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Support GCC 13 (fedora-38) #35092

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mkoeppe opened this issue Feb 12, 2023 · 14 comments
Closed
1 task done

Support GCC 13 (fedora-38) #35092

mkoeppe opened this issue Feb 12, 2023 · 14 comments

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@mkoeppe
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mkoeppe commented Feb 12, 2023

Is there an existing issue for this?

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

Problem Description

fedora-38 already ships GCC 13, which we reject.

Proposed Solution

Updated spkg-configure and hope that nothing needs changes.

Alternatives Considered

N/A

Additional Information

No response

@mkoeppe
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mkoeppe commented Feb 14, 2023

After allowing GCC 13, tox -e docker-fedora-38-minimal reveals:
Building zeromq fails:

  [zeromq-4.3.4]   In file included from /usr/include/c++/13/ext/alloc_traits.h:34,
  [zeromq-4.3.4]                    from /usr/include/c++/13/bits/stl_uninitialized.h:64,
  [zeromq-4.3.4]                    from /usr/include/c++/13/vector:65,
  [zeromq-4.3.4]                    from src/epoll.hpp:37,
  [zeromq-4.3.4]                    from src/poller.hpp:46,
  [zeromq-4.3.4]                    from src/io_object.hpp:36,
  [zeromq-4.3.4]                    from src/ws_engine.hpp:33,
  [zeromq-4.3.4]                    from src/ws_engine.cpp:59:
  [zeromq-4.3.4]   /usr/include/c++/13/bits/alloc_traits.h: In instantiation of 'struct std::__allocator_traits_base::__rebind<zmq::secure_allocator_t<unsigned char>, unsigned char, void>':
  [zeromq-4.3.4]   /usr/include/c++/13/bits/alloc_traits.h:94:11:   required by substitution of 'template<class _Alloc, class _Up> using std::__alloc_rebind = typename std::__allocator_traits_base::__rebind<_Alloc, _Up>::type [with _Alloc = zmq::secure_allocator_t<unsigned char>; _Up = unsigned char]'
  [zeromq-4.3.4]   /usr/include/c++/13/bits/alloc_traits.h:228:8:   required by substitution of 'template<class _Alloc> template<class _Tp> using std::allocator_traits< <template-parameter-1-1> >::rebind_alloc = std::__alloc_rebind<_Alloc, _Tp> [with _Tp = unsigned char; _Alloc = zmq::secure_allocator_t<unsigned char>]'
  [zeromq-4.3.4]   /usr/include/c++/13/ext/alloc_traits.h:126:65:   required from 'struct __gnu_cxx::__alloc_traits<zmq::secure_allocator_t<unsigned char>, unsigned char>::rebind<unsigned char>'
  [zeromq-4.3.4]   /usr/include/c++/13/bits/stl_vector.h:88:21:   required from 'struct std::_Vector_base<unsigned char, zmq::secure_allocator_t<unsigned char> >'
  [zeromq-4.3.4]   /usr/include/c++/13/bits/stl_vector.h:423:11:   required from 'class std::vector<unsigned char, zmq::secure_allocator_t<unsigned char> >'
  [zeromq-4.3.4]   src/curve_client_tools.hpp:64:76:   required from here
  [zeromq-4.3.4]   /usr/include/c++/13/bits/alloc_traits.h:70:31: error: static assertion failed: allocator_traits<A>::rebind_alloc<A::value_type> must be A
  [zeromq-4.3.4]      70 |                         _Tp>::value,
  [zeromq-4.3.4]         |                               ^~~~~
  [zeromq-4.3.4]   /usr/include/c++/13/bits/alloc_traits.h:70:31: note: 'std::integral_constant<bool, false>::value' evaluates to false
  [zeromq-4.3.4]   make[4]: *** [Makefile:6176: src/libzmq_la-ws_engine.lo] Error 1

@mkoeppe
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mkoeppe commented Feb 14, 2023

Also

[givaro-4.1.1] installing. Log file: /sage/logs/pkgs/givaro-4.1.1.log
  [givaro-4.1.1] error installing, exit status 1. End of log file:
  [givaro-4.1.1]      47 |         Degree& operator/=( const uint64_t& e) { _deg/=e; return *this; }
  [givaro-4.1.1]         |                                   ^~~~~~~~
  [givaro-4.1.1]   ./givaro/givdegree.h:47:35: note: 'uint64_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
  [givaro-4.1.1]   make[7]: *** [Makefile:467: givdegree.lo] Error 1
  [givaro-4.1.1]   make[7]: Target 'all' not remade because of errors.

