Bug#984326: sagemath: ftbfs with GCC-11

Matthias Klose doko at debian.org
Wed Mar 3 16:17:12 GMT 2021


Package: src:sagemath
Version: 9.2-2
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11

[This bug is not targeted to the upcoming bullseye release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/sagemath_9.2-2_unstable_gcc11.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
[sagelib-9.2]  3545 | static char __pyx_doc_4sage_9structure_7element_parent[] = "parent(x)\nFile: sage/structure/element.pxd (starting at line 6)\n\n    Return the parent of the element ``x``.\n\n    Usually, this means the mathematical object of which ``x`` is an\n    element.\n\n    INPUT:\n\n    - ``x`` -- an element\n\n    OUTPUT:\n\n    - If ``x`` is a Sage :class:`Element`, return ``x.parent()``.\n\n    - Otherwise, return ``type(x)``.\n\n    .. SEEALSO::\n\n        `Parents, Conversion and Coercion <http://doc.sagemath.org/html/en/tutorial/tour_coercion.html>`_\n        Section in the Sage Tutorial\n\n    EXAMPLES::\n\n        sage: a = 42\n        sage: parent(a)\n        Integer Ring\n        sage: b = 42/1\n        sage: parent(b)\n        Rational Field\n        sage: c = 42.0\n        sage: parent(c)\n        Real Field with 53 bits of precision\n\n    Some more complicated examples::\n\n        sage: x = Partition([3,2,1,1,1])\n        sage: parent(x)\n        Partitions\n        sage: v = vector(RDF, [1,2,3])\n        sage: parent(v)\n        Vector space of dimension 3 over Real Double Field\n\n    The following are not considered to be elements, so the type is\n    returned::\n\n        sage: d = int(42)  # Python int\n        sage: parent(d)\n        <... 'int'>\n        sage: L = list(range(10))\n        sage: parent(L)\n        <... 'list'>\n    ";
[sagelib-9.2]       |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[sagelib-9.2] x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -L/<<PKGBUILDDIR>>/sage/local/lib -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/build/cythonized/sage/ext/interpreters/wrapper_cdf.o -o build/lib.linux-x86_64-3.9/sage/ext/interpreters/wrapper_cdf.cpython-39-x86_64-linux-gnu.so -lpari
[sagelib-9.2] [521/522] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/x86_64-linux-gnu/openblas-pthread/ -I/usr/lib/python3/dist-packages/cysignals -I/<<PKGBUILDDIR>>/sage/build/pkgs/sagelib/src -I/<<PKGBUILDDIR>>/sage/build/pkgs/sagelib/src/sage/ext -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -Ibuild/cythonized -I/<<PKGBUILDDIR>>/sage/local/include -I/usr/include/python3.9 -c build/cythonized/sage/ext/interpreters/wrapper_rdf.c -o build/temp.linux-x86_64-3.9/build/cythonized/sage/ext/interpreters/wrapper_rdf.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c99
[sagelib-9.2] x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -L/<<PKGBUILDDIR>>/sage/local/lib -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/build/cythonized/sage/ext/interpreters/wrapper_el.o -o build/lib.linux-x86_64-3.9/sage/ext/interpreters/wrapper_el.cpython-39-x86_64-linux-gnu.so -lpari
[sagelib-9.2] [522/522] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./sage/cpython -I/usr/lib/python3/dist-packages/cypari2 -I/usr/lib/python3/dist-packages/cysignals -I/<<PKGBUILDDIR>>/sage/build/pkgs/sagelib/src -I/<<PKGBUILDDIR>>/sage/build/pkgs/sagelib/src/sage/ext -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -Ibuild/cythonized -I/<<PKGBUILDDIR>>/sage/local/include -I/usr/include/python3.9 -c build/cythonized/sage/ext/interpreters/wrapper_cc.c -o build/temp.linux-x86_64-3.9/build/cythonized/sage/ext/interpreters/wrapper_cc.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c99
[sagelib-9.2] build/cythonized/sage/ext/interpreters/wrapper_cc.c:4671:18: warning: ‘__pyx_pw_4sage_9structure_7element_3have_same_parent’ defined but not used [-Wunused-function]
