Re: [sage-support] Sage 10.6 - Error during compilation: matplotlib/numpy incompatibility

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Dima Pasechnik

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Apr 24, 2025, 2:04:22 PMApr 24

to sage-support, sage-devel, sage-release, Tobias Diez, Volker Braun

Sage 10.6 was released with numpy 2.2.3, and matplotlib 3.8.0 from 2023, which is incompatible with numpy 2 (the compatibility was added in 3.8.4).

While 10.6.rc0 was released, this problem was noticed (see https://groups.google.com/g/sage-release/c/TkPM0xL2fFA/m/LB0dT9PLAwAJ)

but was not acted upon until 10.6 was out.

I have no idea how this could have happened (besides the lack of testing), and not enough eyes on these things. Volker, do you have an idea how it worked?

(I argued for years that PyPI packages are best pip-installed from PyPI, not with our poor effort to mimick PyPI and version resolving capabilities of PyPI, but I was always shouted down

by these who value status quo.)

Dima

On Thu, Apr 24, 2025 at 8:24 AM Topaze <topa...@gmail.com> wrote:

OK, so I started from scratch. I've got lots of disk space and memory, so I don't know why make stumbled. And twice in the same place, hence my report. But this time I managed to compile without any problem (did make -j 1 (parameter “1”, no more) help?). So compilation went smoothly the third time.
But now sage won't run, as you can see. And it's still something that involves numpy,.
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/home/mainuser/software/sage-10.6/bin/sage-venv-config:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('sagemath-standard==10.6')
Traceback (most recent call last):
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 656, in _build_master
ws.require(__requires__)
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1063, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 890, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 936, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 2.2.3 (/home/mainuser/software/sage-10.6/lib/python3.11/site-packages), Requirement.parse('numpy<2,>=1.21'), {'matplotlib'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/mainuser/software/sage-10.6/bin/sage-venv-config", line 4, in <module>
__import__('pkg_resources').require('sagemath-standard==10.6')
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 3656, in <module>
@_call_aside
^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 3640, in _call_aside
f(*args, **kwargs)
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 3669, in _initialize_master_working_set
working_set = _declare_state('object', 'working_set', WorkingSet._build_master())
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 658, in _build_master
return cls._build_from_requirements(__requires__)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 671, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 890, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 936, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 2.2.3 (/home/mainuser/software/sage-10.6/lib/python3.11/site-packages), Requirement.parse('numpy<2,>=1.21'), {'matplotlib'})
/home/mainuser/software/sage-10.6/bin/sage-notebook:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('sagemath-standard==10.6')
Traceback (most recent call last):
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 656, in _build_master
ws.require(__requires__)
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1063, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 890, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 936, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 2.2.3 (/home/mainuser/software/sage-10.6/lib/python3.11/site-packages), Requirement.parse('numpy<2,>=1.21'), {'matplotlib'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/mainuser/software/sage-10.6/bin/sage-notebook", line 4, in <module>
__import__('pkg_resources').require('sagemath-standard==10.6')
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 3656, in <module>
@_call_aside
^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 3640, in _call_aside
f(*args, **kwargs)
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 3669, in _initialize_master_working_set
working_set = _declare_state('object', 'working_set', WorkingSet._build_master())
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 658, in _build_master
return cls._build_from_requirements(__requires__)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 671, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 890, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/home/mainuser/software/sage-10.6/lib/python3.11/site-packages/pkg_resources/__init__.py", line 936, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 2.2.3 (/home/mainuser/software/sage-10.6/lib/python3.11/site-packages), Requirement.parse('numpy<2,>=1.21'), {'matplotlib'})

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