Make step fails during installation due to certificate problem downloading Patch 2.7.6

[Mike Wirth]

 Just discovered SageMath.  Wonderful!  Did a PhD thesis fifty(!) years ago using MACSYMA over a dialup connection to a TIP and the ARPANET :-)  Great to see an alternative to Mathe$$$ica.
Installing on old MacBook Pro 11,3 (mid-2013) running Sonoma 15.2 (patched with OCLP 2.2.0).  Just upgraded my Python installation to 13.3.2, ran your source install with that in a venv. Fumbled along a bit, but made it through your configure steps.  But when a did a make, it failed while trying to download your patch2.7.6 (See log snippet below).  Complained about certificate issues.  Notes: 1. I do have a GitHub account, but that probably wasn't involved.  2. I did a fresh install of Python 13.3.2 from the official site, INCLUDING the post instal script to update certificates, but ended up not using that image and installed another copy using BREW which put the binary in a more useful place wrt macOS and ZShell.
TIA,
Mike (excited to get SageMath running)
PS: Presume my problem will be obvious to you, so only including a bit of the log.  Can easily send more or try alternative steps.
-------------------------
(pyvenv) mike@Mikes-MacBook-Pro-113 sage % make
make -j4 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: ***
ACLOCAL_PATH=
CPATH=/usr/local/opt/primesieve/include:/usr/local/opt/bdw-gc/include:/usr/local/opt/libpng/include:/usr/local/opt/polymake/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/primesieve/include:/usr/local/opt/bdw-gc/include:/usr/local/opt/libpng/include:/usr/local/opt/polymake/include:/usr/local/opt/ntl/include:/usr/local/opt/bzip2/include:/usr/local/opt/readline/include:/usr/local/include
CPPFLAGS=-I/usr/local/opt/openssl@3/include
CVXOPT_SUITESPARSE_INC_DIR=/usr/local/include/suitesparse
CVXOPT_SUITESPARSE_LIB_DIR=/usr/local/lib
GNUARMEMB_TOOLCHAIN_PATH=/opt/gnuarmemb
HOME=/Users/mike
LANG=en_US.UTF-8
LDFLAGS=-L/usr/local/opt/openssl@3/lib
LIBRARY_PATH=/usr/local/opt/primesieve/lib:/usr/local/opt/bdw-gc/lib:/usr/local/opt/libpng/lib:/usr/local/opt/polymake/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib:/usr/local/opt/primesieve/lib:/usr/local/opt/bdw-gc/lib:/usr/local/opt/libpng/lib:/usr/local/opt/polymake/lib:/usr/local/opt/ntl/lib:/usr/local/opt/bzip2/lib:/usr/local/opt/readline/lib:/usr/local/lib
LOGNAME=mike
MAKE=make -j4
MAKEFLAGS= V=1
MAKELEVEL=1
MANPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/share/man:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/usr/share/man:/Applications/Xcode.app/Contents/Developer/usr/share/man:/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/share/man:
MFLAGS=
OPENSSL_ROOT_DIR=/usr/local/opt/openssl@3
PATH=/Users/mike/sage/sage/build/bin:/Users/mike/sage/sage/src/bin:/Users/mike/sage/sage/local/bin:/usr/local/opt/polymake/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/polymake/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/Users/mike/.pyenv/shims:/usr/local/bin/:/Users/mike/Py3.13.2/pyvenv/bin:/usr/local/opt/openssl@3/bin:/usr/local/sbin:/usr/local/opt/ccache/libexec:/Library/Frameworks/Python.framework/Versions/3.13/bin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/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/Apple/usr/bin:/Library/TeX/texbin:/Applications/Wireshark.app/Contents/MacOS:/Applications/VMware Fusion.app/Contents/Public:/usr/local/go/bin:/Applications/Visual Studio Code.app/Contents/Resources/app/bin:/Users/mike/gn:/Users/mike/go/bin
PKG_CONFIG_PATH=/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/opt/openssl@3/lib/pkgconfig
PWD=/Users/mike/sage/sage/build/make
PYENV_ROOT=/Users/mike/.pyenv
PYENV_SHELL=zsh
PYTHONPATH=/Users/mike/sage/sage/local
SAGE_ENV_CONFIG_SOURCED=1
SAGE_LOCAL=/Users/mike/sage/sage/local
SAGE_LOGFILE=logs/install.log
SAGE_LOGS=/Users/mike/sage/sage/logs/pkgs
SAGE_NUM_THREADS=4
SAGE_NUM_THREADS_PARALLEL=4
SAGE_ORIG_PATH=/usr/local/opt/polymake/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/usr/local/opt/polymake/bin:/usr/local/opt/texinfo/bin:/usr/local/opt/bzip2/bin:/Users/mike/.pyenv/shims:/usr/local/bin/:/Users/mike/Py3.13.2/pyvenv/bin:/usr/local/opt/openssl@3/bin:/usr/local/sbin:/usr/local/opt/ccache/libexec:/Library/Frameworks/Python.framework/Versions/3.13/bin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/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/Apple/usr/bin:/Library/TeX/texbin:/Applications/Wireshark.app/Contents/MacOS:/Applications/VMware Fusion.app/Contents/Public:/usr/local/go/bin:/Applications/Visual Studio Code.app/Contents/Resources/app/bin:/Users/mike/gn:/Users/mike/go/bin
SAGE_ORIG_PATH_SET=True
SAGE_PKGCONFIG=/Users/mike/sage/sage/local/lib/pkgconfig
SAGE_ROOT=/Users/mike/sage/sage
SAGE_SHARE=/Users/mike/sage/sage/local/share
SAGE_SRC=/Users/mike/sage/sage/src
SHELL=/bin/zsh
SHLVL=5
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.IbtgscA1Gu/Listeners
SU2_RUN=/usr/local/bin/
TERM=xterm-256color
TERM_PROGRAM=Apple_Terminal
TERM_PROGRAM_VERSION=455
TERM_SESSION_ID=3A754BB4-4919-4FBE-BDC5-909053096A6F
TMPDIR=/var/folders/77/vchmhm_92yg2wyqntn6snjjh0000gp/T/
USER=mike
VIRTUAL_ENV=/Users/mike/Py3.13.2/pyvenv
VIRTUAL_ENV_PROMPT=pyvenv
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
ZEPHYR_TOOLCHAIN_VARIANT=gnuarmemb
ZPROFILETEST=was run
_=/usr/bin/env
__CFBundleIdentifier=com.apple.Terminal
__CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0
***********************************************
make --no-print-directory patch-SAGE_LOCAL-no-deps
[patch-2.7.6] Attempting to download package patch-2.7.6.tar.gz from mirrors
[patch-2.7.6] https://github.com/sagemath/sage/releases/download/10.6/patch-2.7.6.tar.gz
[patch-2.7.6] [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]
[patch-2.7.6] ERROR [transfer|run:135]: [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)
[patch-2.7.6] https://github.com/sagemath/sage/releases/download/10.5/patch-2.7.6.tar.gz
