You'd apparently want to invoke ./configure in a different way:
./configure --with-python=python3.13
You instead used --with-system-python3, which, as you could see by
./configure -h | grep python3
does a different thing:
--with-system-python3={no|yes (default)|force (exit with an error if no
usable version is found)}
detect and use an existing system python3
As a result, Sage was unable to find a good Python to use, tried to build
its own, failed...
HTH
Dima
On Wed, Oct 22, 2025 at 2:08 PM 'David DeMark' via sage-support <
[email protected]> wrote:
> Hi all, reposting from sage-devel since I didn't get any responses there...
>
> Hi, I've run into some difficulty installing sage from source via cloning
> from github and following the installation guide in the readme.
> Specifically, when running make in step 14, I get a python error saying
> that the culprit is in sage_bootstrap/download/transfer.py in the
> line "opener = urllib.FancyURLopener()"
> Some cursory research indicates this might be a python2/python3 versioning
> issue?
>
> System info and terminal output below. Log files attached.
>
> System info:
> david@FD9N5QF71Y
> ----------------
> OS: macOS Sequoia 15.5 arm64
> Host: MacBook Air (M2, 2022)
> Kernel: Darwin 24.5.0
> Uptime: 3 days, 5 hours, 2 mins
> Packages: 200 (brew), 5 (brew-cask)
> Shell: zsh 5.9
> Display (Color LCD): 2940x1912 @ 2x in 14", 60]
> DE: Aqua
> WM: Quartz Compositor 278.4.7
> WM Theme: Multicolor (Dark)
> Font: .AppleSystemUIFont [System], Helvetica []
> Cursor: Fill - Black, Outline - White (32px)
> Terminal: tmux 3.5a
> CPU: Apple M2 (8) @ 3.50 GHz
> GPU: Apple M2 (8) @ 1.40 GHz [Integrated]
> Memory: 12.75 GiB / 16.00 GiB (80%)
> Swap: 1.58 GiB / 3.00 GiB (53%)
> Disk (/): 137.19 GiB / 228.27 GiB (60%)
> - apfs]
> Local IP (en0): 192.168.3.133/24
> Battery (bq40z651): 71% (9 hours, 20
> mins rema]
> Locale: en_US.UTF-8
>
>
> My terminal output from running make:
>
> david@FD9N5QF71Y sage % make
> /Library/Developer/CommandLineTools/usr/bin/make build/make/Makefile --stop
> make[1]: `build/make/Makefile' is up to date.
> build/bin/sage-logger \
> "cd build/make && ./install 'base-toolchain'"
> logs/install.log
> *** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
> __CF_USER_TEXT_ENCODING=0x1F5:0x0:0x0
> __CFBundleIdentifier=com.googlecode.iterm2
> _=/usr/bin/env
> ACLOCAL_PATH=
> COLORFGBG=15;0
> COLORTERM=truecolor
> COMMAND_MODE=unix2003
>
> CPATH=/opt/homebrew/opt/primesieve/include:/opt/homebrew/opt/bdw-gc/include:/opt/homebrew/opt/libpng/include:/opt/homebrew/opt/ntl/include:/opt/homebrew/opt/bzip2/include:/opt/homebrew/opt/readline/include:/opt/homebrew/include:/opt/homebrew/opt/primesieve/include:/opt/homebrew/opt/bdw-gc/include:/opt/homebrew/opt/libpng/include:/opt/homebrew/opt/ntl/include:/opt/homebrew/opt/bzip2/include:/opt/homebrew/opt/readline/include:/opt/homebrew/include
> CVXOPT_SUITESPARSE_INC_DIR=/opt/homebrew/include/suitesparse
> CVXOPT_SUITESPARSE_LIB_DIR=/opt/homebrew/lib
> DBUS_SESSION_BUS_ADDRESS=unix:path=