[sagelib-9.2]  4671 | static PyObject *__pyx_pw_4sage_9structure_7element_3have_same_parent(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
[sagelib-9.2]       |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[sagelib-9.2] build/cythonized/sage/ext/interpreters/wrapper_cc.c:4670:13: warning: ‘__pyx_doc_4sage_9structure_7element_2have_same_parent’ defined but not used [-Wunused-variable]
[sagelib-9.2]  4670 | static char __pyx_doc_4sage_9structure_7element_2have_same_parent[] = "have_same_parent(left, right) -> bool\nFile: sage/structure/element.pxd (starting at line 111)\n\n    Return ``True`` if and only if ``left`` and ``right`` have the\n    same parent.\n\n    .. WARNING::\n\n        This function assumes that at least one of the arguments is a\n        Sage :class:`Element`. When in doubt, use the slower\n        ``parent(left) is parent(right)`` instead.\n\n    EXAMPLES::\n\n        sage: from sage.structure.element import have_same_parent\n        sage: have_same_parent(1, 3)\n        True\n        sage: have_same_parent(1, 1/2)\n        False\n        sage: have_same_parent(gap(1), gap(1/2))\n        True\n\n    These have different types but the same parent::\n\n        sage: a = RLF(2)\n        sage: b = exp(a)\n        sage: type(a)\n        <... 'sage.rings.real_lazy.LazyWrapper'>\n        sage: type(b)\n        <... 'sage.rings.real_lazy.LazyNamedUnop'>\n        sage: have_same_parent(a, b)\n        True\n    ";
[sagelib-9.2]       |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[sagelib-9.2] build/cythonized/sage/ext/interpreters/wrapper_cc.c:4326:18: warning: ‘__pyx_pw_4sage_9structure_7element_1parent’ defined but not used [-Wunused-function]
[sagelib-9.2]  4326 | static PyObject *__pyx_pw_4sage_9structure_7element_1parent(PyObject *__pyx_self, PyObject *__pyx_v_x) {
[sagelib-9.2]       |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[sagelib-9.2] build/cythonized/sage/ext/interpreters/wrapper_cc.c:4325:13: warning: ‘__pyx_doc_4sage_9structure_7element_parent’ defined but not used [-Wunused-variable]
[sagelib-9.2]  4325 | static char __pyx_doc_4sage_9structure_7element_parent[] = "parent(x)\nFile: sage/structure/element.pxd (starting at line 6)\n\n    Return the parent of the element ``x``.\n\n    Usually, this means the mathematical object of which ``x`` is an\n    element.\n\n    INPUT:\n\n    - ``x`` -- an element\n\n    OUTPUT:\n\n    - If ``x`` is a Sage :class:`Element`, return ``x.parent()``.\n\n    - Otherwise, return ``type(x)``.\n\n    .. SEEALSO::\n\n        `Parents, Conversion and Coercion <http://doc.sagemath.org/html/en/tutorial/tour_coercion.html>`_\n        Section in the Sage Tutorial\n\n    EXAMPLES::\n\n        sage: a = 42\n        sage: parent(a)\n        Integer Ring\n        sage: b = 42/1\n        sage: parent(b)\n        Rational Field\n        sage: c = 42.0\n        sage: parent(c)\n        Real Field with 53 bits of precision\n\n    Some more complicated examples::\n\n        sage: x = Partition([3,2,1,1,1])\n        sage: parent(x)\n        Partitions\n        sage: v = vector(RDF, [1,2,3])\n        sage: parent(v)\n        Vector space of dimension 3 over Real Double Field\n\n    The following are not considered to be elements, so the type is\n    returned::\n\n        sage: d = int(42)  # Python int\n        sage: parent(d)\n        <... 'int'>\n        sage: L = list(range(10))\n        sage: parent(L)\n        <... 'list'>\n    ";