[patch-2.7.6] [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]
[patch-2.7.6] ERROR [transfer|run:135]: [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)
[patch-2.7.6] https://github.com/sagemath/sage/releases/download/10.4/patch-2.7.6.tar.gz
[patch-2.7.6] [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]
[patch-2.7.6] ERROR [transfer|run:135]: [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)
[patch-2.7.6] Downloading the Sage mirror list
[patch-2.7.6] CRITICAL [mirror_list|_refresh:238]: Downloading the mirror list failed, using cached version
[patch-2.7.6] Attempting to download from https://ftp.gnu.org/gnu/patch/patch-2.7.6.tar.gz
[patch-2.7.6] [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]
[patch-2.7.6] ERROR [transfer|run:135]: [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)
[patch-2.7.6] Traceback (most recent call last):
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1787, in open
[patch-2.7.6]     return getattr(self, name)(url)
[patch-2.7.6]            ^^^^^^^^^^^^^^^^^^^^^^^^
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1996, in open_https
[patch-2.7.6]     return self._open_generic_http(self._https_connection, url, data)
[patch-2.7.6]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1945, in _open_generic_http
[patch-2.7.6]     http_conn.request("GET", selector, headers=headers)
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1282, in request
[patch-2.7.6]     self._send_request(method, url, body, headers, encode_chunked)
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1328, in _send_request
[patch-2.7.6]     self.endheaders(body, encode_chunked=encode_chunked)
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1277, in endheaders
[patch-2.7.6]     self._send_output(message_body, encode_chunked=encode_chunked)
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1037, in _send_output
[patch-2.7.6]     self.send(msg)
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 975, in send
[patch-2.7.6]     self.connect()
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1454, in connect
[patch-2.7.6]     self.sock = self._context.wrap_socket(self.sock,
[patch-2.7.6]                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 517, in wrap_socket
[patch-2.7.6]     return self.sslsocket_class._create(
[patch-2.7.6]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1075, in _create
[patch-2.7.6]     self.do_handshake()
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1346, in do_handshake
[patch-2.7.6]     self._sslobj.do_handshake()
[patch-2.7.6] ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)
[patch-2.7.6]
[patch-2.7.6] The above exception was the direct cause of the following exception:
[patch-2.7.6]
[patch-2.7.6] Traceback (most recent call last):
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/tarball.py", line 185, in download
[patch-2.7.6]     Download(url, destination).run()
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/download/transfer.py", line 137, in run
[patch-2.7.6]     raise error
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/download/transfer.py", line 128, in run
[patch-2.7.6]     filename, info = opener.retrieve(
[patch-2.7.6]                      ^^^^^^^^^^^^^^^^
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1821, in retrieve
[patch-2.7.6]     fp = self.open(url, data)
[patch-2.7.6]          ^^^^^^^^^^^^^^^^^^^^
[patch-2.7.6]   File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1793, in open
[patch-2.7.6]     raise OSError('socket error', msg) from msg
[patch-2.7.6] OSError: [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)
[patch-2.7.6]
[patch-2.7.6] During handling of the above exception, another exception occurred:
[patch-2.7.6]
[patch-2.7.6] Traceback (most recent call last):
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/sage-package", line 40, in <module>
[patch-2.7.6]     run()
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/cmdline.py", line 538, in run
[patch-2.7.6]     app.download_cls(*args.package_class,
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/app.py", line 337, in download_cls
[patch-2.7.6]     pc.apply(download_with_args)
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/expand_class.py", line 126, in apply
[patch-2.7.6]     function(package_name, *args, **kwds)
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/app.py", line 329, in download_with_args
[patch-2.7.6]     self.download(package, allow_upstream=allow_upstream)
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/app.py", line 315, in download
[patch-2.7.6]     package.tarball.download(allow_upstream=allow_upstream)
[patch-2.7.6]   File "/Users/mike/sage/sage/build/bin/../sage_bootstrap/tarball.py", line 187, in download
[patch-2.7.6]     raise FileNotMirroredError('tarball does not exist on mirror network and neither at the upstream URL')
[patch-2.7.6] sage_bootstrap.tarball.FileNotMirroredError: tarball does not exist on mirror network and neither at the upstream URL
[patch-2.7.6] ************************************************************************
[patch-2.7.6] Error downloading tarball of patch
[patch-2.7.6] ************************************************************************
[patch-2.7.6] Please email sage-devel (http://groups.google.com/group/sage-devel)
[patch-2.7.6] explaining the problem and including the log files
[patch-2.7.6]   /Users/mike/sage/sage/logs/pkgs/patch-2.7.6.log
[patch-2.7.6] and
[patch-2.7.6]   /Users/mike/sage/sage/config.log
[patch-2.7.6] Describe your computer, operating system, etc.
[patch-2.7.6] ************************************************************************
make[2]: *** [patch-SAGE_LOCAL-no-deps] Error 1
make[1]: *** [/Users/mike/sage/sage/local/var/lib/sage/installed/patch-2.7.6] Error 2
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make base-toolchain'):