@mkoeppe
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mkoeppe commented Feb 14, 2023

Also openblas build fails

make[4]: *** No rule to make target '../libopenblas_haswellp-r0.3.21.a', needed by '../libopenblas_haswellp-r0.3.21.so'.

but that looks more like a makefile concurrency bug

@mkoeppe mkoeppe added this to the sage-10.0 milestone Feb 14, 2023
@enriqueartal
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@mkoeppe
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mkoeppe commented Apr 1, 2023

Thanks for finding these! This looks like what we need.
The givaro link led me to https://src.fedoraproject.org/rpms/givaro/c/9af877e0232db5ca416e77ccd18068497241a5db?branch=rawhide

@mkoeppe
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mkoeppe commented Apr 10, 2023

Also libgd fails to build (it is not accepted from the system).

https://mirror.csclub.uwaterloo.ca/sage/spkg/upstream/libgd/libgd-2.3.2.tar.xz
[......................................................................]
libgd-2.3.2
====================================================
Setting up build directory for libgd-2.3.2
Finished extraction
No patch files found in ../patches
****************************************************
Host system:
Linux 7f0f1cb4e690 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/sage/local/libexec/gcc/x86_64-pc-linux-gnu/12.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ../src/configure --prefix=/sage/local --with-local-prefix=/sage/local --with-system-zlib --without-isl --disable-multilib --disable-nls --disable-libitm --enable-languages=c,c++,fortran   CXX=g++
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 12.2.0 (GCC) 
****************************************************
Package 'libgd' is currently not installed
Uninstalling 'libgd' with legacy uninstaller
rm: cannot remove '/sage/local/lib/libgd.*': No such file or directory
Error during uninstallation of 'libgd': Command '['/sage/build/pkgs/libgd/spkg-legacy-uninstall']' returned non-zero exit status 1.
Configuring libgd-2.3.2
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking the archiver (ar) interface... ar
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... ld
checking if the linker (ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3145728
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking whether ln -s works... yes
checking whether to support xpm... no
checking whether to support tiff... auto
checking for libtiff-4... yes
checking whether to support webp... auto
checking for libwebp... yes
checking whether to support heif... auto
checking for libheif >= 1.7.0... no
checking for heif_get_version in -lheif... no
configure: Disabling support for heif
checking whether to support avif... no
checking for simple visibility declarations... yes
checking whether we are building for a Win32 host... no
checking CFLAGS for maximum warnings... -Wall

** Configuration summary for libgd 2.3.2:

   Support for gd/gd2 images:        yes
   Support for Zlib:                 yes
   Support for PNG library:          yes
   Support for JPEG library:         no
   Support for WebP library:         yes
   Support for HEIF library:         no
   Support for AVIF library:         no
   Support for TIFF library:         yes
   Support for Freetype 2.x library: yes
   Support for Fontconfig library:   no
   Support for Xpm library:          no
   Support for liq library:          no
   Support for complex text:         no
   Support for pthreads:             yes