> HOME=/Users/david
> HOMEBREW_CELLAR=/opt/homebrew/Cellar
> HOMEBREW_PREFIX=/opt/homebrew
> HOMEBREW_REPOSITORY=/opt/homebrew
> INFOPATH=/opt/homebrew/share/info:/opt/homebrew/share/info:
> ITERM_PROFILE=Default
> ITERM_SESSION_ID=w0t0p0:D07654F1-4896-43C9-BD75-F26059297394
> LANG=en_US.UTF-8
> LC_TERMINAL_VERSION=3.6.1
> LC_TERMINAL=iTerm2
>
> LIBRARY_PATH=/opt/homebrew/opt/primesieve/lib:/opt/homebrew/opt/bdw-gc/lib:/opt/homebrew/opt/libpng/lib:/opt/homebrew/opt/ntl/lib:/opt/homebrew/opt/bzip2/lib:/opt/homebrew/opt/readline/lib:/opt/homebrew/lib:/opt/homebrew/opt/primesieve/lib:/opt/homebrew/opt/bdw-gc/lib:/opt/homebrew/opt/libpng/lib:/opt/homebrew/opt/ntl/lib:/opt/homebrew/opt/bzip2/lib:/opt/homebrew/opt/readline/lib:/opt/homebrew/lib
> LOGNAME=david
> MAKE=make
> MAKEFLAGS=l 8.5 - --jobserver-fds=3,4 -j V=1
> MAKELEVEL=1
>
> MANPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/share/man:/Library/Developer/CommandLineTools/usr/share/man:/Library/Developer/CommandLineTools/Toolchains/XcodeDefault.xctoolchain/usr/share/man:
> MFLAGS=-l 8.5 - --jobserver-fds=3,4 -j
> OLDPWD=/Users/david/sage/sage
>
> PATH=/Users/david/sage/sage/build/bin:/Users/david/sage/sage/src/bin:/Users/david/sage/sage/local/bin:/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/Applications/iTerm.app/Contents/Resources/utilities
>
> PKG_CONFIG_PATH=/opt/homebrew/opt/zlib/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/lib/pkgconfig:/opt/homebrew/opt/zlib/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/lib/pkgconfig:
> PWD=/Users/david/sage/sage/build/make
> PYTHONPATH=/Users/david/sage/sage/local
> SAGE_ENV_CONFIG_SOURCED=1
> SAGE_LOCAL=/Users/david/sage/sage/local
> SAGE_LOGFILE=logs/install.log
> SAGE_LOGS=/Users/david/sage/sage/logs/pkgs
> SAGE_NUM_THREADS_PARALLEL=2
> SAGE_NUM_THREADS=2
> SAGE_ORIG_PATH_SET=True
>
> SAGE_ORIG_PATH=/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/Applications/iTerm.app/Contents/Resources/utilities
> SAGE_PKGCONFIG=/Users/david/sage/sage/local/lib/pkgconfig
> SAGE_ROOT=/Users/david/sage/sage
> SAGE_SHARE=/Users/david/sage/sage/local/share
> SAGE_SRC=/Users/david/sage/sage/src
> SHELL=/bin/zsh
> SHLVL=6
> SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.UoD9uhnA7B/Listeners
> TERM_FEATURES=T3LrMSc7UUw9Ts3BFGsSyHNoSxF
> TERM_PROGRAM_VERSION=3.5a
> TERM_PROGRAM=tmux
> TERM_SESSION_ID=w0t0p0:D07654F1-4896-43C9-BD75-F26059297394
> TERM=tmux-256color
>
> TERMINFO_DIRS=/Applications/iTerm.app/Contents/Resources/terminfo:/usr/share/terminfo
> TMPDIR=/var/folders/sl/5g495s_91f3cbgpsj72ct9d00000gn/T/
> TMUX_PANE=%8
> TMUX=/private/tmp/tmux-501/default,1487,0
> USER=david
> XPC_FLAGS=0x0
> XPC_SERVICE_NAME=0
> ***********************************************
> make --no-print-directory toolchain
> make[2]: Nothing to be done for `toolchain'.
> Sage build/upgrade complete!
> /Library/Developer/CommandLineTools/usr/bin/make all-start
> /Library/Developer/CommandLineTools/usr/bin/make build/make/Makefile --stop
> make[2]: `build/make/Makefile' is up to date.
