.linux-x86_64-cpython-311/sage/tests/stl_vector.cpython-311-x86_64-linux-gnu.so -lpari
[spkg-install]     error: command '/home/bagas/miniconda3/envs/sagemath/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
[spkg-install]     error: subprocess-exited-with-error
[spkg-install]     
[spkg-install]     × python setup.py develop did not run successfully.
[spkg-install]     │ exit code: 1
[spkg-install]     ╰─> See above for output.
[spkg-install]     
[spkg-install]     note: This error originates from a subprocess, and is likely not a problem with pip.
[spkg-install]     full command: /home/bagas/miniconda3/envs/sagemath/bin/python3 -c '
[spkg-install]     exec(compile('"'"''"'"''"'"'
[spkg-install]     # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
[spkg-install]     #
[spkg-install]     # - It imports setuptools before invoking setup.py, to enable projects that directly
[spkg-install]     #   import from `distutils.core` to work with newer packaging standards.
[spkg-install]     # - It provides a clear error message when setuptools is not installed.
[spkg-install]     # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
[spkg-install]     #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
[spkg-install]     #     manifest_maker: standard file '"'"'-c'"'"' not found".
[spkg-install]     # - It generates a shim setup.py, for handling setup.cfg-only projects.
[spkg-install]     import os, sys, tokenize
[spkg-install]     
[spkg-install]     try:
[spkg-install]         import setuptools
[spkg-install]     except ImportError as error:
[spkg-install]         print(
[spkg-install]             "ERROR: Can not execute `setup.py` since setuptools is not available in "
[spkg-install]             "the build environment.",
[spkg-install]             file=sys.stderr,
[spkg-install]         )
[spkg-install]         sys.exit(1)
[spkg-install]     
[spkg-install]     __file__ = %r
[spkg-install]     sys.argv[0] = __file__
[spkg-install]     
[spkg-install]     if os.path.exists(__file__):
[spkg-install]         filename = __file__
[spkg-install]         with tokenize.open(__file__) as f:
[spkg-install]             setup_py_code = f.read()
[spkg-install]     else:
[spkg-install]         filename = "<auto-generated setuptools caller>"
[spkg-install]         setup_py_code = "from setuptools import setup; setup()"
[spkg-install]     
[spkg-install]     exec(compile(setup_py_code, filename, "exec"))
[spkg-install]     '"'"''"'"''"'"' % ('"'"'/home/bagas/repo/sagemath/src/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' --no-user-cfg develop --no-deps
[spkg-install]     cwd: /home/bagas/repo/sagemath/src/
[spkg-install] error: subprocess-exited-with-error
[spkg-install] 
[spkg-install] × python setup.py develop did not run successfully.
[spkg-install] │ exit code: 1
[spkg-install] ╰─> See above for output.
[spkg-install] 
[spkg-install] note: This error originates from a subprocess, and is likely not a problem with pip.
[spkg-install] *************************************************************************************
[spkg-install] Error installing sagelib-10.4.beta6
[spkg-install] *************************************************************************************

It looks like this is build regression (last time I build sage is 10.4.beta3), but then I recreated conda env before building (thus with newer conda packages).

Checklist

• I have searched the existing issues for a bug report that matches the one I want to file, without success.
• I have read the documentation and troubleshoot guide

[mkoeppe]

The actual error from the log file:

[spkg-install]     building 'sage.matroids.graphic_matroid' extension
[spkg-install]     /home/bagas/miniconda3/envs/sagemath/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -fPIC -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bagas/miniconda3/envs/sagemath/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -fPIC -Isage/data_structures -Isage/cpython -I/home/bagas/miniconda3/envs/sagemath/lib/python3.11/site-packages/cysignals -I/home/bagas/repo/sagemath/src -I/home/bagas/miniconda3/envs/sagemath/lib/python3.11/site-packages/numpy/core/include -I/home/bagas/miniconda3/envs/sagemath/include/python3.11 -I/home/bagas/miniconda3/envs/sagemath/include/python3.11 -c sage/matroids/graphic_matroid.c -o build/temp.linux-x86_64-cpython-311/sage/matroids/graphic_matroid.o
[spkg-install]     sage/matroids/graphic_matroid.c: In function '__pyx_f_4sage_8matroids_15graphic_matroid_14GraphicMatroid__has_minor':
[spkg-install]     sage/matroids/graphic_matroid.c:23551:234: error: macro "minor" passed 3 arguments, but takes just 1

Fixed in:

• Avoid conflict with macro minor #38033

[bagasme]

The actual error from the log file:

[spkg-install]     building 'sage.matroids.graphic_matroid' extension
[spkg-install]     /home/bagas/miniconda3/envs/sagemath/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -fPIC -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bagas/miniconda3/envs/sagemath/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/bagas/miniconda3/envs/sagemath/include -fPIC -Isage/data_structures -Isage/cpython -I/home/bagas/miniconda3/envs/sagemath/lib/python3.11/site-packages/cysignals -I/home/bagas/repo/sagemath/src -I/home/bagas/miniconda3/envs/sagemath/lib/python3.11/site-packages/numpy/core/include -I/home/bagas/miniconda3/envs/sagemath/include/python3.11 -I/home/bagas/miniconda3/envs/sagemath/include/python3.11 -c sage/matroids/graphic_matroid.c -o build/temp.linux-x86_64-cpython-311/sage/matroids/graphic_matroid.o
[spkg-install]     sage/matroids/graphic_matroid.c: In function '__pyx_f_4sage_8matroids_15graphic_matroid_14GraphicMatroid__has_minor':
[spkg-install]     sage/matroids/graphic_matroid.c:23551:234: error: macro "minor" passed 3 arguments, but takes just 1

Fixed in:

* [Avoid conflict with macro `minor` #38033](https://github.com/sagemath/sage/pull/38033)

#38033 fixed the issue for me.