[sagelib-9.2]       |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[sagelib-9.2] x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -L/<<PKGBUILDDIR>>/sage/local/lib -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/build/cythonized/sage/ext/interpreters/wrapper_rdf.o -L/usr/lib/x86_64-linux-gnu/openblas-pthread/ -lgsl -lopenblas -lm -o build/lib.linux-x86_64-3.9/sage/ext/interpreters/wrapper_rdf.cpython-39-x86_64-linux-gnu.so -lpari
[sagelib-9.2] In function ‘__pyx_pf_4sage_3ext_12interpreters_10wrapper_cc_10Wrapper_cc_4__call__’,
[sagelib-9.2]     inlined from ‘__pyx_pw_4sage_3ext_12interpreters_10wrapper_cc_10Wrapper_cc_5__call__’ at build/cythonized/sage/ext/interpreters/wrapper_cc.c:4000:13:
[sagelib-9.2] build/cythonized/sage/ext/interpreters/wrapper_cc.c:4120:15: warning: ‘interp_cc’ accessing 64 bytes in a region of size 32 [-Wstringop-overflow=]
[sagelib-9.2]  4120 |   __pyx_t_2 = interp_cc(__pyx_v_c_args, ((__mpc_struct *)__pyx_v_retval->__pyx___re), __pyx_v_self->_constants, __pyx_v_self->_py_constants, __pyx_v_self->_stack, __pyx_v_self->_code, ((PyObject *)__pyx_v_self->_domain)); if (unlikely(__pyx_t_2 == ((int)0) && PyErr_Occurred())) __PYX_ERR(0, 114, __pyx_L1_error)
[sagelib-9.2]       |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[sagelib-9.2] build/cythonized/sage/ext/interpreters/wrapper_cc.c: In function ‘__pyx_pw_4sage_3ext_12interpreters_10wrapper_cc_10Wrapper_cc_5__call__’:
[sagelib-9.2] build/cythonized/sage/ext/interpreters/wrapper_cc.c:4120:15: note: referencing argument 2 of type ‘__mpc_struct *’
[sagelib-9.2] In file included from build/cythonized/sage/ext/interpreters/wrapper_cc.c:2980:
[sagelib-9.2] /<<PKGBUILDDIR>>/sage/build/pkgs/sagelib/src/sage/ext/interpreters/interp_cc.c:8:5: note: in a call to function ‘interp_cc’
[sagelib-9.2]     8 | int interp_cc(mpc_t* args,
[sagelib-9.2]       |     ^~~~~~~~~
[sagelib-9.2] x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -L/<<PKGBUILDDIR>>/sage/local/lib -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/build/cythonized/sage/ext/interpreters/wrapper_cc.o -lmpfr -lmpc -lgmp -o build/lib.linux-x86_64-3.9/sage/ext/interpreters/wrapper_cc.cpython-39-x86_64-linux-gnu.so -lpari
[sagelib-9.2] x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -L/<<PKGBUILDDIR>>/sage/local/lib -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/build/cythonized/sage/ext/interpreters/wrapper_rr.o -lmpfr -lgmp -o build/lib.linux-x86_64-3.9/sage/ext/interpreters/wrapper_rr.cpython-39-x86_64-linux-gnu.so -lpari
[sagelib-9.2] g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -L/<<PKGBUILDDIR>>/sage/local/lib -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/build/cythonized/sage/graphs/base/boost_graph.o -o build/lib.linux-x86_64-3.9/sage/graphs/base/boost_graph.cpython-39-x86_64-linux-gnu.so -lpari
[sagelib-9.2] error: command '/usr/bin/gcc' failed with exit code 1
[sagelib-9.2] 
[sagelib-9.2] real	33m26.828s
[sagelib-9.2] user	129m21.281s
[sagelib-9.2] sys	1m29.504s
make[8]: *** [Makefile:2163: sagelib-no-deps] Error 1
make[7]: *** [Makefile:2163: /<<PKGBUILDDIR>>/sage/local/var/lib/sage/installed/sagelib-9.2] Error 2
make[6]: *** [Makefile:1771: all-build] Error 2
make[6]: Leaving directory '/<<PKGBUILDDIR>>/sage/build/make'

real	33m30.916s
user	129m26.955s
sys	1m31.791s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-build'):

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[5]: *** [Makefile:33: all-build] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/sage'
make[4]: *** [Makefile:16: build] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/sage'
make[3]: *** [debian/rules:70: override_dh_auto_build-arch] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [debian/rules:40: build] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:40: install] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:40: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2



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