Jupiter Server fails to start on macOS Catalina

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Eric Martin

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Jan 6, 2020, 5:04:35 AM1/6/20
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After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking the Sage icon immediately results in a window popping up with the message: "Jupiter Server fails to start. For some reason the Jupiter server ailed to start. Please check the log for clues, and have that information handy when asking for help." The log shows:

Rewriting paths for your new installation directory
===================================================

This might take a few minutes but only has to be done once.

patching /Applications/SageMath-9.0.app/Contents/Resources/sage/build/make/Makefile-auto
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/config.status
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/2to3-3.7
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ESingular
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/NRswitchg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/QuadraticSieve
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/R
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Rscript
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Singular
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/TSingular
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/addedgeg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency_gmp
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces_gmp
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/amtog
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/annotate
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/biplabg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cas_help
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/catg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec_gmp
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cl
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/complg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/converseg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/copyg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/countg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cu2
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubex
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubhamg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/curve_keygen
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cygdb
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cysignals-CSI
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cython
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cythonize
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/deledgeg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/delptg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/directg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dreadnaut
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretodot
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretog
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install-3.7
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl-config
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecm
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/f2py
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/f2py3
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/f2py3.7
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fai
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fflas-ffpack-config
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fourier
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fourier_gmp
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fplll
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/freetype-config
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/futurize
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gac
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gac-e
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gap-bin
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gcc-ar
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gcc-nm
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gcc-ranlib
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gcov
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gcov-dump
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gcov-tool
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gd2copypal
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gd2togif
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gd2topng
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gdcmpgif
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gdlib-config
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gdparttopng
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gdtopng
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/genbg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/genbgL
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/geng
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/genquarticg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/genrang
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/genspecialg
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gentourng
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gfan
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gfortran
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/giftogd2
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/givaro-config
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/givaro-makefile
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/glpsol
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gp-2.11
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gphelp
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gsl-config
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gsl-histogram
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/gsl-randist
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/hamheuristic
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/hevea2mml
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/icas
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/idle3.7
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/iptest
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/iptest3
patching /Applications/SageMath-9.0.app/Contents/Resources/sa

(Indeed, log ends in "patching /Applications/SageMath-9.0.app/Contents/Resources/sa").

Ralph Martin

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Jan 6, 2020, 7:18:30 AM1/6/20
to sage-support
I confirm that Jupyter does not start. My log shows the following output

[I 18:14:07.652 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
[I 18:14:07.842 NotebookApp] Serving notebooks from local directory: /Users/ralph/Documents/Sage Jupyter Notebooks
[I 18:14:07.842 NotebookApp] The Jupyter Notebook is running at:
[I 18:14:07.843 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 18:14:07.847 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///Users/ralph/Library/Jupyter/runtime/nbserver-11902-open.html
    Or copy and paste one of these URLs:
[I 18:14:24.013 NotebookApp] Creating new notebook in 
[I 18:14:24.692 NotebookApp] Kernel started: 35543d18-9b4d-44d6-9234-fde888a4951e
[I 18:14:26.123 NotebookApp] Adapting to protocol v5.1 for kernel 35543d18-9b4d-44d6-9234-fde888a4951e
[I 18:15:11.689 NotebookApp] Saving file at /Untitled.ipynb
[I 18:15:48.066 NotebookApp] Starting buffering for 35543d18-9b4d-44d6-9234-fde888a4951e:08c6751af6b3477893d056fe2cc9c4c7
[I 18:15:48.379 NotebookApp] Kernel shutdown: 35543d18-9b4d-44d6-9234-fde888a4951e
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted

Dima Pasechnik

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Jan 6, 2020, 7:23:52 AM1/6/20
to sage-support


On Mon, 6 Jan 2020, 13:18 Ralph Martin, <ralphr...@gmail.com> wrote:
I confirm that Jupyter does not start. My log shows the following output

[I 18:14:07.652 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
[I 18:14:07.842 NotebookApp] Serving notebooks from local directory: /Users/ralph/Documents/Sage Jupyter Notebooks
[I 18:14:07.842 NotebookApp] The Jupyter Notebook is running at:
[I 18:14:07.843 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 18:14:07.847 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///Users/ralph/Library/Jupyter/runtime/nbserver-11902-open.html
    Or copy and paste one of these URLs:

does this URL work?

