Apparently Sage lost Python

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Anita Rojas

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Apr 3, 2020, 11:11:03 PM4/3/20
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Hi! I am far away of being a OSX guru, but I managed to get my SAGE working. 

It use to work properly but now I got the following message:


Error: Tried to use Sage's Python which was not yet installed.

If this was called from an spkg-install script for another 

package you should add $(PYTHON) as a dependency in 

build/pkgs/<pkg>/dependencies


I looked for solutions but I could not find answers. I would appreciate help.


Best,

Anita

Dima Pasechnik

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Apr 3, 2020, 11:13:49 PM4/3/20
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Probably a MacOS update broke your Sage installation.

If so, reinstalling might be the only  known way to fix this.


Best,

Anita

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Anita Rojas

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Apr 3, 2020, 11:47:53 PM4/3/20
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Thanks a lot!
I am installing a new version of sage. I have received several times (more than 20) a message like

macOS no puede verificar el desarrollador de la app “_sha3.cpython-37m-darwin.so”. ¿Seguro que quieres abrirla?

Which means that the developer is unknown and it asks me if I want to open it. It is a warning of malware. I have authorize its installation, but I have been doing this one by one...is it ok? or usual?

Thanks, and I am sorry for bothering you but I use sage regularly and I do not want to lose it.
Best,
Anita



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Anita M. Rojas
Departamento de Matemáticas
Facultad de Ciencias
Universidad de Chile

Dima Pasechnik

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Apr 3, 2020, 11:54:48 PM4/3/20
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yes, this is an issue due to Apple "improving" their security in the latest MacOS.

I believe there are instructions on

and perhaps other posts there.

Anita Rojas

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Apr 4, 2020, 12:25:46 AM4/4/20
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Thanks. I did:
sudo spctl --master-disable
and it worked. I have a question: Did I leave my computer vulnerable by doing so?

Second: I was used to use notebook() but it did not work. 

Deep thanks for your help
Anita





Dima Pasechnik

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Apr 4, 2020, 1:12:13 AM4/4/20
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On Sat, 4 Apr 2020, 12:25 Anita Rojas, <roja...@gmail.com> wrote:
Thanks. I did:
sudo spctl --master-disable
and it worked. I have a question: Did I leave my computer vulnerable by doing so?

it depends upon settings of your usual account. If it allows password-less automatic installation of random stuff from the net, then yes...


Second: I was used to use notebook() but it did not work. .
start Sage in the terminal as

sage -n 

to get Jupyter notebook - or a convertor from sagenb (which is Python 2 only, so it is being retired)

Anita Rojas

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Apr 4, 2020, 9:10:35 AM4/4/20
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Thanks. Still not working :(
Now I got:

500 : Internal Server Error

in Chrome browser. 
What should I do?
Sorry and deep thanks. 

Dima Pasechnik

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Apr 4, 2020, 12:41:23 PM4/4/20
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On Sat, Apr 4, 2020 at 9:10 PM Anita Rojas <roja...@gmail.com> wrote:
>
> Thanks. Still not working :(
> Now I got:
>
> 500 : Internal Server Error
>
> in Chrome browser.
> What should I do?

please post more details.
e.g. if I try running "sage -n"
in the terminal I see something like this:


$ ./sage -n
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.1.beta9, Release Date: 2020-03-29 │
│ Using Python 3.7.3. Type "help()" for help. │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable. ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
Please wait while the SageNB export server starts...
[I 00:38:22.448 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
[I 00:38:22.684 NotebookApp] Serving notebooks from local directory:
/home/dimpase/sage
[I 00:38:22.684 NotebookApp] The Jupyter Notebook is running at:
[I 00:38:22.684 NotebookApp]
http://localhost:8888/?token=5f633ab1a08a1d6abc180d567fc05d5158ba41652359faa2
[I 00:38:22.684 NotebookApp] Use Control-C to stop this server and
shut down all kernels (twice to skip confirmation).
[C 00:38:22.975 NotebookApp]

To access the notebook, open this file in a browser:
file:///run/user/1000/jupyter/nbserver-10489-open.html
Or copy and paste one of these URLs:
http://localhost:8888/?token=5f633ab1a08a1d6abc180d567fc05d5158ba41652359faa2

Please post what you're seeing.


As well,

you might try running

sage -n jupyter

which should directly launch a jupyter notebook
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAFV-Ve0YANV4Zan%2B_guhBxViF-55QActPFKiFsx34gKkkan-RA%40mail.gmail.com.

rana-aere

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Apr 4, 2020, 1:34:11 PM4/4/20
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I guess your computer is left vulnerable.
So you should use
```
sudo spctl --master-enable
```

We are fixing slow start-up of Sagemath and also problems of permissions.
SageMath-8.9 is OK for MacOS upto MacOS Mojave.
SageMath-9.0 needs techniques for installation on MacOS Mojave.
Many people complains problems of SageMath-9.0 on MacOS Catalina.
I only understood two or three symptoms reported but I located one essential problem.