> build/bin/sage-logger \
> "cd build/make && ./install 'all-start'" logs/install.log
> *** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
> __CF_USER_TEXT_ENCODING=0x1F5:0x0:0x0
> __CFBundleIdentifier=com.googlecode.iterm2
> _=/usr/bin/env
> ACLOCAL_PATH=
> COLORFGBG=15;0
> COLORTERM=truecolor
> COMMAND_MODE=unix2003
>
> CPATH=/opt/homebrew/opt/primesieve/include:/opt/homebrew/opt/bdw-gc/include:/opt/homebrew/opt/libpng/include:/opt/homebrew/opt/ntl/include:/opt/homebrew/opt/bzip2/include:/opt/homebrew/opt/readline/include:/opt/homebrew/include:/opt/homebrew/opt/primesieve/include:/opt/homebrew/opt/bdw-gc/include:/opt/homebrew/opt/libpng/include:/opt/homebrew/opt/ntl/include:/opt/homebrew/opt/bzip2/include:/opt/homebrew/opt/readline/include:/opt/homebrew/include
> CVXOPT_SUITESPARSE_INC_DIR=/opt/homebrew/include/suitesparse
> CVXOPT_SUITESPARSE_LIB_DIR=/opt/homebrew/lib
> DBUS_SESSION_BUS_ADDRESS=unix:path=
> HOME=/Users/david
> HOMEBREW_CELLAR=/opt/homebrew/Cellar
> HOMEBREW_PREFIX=/opt/homebrew
> HOMEBREW_REPOSITORY=/opt/homebrew
> INFOPATH=/opt/homebrew/share/info:/opt/homebrew/share/info:
> ITERM_PROFILE=Default
> ITERM_SESSION_ID=w0t0p0:D07654F1-4896-43C9-BD75-F26059297394
> LANG=en_US.UTF-8
> LC_TERMINAL_VERSION=3.6.1
> LC_TERMINAL=iTerm2
>
> LIBRARY_PATH=/opt/homebrew/opt/primesieve/lib:/opt/homebrew/opt/bdw-gc/lib:/opt/homebrew/opt/libpng/lib:/opt/homebrew/opt/ntl/lib:/opt/homebrew/opt/bzip2/lib:/opt/homebrew/opt/readline/lib:/opt/homebrew/lib:/opt/homebrew/opt/primesieve/lib:/opt/homebrew/opt/bdw-gc/lib:/opt/homebrew/opt/libpng/lib:/opt/homebrew/opt/ntl/lib:/opt/homebrew/opt/bzip2/lib:/opt/homebrew/opt/readline/lib:/opt/homebrew/lib
> LOGNAME=david
> MAKE=make
> MAKEFLAGS=l 8.5 - --jobserver-fds=3,4 -j V=1
> MAKELEVEL=2
>
> MANPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/share/man:/Library/Developer/CommandLineTools/usr/share/man:/Library/Developer/CommandLineTools/Toolchains/XcodeDefault.xctoolchain/usr/share/man:
> MFLAGS=-l 8.5 - --jobserver-fds=3,4 -j
> OLDPWD=/Users/david/sage/sage
>
> PATH=/Users/david/sage/sage/build/bin:/Users/david/sage/sage/src/bin:/Users/david/sage/sage/local/bin:/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/Applications/iTerm.app/Contents/Resources/utilities
>
> PKG_CONFIG_PATH=/opt/homebrew/opt/zlib/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/lib/pkgconfig:/opt/homebrew/opt/zlib/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/lib/pkgconfig:
> PWD=/Users/david/sage/sage/build/make
> PYTHONPATH=/Users/david/sage/sage/local
> SAGE_ENV_CONFIG_SOURCED=1
> SAGE_LOCAL=/Users/david/sage/sage/local
> SAGE_LOGFILE=logs/install.log
> SAGE_LOGS=/Users/david/sage/sage/logs/pkgs
> SAGE_NUM_THREADS_PARALLEL=2
> SAGE_NUM_THREADS=2
> SAGE_ORIG_PATH_SET=True
>
> SAGE_ORIG_PATH=/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/opt/texinfo/bin:/opt/homebrew/opt/bzip2/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/Applications/iTerm.app/Contents/Resources/utilities
> SAGE_PKGCONFIG=/Users/david/sage/sage/local/lib/pkgconfig
> SAGE_ROOT=/Users/david/sage/sage
> SAGE_SHARE=/Users/david/sage/sage/local/share
> SAGE_SRC=/Users/david/sage/sage/src
> SHELL=/bin/zsh
> SHLVL=6
> SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.UoD9uhnA7B/Listeners
> TERM_FEATURES=T3LrMSc7UUw9Ts3BFGsSyHNoSxF
> TERM_PROGRAM_VERSION=3.5a
> TERM_PROGRAM=tmux
> TERM_SESSION_ID=w0t0p0:D07654F1-4896-43C9-BD75-F26059297394
> TERM=tmux-256color
>
> TERMINFO_DIRS=/Applications/iTerm.app/Contents/Resources/terminfo:/usr/share/terminfo
> TMPDIR=/var/folders/sl/5g495s_91f3cbgpsj72ct9d00000gn/T/
> TMUX_PANE=%8
> TMUX=/private/tmp/tmux-501/default,1487,0
> USER=david
> XPC_FLAGS=0x0
> XPC_SERVICE_NAME=0
> ***********************************************
> make --no-print-directory
> /Users/david/sage/sage/local/var/lib/sage/installed/.dummy
> make[3]: `/Users/david/sage/sage/local/var/lib/sage/installed/.dummy' is
> up to date.
> make --no-print-directory
> /Users/david/sage/sage/local/var/lib/sage/installed/.dummy
> make[3]: `/Users/david/sage/sage/local/var/lib/sage/installed/.dummy' is
> up to date.