[...]
Building libgd-2.3.2
Making all in src
make  all-am
gcc -DHAVE_CONFIG_H -I.   -I/sage/local/include   -I/usr/include/libpng16  -I/sage/local/include -I/sage/local/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread     -I/usr/include/webp   -g -g -O2 -fvisibility=hidden -Wall -c -o gdcmpgif.o gdcmpgif.c
[...]
  [libgd-2.3.2]   /usr/bin/bash ../libtool  --tag=CC   --mode=link gcc  -g -g -O2 -fvisibility=hidden -Wall  -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib  -o giftogd2 giftogd2.o libgd.la  -lm  -L/sage/local/lib -lz   -lpng16 -lz  -L/sage/local/lib -lfreetype   -ltiff   -lwebp -lsharpyuv 
  [libgd-2.3.2]   libtool: link: gcc -g -g -O2 -fvisibility=hidden -Wall -Wl,-rpath-link -Wl,/sage/local/lib -Wl,-rpath -Wl,/sage/local/lib -Wl,-rpath-link -Wl,/sage/local/lib -Wl,-rpath -Wl,/sage/local/lib -o .libs/giftogd2 giftogd2.o  -L/sage/local/lib ./.libs/libgd.so -lm -lpng16 -lz -lfreetype -ltiff -lwebp -lsharpyuv -Wl,-rpath -Wl,/sage/local/lib
  [libgd-2.3.2]   /usr/bin/ld: /usr/lib64/libharfbuzz.so.0: undefined reference to `FT_Get_Transform'
  [libgd-2.3.2]   /usr/bin/ld: /usr/lib64/libharfbuzz.so.0: undefined reference to `FT_Get_Color_Glyph_Paint'
  [libgd-2.3.2]   /usr/bin/ld: /usr/lib64/libharfbuzz.so.0: undefined reference to `FT_Get_Color_Glyph_ClipBox'
  [libgd-2.3.2]   /usr/bin/ld: /usr/lib64/libharfbuzz.so.0: undefined reference to `FT_Get_Paint_Layers'
  [libgd-2.3.2]   /usr/bin/ld: /usr/lib64/libharfbuzz.so.0: undefined reference to `FT_Get_Colorline_Stops'
  [libgd-2.3.2]   /usr/bin/ld: /usr/lib64/libharfbuzz.so.0: undefined reference to `FT_Get_Paint'
  [libgd-2.3.2]   collect2: error: ld returned 1 exit status
  [libgd-2.3.2]   make[5]: *** [Makefile:859: giftogd2] Error 1
  [libgd-2.3.2]   make[5]: Target 'all-am' not remade because of errors.
  [libgd-2.3.2]   make[4]: *** [Makefile:644: all] Error 2
  [libgd-2.3.2]   Making all in config
  [libgd-2.3.2]   make[4]: Nothing to be done for 'all'.
  [libgd-2.3.2]   Making all in tests
  [libgd-2.3.2]   make[4]: Nothing to be done for 'all'.
  [libgd-2.3.2]   make[4]: Nothing to be done for 'all-am'.
  [libgd-2.3.2]   make[3]: *** [Makefile:426: all-recursive] Error 1
  [libgd-2.3.2]   make[3]: Target 'all' not remade because of errors.
  [libgd-2.3.2]   ********************************************************************************
  [libgd-2.3.2]   Error building libgd-2.3.2
  [libgd-2.3.2]   ********************************************************************************

@enriqueartal
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Fedora 38 uses libgd-2.3.3 (actually also Fedora 37)

@mkoeppe
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mkoeppe commented Apr 10, 2023

I'm already preparing an upgrade PR

@enriqueartal
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After upgrading to Fedora 38, an incremental building of the develop branch (actually one of my branches merged with develop) failed; though openblas was in the system it tried to compile with a failure libopenblas_atomp-r0.3.21.a] Bus error (core dumped). Actually it compiled gfortran 12; I changed to admit gfortran 13 with the same failure. After make distclean everything is fine, it took gfortran and openblas from the system

vbraun pushed a commit that referenced this issue Apr 28, 2023
    
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Part of the fix for #35092.
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URL: #35415
Reported by: Matthias Köppe
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@mkoeppe mkoeppe modified the milestones: sage-10.0, sage-10.1 May 20, 2023
vbraun pushed a commit that referenced this issue May 22, 2023
…pport

    
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Just released: https://github.com/4ti2/4ti2/releases/tag/Release_1_6_10,
with portability fixes, in particular for:
- #35092
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URL: #35570
Reported by: Matthias Köppe
Reviewer(s): Dima Pasechnik
@mkoeppe mkoeppe modified the milestones: sage-10.1, sage-10.2 Aug 20, 2023
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mkoeppe commented Sep 28, 2023