* package:         patch-2.7.6
  last build time: Feb 5 23:44
  log file:        /Users/mike/sage/sage/logs/pkgs/patch-2.7.6.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: *** [base-toolchain] Error 1
(pyvenv) mike@Mikes-MacBook-Pro-113 sage % 

[Dima Pasechnik]

Hi,

few thing you ought to consider with your setup.

We presently don't really support installing Sage in a venv

(this is being worked on, but it's far from being ready for general use)

Basically, Sage will create its own venv instead.

Then, we're not supporting Python 3.13 yet.

You can use 3.12 instead, then it will be used.

(and not built from sources, something which is broken on macOS a.t.m.)

It seems you're using Homebrew, no? You certainly don't need to build "patch" then,

just install a Homebrew patch.

The way to use it with as many packages it has, not only non-python ones,

is to run

source .homebrew-build-env # needed anyway

and run

./configure ---enable-system-site-packages # site is for Python packages in the env. of your python3

HTH

Dima

[Mike Wirth]

Thanks.  Will give it a try.

 Mike

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[Mike Wirth]

Thanks Guillermo and Dima for the quick responses.  I got SageMath up and running by:

1. Removing the duplicate Python 3.13.2 installation (downloaded from python.org)
2. Left the Python 3.13.2 installation done by pyenv in place.
3. Did an install of Python 3.12.9 with pyenv and made it global
4. Cleaned up my .zshrc and .zprofile files
5. Installing SageMath from the Mac binary

Now working through the tutorial (using source from the web docs and pasting into a new Jupyter notebook), finding an occasional issue, e.g.

latex(k)
\frac{36}{20 \, \sqrt{73} + 36 i \, \sqrt{3} + 27}

yields an "unexpected indent error", positioned after the i.  (Have to be careful copy-pasting the source to avoid syntactic issues.)

BTW, where is the "Tutorial" Jupyter notebook.  Docs say it should be under the Help menu command.  Not there.

Thanks again,

Mike

[Hilbert_not_Dilbert]

Good grief. Can’t we just get the usual .exe-installer download that nearly every other program on the planet offers?

There are already enough problems with SageMath to dissuade migration from Mathematica, etc. We shouldn’t also need a degree in CS to install the program.

Brent

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[Dima Pasechnik]

Of course if you have a few millions to donate to the project, we will be able to provide the users with the most beautiful installation experience, with visuals and music. After several years of work. The result will still have bugs, of course.

The follow-ups please to sage-...@googlegroups.com