How do I report a bug in Sage 9.2 (app version) for macOS?

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Murray Eisenberg

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Nov 10, 2020, 10:46:13 AM11/10/20
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This concerns the missing openssl for python3, which prevents the jupyter server from starting under macOS Catalina 10.15.7.

How/where report this as a bug?

Samuel Lelievre

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Nov 10, 2020, 12:12:43 PM11/10/20
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2020-11-10 15:46:13 UTC, Murray Eisenberg:
The current licence of OpenSSL prevents us from shipping it.

OpenSSL is changing its licence starting with OpenSSL 3,
currently in alpha stage, with alpha8 recently released:


(see also this blog post about alpha7)


and the work needed before releasing beta1 is tracked at


Upgrading to OpenSSL 3 in Sage is tracked at

- Sage Trac ticket 29555
  Upgrade to OpenSSL 3.0 and make it a standard package
  https://trac.sagemath.org/ticket/29555

In the meanwhile, after downloading Sage binaries for macOS,
you can repair them using the "fix_mac_sage" script available at:

    https://github.com/3-manifolds/fix_mac_sage/

Hope this helps.  Kind regards,  --Samuel

Dima Pasechnik

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Nov 10, 2020, 12:13:53 PM11/10/20
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I can only lament about the sorry state of macOS binaries support for
9.2 on macOS 10.15.7.
I get

“python3.8” cannot be opened because the developer cannot be verified.

already in a terminal session.

What works for me, totally hassle-free, is Conda. See
https://doc.sagemath.org/html/en/installation/conda.html
TL; DR

1. install Miniconda (using a Python 3.8 installer from
https://docs.conda.io/en/latest/miniconda.html#macosx-installers )
1.1. Open a new Terminal. Conda should be active there (you'll see
(base) in the prompt)
2. conda install mamba -c conda-forge # installs mamba
3. mamba create -n sage sage -c conda-forge # replaces "conda create..."
4. conda activate sage
5. sage -n # launches a Jupyter
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Dima Pasechnik

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Nov 10, 2020, 12:15:26 PM11/10/20
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I'd just stop recommending the use of our macOS binaries until the
signing issue is solved.
Use Conda.

>
> Hope this helps. Kind regards, --Samuel
>
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Matthias Koeppe

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Nov 10, 2020, 1:11:38 PM11/10/20
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On Tuesday, November 10, 2020 at 9:15:26 AM UTC-8, Dima Pasechnik wrote:

I'd just stop recommending the use of our macOS binaries until the
signing issue is solved.
Use Conda.


+1. 

In fact, I would suggest that we stop publishing macOS binaries until then.






Murray Eisenberg

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Nov 10, 2020, 2:09:43 PM11/10/20
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I get an unexpected error doing that (with conda/anaconda already installed):

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 900, in exception_converter
        raise e
      File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 894, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 853, in _wrapped_main
        result = do_call(args, p)
      File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 741, in do_call
        exit_code = create(args, parser)
      File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 620, in create
        return install(args, parser, "create")
      File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py", line 570, in install
        downloaded = transaction.prompt(PackageCacheData.first_writable().pkgs_dir, repos)
    RuntimeError: Download error (6) Couldn't resolve host name [https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2]

`$ /opt/anaconda3/bin/mamba create -n sage sage -c conda-forge`

  environment variables:
                 CIO_TEST=<not set>
                CLASSPATH=:/Library/Java/Extensions/mysql-connector-java-
                          bin.jar:/Users/murray/Library/texmf/texhyphj
               CONDA_ROOT=/opt/anaconda3
           CURL_CA_BUNDLE=<not set>
              EVOLVERPATH=/Users/Shared/ApplicationDocs/Math/Evolver/fe:/Users/Shared/Applicatio
                          nDocs/Math/Evolver/doc
                 INFOPATH=/Applications/Macaulay2/Macaulay2-1.13/share/info
          LD_LIBRARY_PATH=/Applications/Macaulay2/Macaulay2-1.13/lib
                  MANPATH=/opt/local/share/man::/Applications/Macaulay2/Macaulay2-1.13/share/man
                     PATH=/Users/murray/.local/bin:/Users/murray/.elan/bin:/opt/anaconda3/bin:/o
                          pt/local/lib/mysql8/bin:/Library/TeX/texbin:/opt/local/bin:/opt/local/
                          sbin:/opt/local/apache2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sb
                          in:/Library/TeX/texbin:/usr/local/share/dotnet:/opt/local/bin:/opt/X11
                          /bin:~/.dotnet/tools:/Library/Apple/usr/bin:/Library/Frameworks/Mono.f
                          ramework/Versions/Current/Commands:/usr/local/sbin:/opt/local/Library/
                          Frameworks/Python.framework/Versions/3.8/lib:/Library/Frameworks/Pytho
                          n.framework/Versions/3.7/bin:/Library/Frameworks/Python.framework/Vers
                          ions/3.6/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Ap
                          plications/Postgres.app/Contents/Versions/latest/bin:/Users/murray/Lib
                          rary/Application Support/GoodSync:/Users/murray/bin:/Users/murray/bin/
                          shell:/Users/murray/bin/python:/Applications/Julia-1.5.app/Contents/Re
                          sources/julia/bin:/Applications/Math/Singular/Contents/bin:/Applicatio
                          ns/Math/Singular/Contents/bin/lib:/Library/PostgreSQL/12/bin:/Applicat
                          ions/Macaulay2/Macaulay2-1.13/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : None
       user config file : /Users/murray/.condarc
 populated config files : 
          conda version : 4.9.1
    conda-build version : 3.18.11
         python version : 3.8.3.final.0
       virtual packages : __osx=10.15.7=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/anaconda3/pkgs
                          /Users/murray/.conda/pkgs
       envs directories : /opt/anaconda3/envs
                          /Users/murray/.conda/envs
               platform : osx-64
             user-agent : conda/4.9.1 requests/2.24.0 CPython/3.8.3 Darwin/19.6.0 OSX/10.15.7
                UID:GID : 501:20
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

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Murray Eisenberg

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Nov 10, 2020, 2:09:50 PM11/10/20
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How does one use the conda binaries instead?

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Isuru Fernando

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Nov 10, 2020, 2:18:40 PM11/10/20
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Dima Pasechnik

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Nov 10, 2020, 2:19:07 PM11/10/20
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Anaconda is a different serpent :-)
I don't think it was tested, no idea if it would work.
If you install miniconda, it will go to /opt/miniconda3/ - so it's a
different tree.
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