On fedora-38-minimal, openblas 0.3.23 still fails to build

 [openblas-0.3.23]   ar: ../libopenblasp-r0.3.23.a(dsyevd.o):2: unexpected character `\016' in S-record file
  [openblas-0.3.23]   bfd plugin: ../libopenblasp-r0.3.23.a: file too short
  [openblas-0.3.23]   ar: ../libopenblasp-r0.3.23.a(dsyevd.o):2: unexpected character `\016' in S-record file
  [openblas-0.3.23]   make[4]: warning: -j2 forced in submake: resetting jobserver mode.
  [openblas-0.3.23]   ./gensymbol linktest  x86_64 _ 0 0 0 0 0 0 "" "" 1 0 1 1 1 1 > linktest.c
  [openblas-0.3.23]   gcc -g -O2 -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=2 -DMAX_PARALLEL_NUMBER=1 -DUSE_TLS -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.23\" -UASMNAME -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I. -O2 -DSMALL_MATRIX_OPT -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=2 -DMAX_PARALLEL_NUMBER=1 -DUSE_TLS -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.23\" -UASMNAME -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I.. -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib  -shared -o ../libopenblasp-r0.3.23.so \
  [openblas-0.3.23]   -Wl,--whole-archive ../libopenblasp-r0.3.23.a -Wl,--no-whole-archive \
  [openblas-0.3.23]   -Wl,-soname,libopenblas.so.0 -lm -lpthread -lgfortran -lm -lpthread -lgfortran
  [openblas-0.3.23]   /usr/bin/ld: ../libopenblasp-r0.3.23.a: member ../libopenblasp-r0.3.23.a(saxpy.o) in archive is not an object
  [openblas-0.3.23]   collect2: error: ld returned 1 exit status
  [openblas-0.3.23]   make[4]: *** [Makefile:195: ../libopenblasp-r0.3.23.so] Error 1
  [openblas-0.3.23]   make[4]: Target 'so' not remade because of errors.
  [openblas-0.3.23]   make[3]: *** [Makefile:132: shared] Error 2

https://github.com/sagemath/sage/actions/runs/6207962004/job/16858997112

Same in fedora-39-minimal - https://github.com/sagemath/sage/actions/runs/6207962004/job/16858997196

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In Fedora 38, system openblas seems to work

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mkoeppe commented Sep 28, 2023

Yes, we know that it does. Above failure is for building the SPKG.

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mkoeppe commented Sep 29, 2023

I tried building 0.3.24, same result.
But it succeeded when I used MAKE="make -j1".
So there seems to a parallelization bug in the makefile

vbraun pushed a commit to vbraun/sage that referenced this issue Oct 1, 2023
    
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<!-- Why is this change required? What problem does it solve? -->
To fix build on fedora-39-minimal, archlinux-latest-{minimal,standard},
opensuse-tumbleweed-minimal - as seen in
https://github.com/scipopt/SCIP-SDP/actions/runs/5203680653
(scipopt/SCIP-SDP#6)

Tests at https://github.com/mkoeppe/SCIP-SDP/actions/runs/5298512526
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Part of:
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### ⌛ Dependencies

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- Depends on sagemath#35785 (merged here)

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URL: sagemath#35786
Reported by: Matthias Köppe
Reviewer(s): Dima Pasechnik
vbraun pushed a commit that referenced this issue Oct 8, 2023
    
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To fix build on fedora-39-minimal, archlinux-latest-{minimal,standard},
opensuse-tumbleweed-minimal - as seen in
https://github.com/scipopt/SCIP-SDP/actions/runs/5203680653
(scipopt/SCIP-SDP#6)

Tests at https://github.com/mkoeppe/SCIP-SDP/actions/runs/5298512526
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- Depends on #35785 (merged here)

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URL: #35786
Reported by: Matthias Köppe
Reviewer(s): Dima Pasechnik
vbraun pushed a commit to vbraun/sage that referenced this issue Nov 9, 2023
… out broken tests in setup

    
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Patches generated from
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- Fixes sagemath#36027
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URL: sagemath#36663
Reported by: Matthias Köppe
Reviewer(s): John H. Palmieri, Matthias Köppe
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mkoeppe commented Nov 19, 2023

With #36663 and #36712 merged, we can close it as completed.

@mkoeppe mkoeppe closed this as completed Nov 19, 2023
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