Note that I also have nothing with sage_setup, and the scripts are in the Sage's venv. You do have sage_setup, and your files are not in a Sage venv.
Seeing the output of ./config.status --config, and the contents of config.log, might help to understand more. On Sun, Mar 1, 2026 at 3:22 PM Dima Pasechnik <[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. 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/CAAWYfq0OZ9nyOFOZPfmaQ8gdZKN3yN1CfuKFx_orxSnQVD4gmA%40mail.gmail.com.
