Using --enable-system-site-packages does change things. I still see the warning about the missing file. But now the file is actually missing, so I guess I can ignore the warning. That is progress.
The core problem I am seeing now is that the gap object is not working in 10.9beta7. This is definitely a regression from 10.8. With 10.8, using the identical build setup, I can do: sage: gap.FreeGroup(3) Group( [ f1, f2, f3 ] ) But with 10.9beta7 I get a RuntimeError: sage: gap.FreeGroup(3) -------------------------------------------------------------------------- - [ ,,, traceback details removed ...] RuntimeError: Gap produced error output Error, FreeGroup: function is not yet defined executing __SAGE_LAST__:="__SAGE_LAST__";;FreeGroup(\$sage1);; This is a problem with the GAP interface, not with GAP: $ sage/sage -gap ┌───────┐ GAP 4.14.0 of 2024-12-05 │ GAP │ https://www.gap-system.org └───────┘ Architecture: x86_64-pc-linux-gnu-default64-kv9 Configuration: gmp 6.3.0, GASMAN, readline Loading the library and packages ... Packages: GAPDoc 1.6.7, PrimGrp 3.4.4, SmallGrp 1.5.4, TransGrp 3.6.5 Try '??help' for help. See also '?copyright', '?cite' and '?authors' gap> F := FreeGroup(3); <free group on the generators [ f1, f2, f3 ]> gap> - Marc On Monday, March 2, 2026 at 9:10:34 AM UTC-6 Marc Culler wrote: > I colored that line red to make it easier for you to see that > * ./local/var/lib/sage/scripts/sagelib/spkg-requirements.txt* > is there in the list. > > OK. I will see what happens if I add that. I think that should only > change the pyvenv.cfg file. But you are probably trying to tell me that > the sage build system inspects the pyvenv.cfg file and makes different > decisions depending on what it finds there. > > My files are in a sage venv. However the sage venv is actually the same > as sage/local. > > Since I have to build my own python now, I simply install it in sage/local > before building sage. That worked fine for Sage 10.7 and 10.8. I think it > works fine with 10.9, as well. The only problem I am seeing is that I get > these weird reports of files not existing when in fact they do exist. The > resulting sage runs fine (unless I try to create a Gap FreeGroup). > > - Marc > > On Sunday, March 1, 2026 at 3:23:44 PM UTC-6 [email protected] wrote: > >> In my case these are the only packages installed by Sage, the rest come >> from the "system", via >> >> ./configure --enable-system-site-packages >> >> Why is there a red line below, is it a hanging link? >> >> >> >> On March 1, 2026 12:50:24 PM CST, Marc Culler <[email protected]> wrote: >> >>> I see: >>> >>> find . -name spkg-requirements.txt >>> ./local/var/lib/sage/scripts/comm/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pytest/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/distlib/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/ipykernel/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/filelock/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pybind11/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pathspec/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pure_eval/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/tornado/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pyproject_api/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/requests/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/gmpy2/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pyparsing/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/conway_polynomials/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pytz/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/virtualenv/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/primecountpy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/tzdata/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/wheel/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/asttokens/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/networkx/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/meson/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/ipywidgets/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pytz_deprecation_shim/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pexpect/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/memory_allocator/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pyproject_hooks/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pygments/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinxcontrib_htmlhelp/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sage_setup/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/exceptiongroup/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/py/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cython/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/entrypoints/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/flit_core/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/parso/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/debugpy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cachetools/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/tox/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinx_inline_tabs/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/contourpy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/hatch_vcs/spkg-requirements.txt >>> >>> ./local/var/lib/sage/scripts/sage_numerical_backends_coin/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sortedcontainers/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pytest_xdist/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/alabaster/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/roman_numerals/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pip/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/gast/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/decorator/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/python_build/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cffi/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cycler/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/idna/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/beautifulsoup4/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/markupsafe/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cvxopt/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pythran/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/attrs/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/jinja2/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/chardet/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pycparser/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cypari/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/trove_classifiers/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/snowballstemmer/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/imagesize/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/jedi/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/iniconfig/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pynormaliz/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pyzmq/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/docutils/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pycosat/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/furo/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/numpy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pyproject_metadata/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/packaging/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinx_copybutton/spkg-requirements.txt >>> *./local/var/lib/sage/scripts/sagelib/spkg-requirements.txt* >>> ./local/var/lib/sage/scripts/charset_normalizer/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/editables/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pkgconfig/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinxcontrib_jsmath/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinxcontrib_qthelp/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/colorama/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/setuptools/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/dateutil/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/lrcalc_python/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cppy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/fpylll/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/urllib3/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/prompt_toolkit/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/kiwisolver/spkg-requirements.txt >>> >>> ./local/var/lib/sage/scripts/sphinxcontrib_websupport/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/meson_python/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/beniget/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/mpmath/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sage_docbuild/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/setuptools_scm/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/fonttools/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinx/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/six/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/platformdirs/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/gnumake_tokenpool/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/calver/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/stack_data/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/appdirs/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/jupyterlab_widgets/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/wcwidth/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/hypothesis/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/widgetsnbextension/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/matplotlib/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sagetex/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/cysignals/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pyrsistent/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/matplotlib_inline/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/scipy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/soupsieve/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/traitlets/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/tzlocal/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pillow/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pplpy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sympy/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinxcontrib_devhelp/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pluggy/spkg-requirements.txt >>> >>> ./local/var/lib/sage/scripts/sphinxcontrib_applehelp/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/babel/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/nest_asyncio/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/ply/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/jupyter_core/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/execnet/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/ptyprocess/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pysingular/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pytest_mock/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/certifi/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/psutil/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/executing/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/pickleshare/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/sphinx_basic_ng/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/zipp/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/ipython_genutils/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/hatchling/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/hatch_readme/spkg-requirements.txt >>> >>> ./local/var/lib/sage/scripts/sphinxcontrib_serializinghtml/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/jupyter_client/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/p_group_cohomology/spkg-requirements.txt >>> ./local/var/lib/sage/scripts/ipython/spkg-requirements.txt >>> >>> On Sunday, March 1, 2026 at 12:00:05 PM UTC-6 [email protected] wrote: >>> >>>> Besides, sagelib doesn't have spkg-requirements.txt, nor it has >>>> any sage/scripts/sagelib/ >>>> You're doing something non-standard, and without full details it's hard >>>> to say anything meaningful. >>>> sagelib is a not like the rest of the packages, anyway. >>>> >>>> >>>> In my SAGEROOT I see >>>> >>>> $ find . -name spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/jupyter_events/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/gnumake_tokenpool/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/tzdata/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/nbconvert/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/overrides/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/jupyterlab_mathjax2/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/types_python_dateutil/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/jupyter_server/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/pickleshare/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/mpmath/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/jupyter_sphinx/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/sagetex/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/jupyterlab_server/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/jupyter_lsp/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/notebook_shim/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/pytz_deprecation_shim/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/jupyterlab/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/ipympl/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/notebook/spkg-requirements.txt >>>> >>>> ./local/var/lib/sage/venv-python3.13/var/lib/sage/scripts/sagenb_export/spkg-requirements.txt >>>> >>>> On Sun, Mar 1, 2026 at 11:25 AM Dima Pasechnik <[email protected]> >>>> wrote: >>>> >>>>> >>>>> >>>>> On Sun, Mar 1, 2026 at 11:19 AM Marc Culler <[email protected]> >>>>> wrote: >>>>> >>>>>> There is really only one file reported as >>>>>> missing:: sage/local/var/lib/sage/scripts/sagelib/spkg-requirements.txt. >>>>>> The other one is the directory containing that file. >>>>>> >>>>>> I did run ./bootstrap, of course. And it created the directory and >>>>>> the file. Moreover, both the directory and the file still exist and are >>>>>> both readable. >>>>>> >>>>> >>>>> Does /var/tmp/sage-10.9/local/var/lib/sage/scripts/sagelib exist? >>>>> (but you see "Directory >>>>> /var/tmp/sage-10.9/local/var/lib/sage/scripts/sagelib not found" ?) >>>>> >>>>> /var/tmp doesn't sound like something our build system uses normally. >>>>> IMHO all happens in SAGEROOT/build/sage-distro/ >>>>> >>>>> Dima >>>>> >>>>> >>>>> >>>>>> But if I verify that they exist, and then run make doc-html, it >>>>>> reports them both as missing. There is something wrong with the test. >>>>>> I >>>>>> wish I knew where the test was. >>>>>> >>>>>> - Marc >>>>>> >>>>>> >>>>>> >>>>>> On Saturday, February 28, 2026 at 2:21:55 PM UTC-6 [email protected] >>>>>> wrote: >>>>>> >>>>>>> some of these are generated by ./bootstrap >>>>>>> You need to run it either directly, or via make (the latter might be >>>>>>> flaky) >>>>>>> >>>>>>> >>>>>>> On February 28, 2026 1:08:10 PM CST, Marc Culler <[email protected]> >>>>>>> wrote: >>>>>>> >>>>>>>> I just tried make doc-html. I get: >>>>>>>> >>>>>>>> [sagelib-10.9.beta7] Warning: File >>>>>>>> /var/tmp/sage-10.9/local/var/lib/sage/scripts/sagelib/spkg-requirements.txt >>>>>>>> >>>>>>>> not found >>>>>>>> [sagelib-10.9.beta7] Warning: Directory >>>>>>>> /var/tmp/sage-10.9/local/var/lib/sage/scripts/sagelib not found >>>>>>>> [sagelib-10.9.beta7] Removing stamp file >>>>>>>> /var/tmp/sage-10.9/local/var/lib/sage/installed/sagelib-10.9.beta7 >>>>>>>> [sagelib-10.9.beta7] [spkg-install] Installing sagelib-10.9.beta7 >>>>>>>> [sagelib-10.9.beta7] [spkg-install] * Building wheel... >>>>>>>> >>>>>>>> Are the missing files in sage/scripts treated as missing >>>>>>>> dependencies? Why would they be missing? I did not delete them. >>>>>>>> >>>>>>>> - Marc >>>>>>>> >>>>>>>> On Sat, Feb 28, 2026 at 1:03 PM Dima Pasechnik <[email protected]> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> For me, >>>>>>>>> >>>>>>>>> make doc-html >>>>>>>>> >>>>>>>>> does the right thing, building html docs, without extra work >>>>>>>>> (after `make` is done). >>>>>>>>> If one needs the docs, it makes sense to run >>>>>>>>> the above straight away, it's a bit quicker, as it avoids extra >>>>>>>>> regeneration of docs ninja targets by meson. >>>>>>>>> >>>>>>>>> Dima >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On February 28, 2026 11:13:44 AM CST, Marc Culler < >>>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>>> When I build sage with make the last step is to build sagelib. >>>>>>>>>> If I then run >>>>>>>>>> make sagemath_doc_html >>>>>>>>>> it rebuilds the sagelib that it just finished building before >>>>>>>>>> starting to build the documentation. >>>>>>>>>> >>>>>>>>>> Why? >>>>>>>>>> >>>>>>>>>> - Marc >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>> You received this message because you are subscribed to a topic in >>>>>>>>> the Google Groups "sage-devel" group. >>>>>>>>> To unsubscribe from this topic, visit >>>>>>>>> https://groups.google.com/d/topic/sage-devel/dVVleHx0xP0/unsubscribe >>>>>>>>> . >>>>>>>>> To unsubscribe from this group and all its topics, send an email >>>>>>>>> to [email protected]. >>>>>>>>> To view this discussion visit >>>>>>>>> https://groups.google.com/d/msgid/sage-devel/FEA68B7E-8D2F-4957-A43A-D2FA9A0263BA%40gmail.com >>>>>>>>> >>>>>>>>> <https://groups.google.com/d/msgid/sage-devel/FEA68B7E-8D2F-4957-A43A-D2FA9A0263BA%40gmail.com?utm_medium=email&utm_source=footer> >>>>>>>>> . >>>>>>>>> >>>>>>>> -- >>>>>> >>>>> You received this message because you are subscribed to the Google >>>>>> Groups "sage-devel" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to [email protected]. >>>>>> To view this discussion visit >>>>>> https://groups.google.com/d/msgid/sage-devel/48b8a758-b896-40ca-ac56-6fccfcef31fcn%40googlegroups.com >>>>>> >>>>>> <https://groups.google.com/d/msgid/sage-devel/48b8a758-b896-40ca-ac56-6fccfcef31fcn%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>> . >>>>>> >>>>> -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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