> make --no-print-directory
> /Users/david/sage/sage/local/var/lib/sage/installed/.dummy
> make[3]: `/Users/david/sage/sage/local/var/lib/sage/installed/.dummy' is
> up to date.
> make --no-print-directory
> /Users/david/sage/sage/local/var/lib/sage/installed/.dummy
> make[3]: `/Users/david/sage/sage/local/var/lib/sage/installed/.dummy' is
> up to date.
> make --no-print-directory all-sage-docs all-sage
> make --no-print-directory python3-SAGE_VENV-no-deps
> if [ -d '/Users/david/sage/sage/local/var/lib/sage/venv-python3.12.5' ];
> then sage-spkg-uninstall setuptools
> '/Users/david/sage/sage/local/var/lib/sage/venv-python3.12.5'; fi
> [python3-3.12.5] Attempting to download package Python-3.12.5.tar.xz from
> mirrors
> [python3-3.12.5]
> https://github.com/sagemath/sage/releases/download/10.7/Python-3.12.5.tar.xz
> [python3-3.12.5] Traceback (most recent call last):
> [python3-3.12.5] File "/Users/david/sage/sage/build/bin/sage-package",
> line 40, in <module>
> [python3-3.12.5] run()
> [python3-3.12.5] ~~~^^
> [python3-3.12.5] File
> "/Users/david/sage/sage/build/bin/../sage_bootstrap/cmdline.py", line 538,
> in run
> [python3-3.12.5] app.download_cls(*args.package_class,
> [python3-3.12.5] ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] has_files=args.has_files,
> no_files=args.no_files,
> [python3-3.12.5]
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] exclude=args.exclude,
> [python3-3.12.5] ^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] allow_upstream=args.allow_upstream,
> [python3-3.12.5] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] on_error=args.on_error)
> [python3-3.12.5] ^^^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] File
> "/Users/david/sage/sage/build/bin/../sage_bootstrap/app.py", line 337, in
> download_cls
> [python3-3.12.5] pc.apply(download_with_args)
> [python3-3.12.5] ~~~~~~~~^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] File
> "/Users/david/sage/sage/build/bin/../sage_bootstrap/expand_class.py", line
> 126, in apply
> [python3-3.12.5] function(package_name, *args, **kwds)
> [python3-3.12.5] ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] File
> "/Users/david/sage/sage/build/bin/../sage_bootstrap/app.py", line 329, in
> download_with_args
> [python3-3.12.5] self.download(package, allow_upstream=allow_upstream)
> [python3-3.12.5] ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] File
> "/Users/david/sage/sage/build/bin/../sage_bootstrap/app.py", line 315, in
> download
> [python3-3.12.5]
> package.tarball.download(allow_upstream=allow_upstream)
> [python3-3.12.5]
> ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] File
> "/Users/david/sage/sage/build/bin/../sage_bootstrap/tarball.py", line 175,
> in download
> [python3-3.12.5] Download(url, destination).run()
> [python3-3.12.5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
> [python3-3.12.5] File
> "/Users/david/sage/sage/build/bin/../sage_bootstrap/download/transfer.py",
> line 123, in run
> [python3-3.12.5] opener = urllib.FancyURLopener()
> [python3-3.12.5] ^^^^^^^^^^^^^^^^^^^^^
> [python3-3.12.5] AttributeError: module 'urllib.request' has no attribute
> 'FancyURLopener'
> [python3-3.12.5]
> ************************************************************************
> [python3-3.12.5] Error downloading tarball of python3
> [python3-3.12.5]
> ************************************************************************
> [python3-3.12.5] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
> [python3-3.12.5] explaining the problem and including the log files
> [python3-3.12.5] /Users/david/sage/sage/logs/pkgs/python3-3.12.5.log
> [python3-3.12.5] and
> [python3-3.12.5] /Users/david/sage/sage/config.log
> [python3-3.12.5] Describe your computer, operating system, etc.
> [python3-3.12.5]
> ************************************************************************
> make[4]: *** [python3-SAGE_VENV-no-deps] Error 1
> make[3]: ***
> [/Users/david/sage/sage/local/var/lib/sage/venv-python3.12.5/var/lib/sage/installed/python3-3.12.5]
> Error 2
> make[2]: *** [all-start] Error 2
> ***************************************************************
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> * package: python3-3.12.5
> last build time: Oct 18 22:52
> log file: /Users/david/sage/sage/logs/pkgs/python3-3.12.5.log
>
> 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[1]: *** [all-start] Error 1
> make: *** [all] Error 2
>
> --
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