So, we are in a rather transient situation.

For the user's of sagenb notebook, I'd rather recommend to use SageMath-8.9 while
waiting for SageMath get OK with Catalina. I think you are in this category.

For MacOS freak, I recommend to try the following procedure in the same account:
(This works for MacOS Mojave. On the other hand, no one reported it to work on Catalina.)
(1) Copy SageMath-9.0 from disk-image to /Applications. Do not double click it at this moment.
(2) Open /Applications/Utilities/Terminal.app
(3) In the terminal window, issue the following command
```
myhome$ /Applications/SageMath-9.0.app/sage
```
(4) Quit sage after the sage-prompt asks you for input something.
(5) Diable verification by "sudo spctl --master-disable".
(6) Double click /Applications/SageMath-9.0.app
(7) Specify your folder for Sagemath when a dialogue asks it.
     This folder is something close to the folder tree  ~/.sage of notebooks.
     But it must be different from ~/.sage.
     Sagemath does not start-up on Catalina if this folder is not specified at the dialogue.
(8) If Sagemath opened a web-page of jupyter notebook
     and you verify this page accept programs of Sagemath (e.g. print("hello") ),
     then quit Sagemath by the menu.
(9) Use " sudo spctl --master-enable" to restart protection.

I guess this explanation gives an impression of a gap between (7) and (8).
This is because we are still fighting the problem behind (7).

If you are in this category, I welcome claims from you.

Alternatively, if you want to go to new versions of Sagemath,
please wait for Sagemath-9.1.


2020年4月4日土曜日 13時25分46秒 UTC+9 Anita Rojas:
Thanks. I did:
sudo spctl --master-disable
and it worked. I have a question: Did I leave my computer vulnerable by doing so?

Second: I was used to use notebook() but it did not work. 

Deep thanks for your help
Anita

...

Anita Rojas

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Apr 5, 2020, 10:17:02 AM4/5/20
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Thanks. I tried "sage -n Jupyter", and my browser opened but without success in entering SAGE.
I will install SAGA 8.1 to see if it works. 
Here is the message I got once typing "sage -n":
---------------

sage: notebook()

---------------------------------------------------------------------------

ModuleNotFoundError                       Traceback (most recent call last)

<ipython-input-1-b5959bb24428> in <module>()

----> 1 notebook()


/Applications/SageMath/local/lib/python3.7/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport.__call__ (build/cythonized/sage/misc/lazy_import.c:3684)()

    351             True

    352         """

--> 353         return self.get_object()(*args, **kwds)

    354 

    355     def __repr__(self):


/Applications/SageMath/local/lib/python3.7/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport.get_object (build/cythonized/sage/misc/lazy_import.c:2347)()

    186         if likely(self._object is not None):

    187             return self._object

--> 188         return self._get_object()

    189 

    190     cpdef _get_object(self):


/Applications/SageMath/local/lib/python3.7/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport._get_object (build/cythonized/sage/misc/lazy_import.c:2586)()

    218         elif self._at_startup and not startup_guard:

    219             print('Option ``at_startup=True`` for lazy import {0} not needed anymore'.format(self._name))

--> 220         self._object = getattr(__import__(self._module, {}, {}, [self._name]), self._name)

    221         name = self._as_name

    222         if self._deprecation is not None:


ModuleNotFoundError: No module named 'sagenb'







Dima Pasechnik

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Apr 5, 2020, 10:31:56 AM4/5/20
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On Sun, Apr 5, 2020 at 10:16 PM Anita Rojas <roja...@gmail.com> wrote:
>
> Thanks. I tried "sage -n Jupyter", and my browser opened but without success in entering SAGE.

At least on Linux, it must be jupyter, not Jupyter

Once again, to get an idea what goes wrong, we need to see the
messages you get in the terminal after you started this.




> I will install SAGA 8.1 to see if it works.
9.1 ?
It's not ready yet.


> Here is the message I got once typing "sage -n":

yes, this is expected.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAFV-Ve0dr8htv4q-f9%3D5ymM6_6aG_xjJOAXCPF64tJyfFgfSqA%40mail.gmail.com.

Anita Rojas

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Apr 5, 2020, 11:08:28 AM4/5/20
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Sorry. Here is the message once typing sage -n jupyter
-----------

Please wait while the Sage Jupyter Notebook server starts...