[I 18:14:24.013 NotebookApp] Creating new notebook in 
[I 18:14:24.692 NotebookApp] Kernel started: 35543d18-9b4d-44d6-9234-fde888a4951e
[I 18:14:26.123 NotebookApp] Adapting to protocol v5.1 for kernel 35543d18-9b4d-44d6-9234-fde888a4951e
[I 18:15:11.689 NotebookApp] Saving file at /Untitled.ipynb
[I 18:15:48.066 NotebookApp] Starting buffering for 35543d18-9b4d-44d6-9234-fde888a4951e:08c6751af6b3477893d056fe2cc9c4c7
[I 18:15:48.379 NotebookApp] Kernel shutdown: 35543d18-9b4d-44d6-9234-fde888a4951e
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted

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slelievre

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Jan 6, 2020, 8:44:19 AM1/6/20
to sage-support

Mon 2020-01-06 10:04:35 UTC, Eric Martin:
After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking
the Sage icon immediately results in a window popping up with the message:
"Jupiter Server fails to start. For some reason the Jupiter server ailed to start.
[...]

Try running the following commands in a terminal:
    
    APP=/Applications/SageMath-9.0.app
    xattr -dr com.apple.quarantine $APP

If it says you don't have the permissions for that,
try the same with "sudo" as follows:

    APP=/Applications/SageMath-9.0.app
    sudo xattr -dr com.apple.quarantine $APP

Murray Eisenberg

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Jan 6, 2020, 10:07:35 AM1/6/20
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I separately reported the same behavior -- the Jupyter server not starting with SageMath-9.0 -- and so tried the suggestion of 

APP=/Applications/SageMath-9.0.app 

xattr -dr com.apple.quarantine $APP


reportedthe latter both as shown and with "sudo". 


This does not fix the problem!

Ralph Martin

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Jan 6, 2020, 12:03:02 PM1/6/20
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I also gave Sage Full Disk Access (in Security -> Privacy preference pane), as well as using xattr, as it seemed unable to access certain directories.
 
Sage now does start Jupyter.

Eric Martin

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Jan 6, 2020, 1:13:50 PM1/6/20
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Same behaviour, with the same log, also after giving Sage Full Disk Access as suggested by Ralf Martin.

Murray Eisenberg

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Jan 6, 2020, 2:35:25 PM1/6/20
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Giving SageMath-9.0 full disk access works for me, too.

It seems like a rather blunt solution for getting around Catalina's increased security!

Is it full disk access that's really required? Or just the ability to launch a terminal process?


On Monday, January 6, 2020 at 5:04:35 AM UTC-5, Eric Martin wrote:

Stefano Brocco

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Jan 6, 2020, 4:35:46 PM1/6/20
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Same as Martin for me too...

Stefano Brocco

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Jan 6, 2020, 5:01:33 PM1/6/20
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There is more to it: after doing all of the above, plus removing both ~/.sage and org.sagemath.Sage.plist, the jupyter did start. Unfortunately I don't know if the critical step in my case was the removal of ~/.sage or of the plist file.


On Monday, January 6, 2020 at 1:13:50 PM UTC-5, Eric Martin wrote:

Eric Martin

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Jan 6, 2020, 5:14:45 PM1/6/20
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I did not have ~/.sage. Removed org.sagemath.Sage.plist, but no difference for me.

Jinsong Xu

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Feb 16, 2020, 4:30:43 PM2/16/20
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I have the same problem and log as Martin. After giving Sage Full Disk Access as well as using xattr and sudo, it still does work.

Is there any other way to launch it?

Dima Pasechnik

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Feb 16, 2020, 5:18:25 PM2/16/20
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maybe trying the terminal version:
http://www.mirrorservice.org/sites/www.sagemath.org/osx/intel/sage-9.0-OSX_10.15.2-x86_64.tar.bz2

is a better idea. After the installation, one can
run, in terminal, in the place where you have it installed,

./sage -n

to launch Jupyter
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Dan Brooks

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Apr 5, 2020, 6:01:56 PM4/5/20
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I had the same problem as the OP. Jupyter Server would not start after install of the .app.dmg package. 

I can report success launching Sage from the Applications icon after the following steps:

1) Grant Full Disk Access in System Preferences->Security->Privacy (as suggested previously)

2) Launch Sage from the command line in the executable's installed directory. In a terminal window:

cd /Applications/SageMath-9.0.app
./sage -n



3) The executable should "patch" or rewrite all of the required paths to match their actual locations in your particular Catalina install. 
    After that, it should open a Jupyter tab in Safari.

4) When you see the Jupyter tab in Safari: 
     click the Quit button. This will stop the Jupyter Server, but that's ok. 

5) Launch Sage using Applications->SageMath-9.0. 

All should be well at this point, but your actual mileage may vary. Hope this helps. 

G C

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May 27, 2020, 4:27:26 AM5/27/20
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I had the same problems and it worked only after following Dan Brooks suggestion. Note that I could launch the jupyter server with MathSage working properly through the terminal with sage -n jupyter. Only launching through the MathSage icon was not working and was leading to the message reported by Eric Martin.
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