[I 11:06:33.649 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js

[I 11:06:33.944 NotebookApp] Serving notebooks from local directory: /Users/anirojas

[I 11:06:33.944 NotebookApp] The Jupyter Notebook is running at:

[I 11:06:33.944 NotebookApp] http://localhost:8888/?token=fffae97f554fd98928c0aa84067eb7f2738ba70e8fa14b47

[I 11:06:33.944 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

[C 11:06:33.962 NotebookApp] 

    

    To access the notebook, open this file in a browser:

        file:///Users/anirojas/Library/Jupyter/runtime/nbserver-8335-open.html

    Or copy and paste one of these URLs:

        http://localhost:8888/?token=fffae97f554fd98928c0aa84067eb7f2738ba70e8fa14b47

-----------------

My browser opens with:


http://localhost:8888/tree


I am downloading sage 8.8 (sorry!)


Thanks again





Anita Rojas

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Apr 5, 2020, 11:13:58 AM4/5/20
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Yes. Thanks. I manage in less than enough in MacOS. I will try to install 8.9 version. I'll report if this works.
Could be useful to other user 

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rana-aere

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Apr 5, 2020, 11:16:06 AM4/5/20
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Yes, version <= 8.9 is the solution for now.
If the number of notebooks is not too large, upgrading sagenb notebooks to jupyter notebooks
might be a good idea.
In the next release, the error messages will not be missing.
In that time please try "sage --notebook=export --list"
and "sage --notebook=export ----ipynb TARGETFILENAME admin:NN"
for upgrading notebooks.

2020年4月5日日曜日 23時17分02秒 UTC+9 Anita Rojas:
Thanks. I tried "sage -n Jupyter", and my browser opened but without success in entering SAGE.
I will install SAGA 8.1 to see if it works. 
Here is the message I got once typing "sage -n":
---------------

sage: notebook()

---------------------------------------------------------------------------

ModuleNotFoundError                       Traceback (most recent call last)

<ipython-input-1-b5959bb24428> in <module>()

----> 1 notebook()



ModuleNotFoundError: No module named 'sagenb'

...

Dima Pasechnik

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Apr 5, 2020, 11:16:13 AM4/5/20
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On Sun, Apr 5, 2020 at 11:08 PM Anita Rojas <roja...@gmail.com> wrote:
>
> Sorry. Here is the message once typing sage -n jupyter
> -----------
>
> Please wait while the Sage Jupyter Notebook server starts...
>
> [I 11:06:33.649 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
>
> [I 11:06:33.944 NotebookApp] Serving notebooks from local directory: /Users/anirojas
>
> [I 11:06:33.944 NotebookApp] The Jupyter Notebook is running at:
>
> [I 11:06:33.944 NotebookApp] http://localhost:8888/?token=fffae97f554fd98928c0aa84067eb7f2738ba70e8fa14b47
>
> [I 11:06:33.944 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
>
> [C 11:06:33.962 NotebookApp]
>
>
>
> To access the notebook, open this file in a browser:
>
> file:///Users/anirojas/Library/Jupyter/runtime/nbserver-8335-open.html
>
> Or copy and paste one of these URLs:
>
> http://localhost:8888/?token=fffae97f554fd98928c0aa84067eb7f2738ba70e8fa14b47
>
> -----------------
>
> My browser opens with:
>
>
> http://localhost:8888/tree

and what happens if you open

http://localhost:8888/?token=fffae97f554fd98928c0aa84067eb7f2738ba70e8fa14b47

as suggested in the message above?
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAFV-Ve1am0cu61P8LXp0cY9a8tR3PtgBngR%3Dp6Hj%3DYkLOJ5k%3Dg%40mail.gmail.com.

rana-aere

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Apr 5, 2020, 11:31:24 AM4/5/20
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I guess it is about the page of title "Home".
We do not have access to sagenb notebooks.
Instead we have access to jupyter notebooks.
For the current situation, you do not have any noebooks.
That is why no notebook is listed in the page.
You can try "New" button at the upper right corner below the grey horizontal line.
If you play with some little program in the new notebook,
it might be a good chance to test upgrading sagenb notebooks.

This "upgrade" is only possible from command line.
The two relevant "sage --notebook=export --list" and "sage --notebook=export ----ipynb TARGETFILENAME admin:NN". The former prints a list of sagenb notebooks.
An example is here.

```

Unique ID       | Notebook Name

-------------------------------------------------------------------------------

admin:0         | Save 30% by Sagemath  (~/Manuals/SageTutorial9.0.pdf)

admin:1         | "Rabbit's population" $F_n$ is like $((1+\sqrt{5})/2)^n$!

admin:2         | Integral #1: $f(x)=\frac{1}{\sqrt{1-x^2}}$, $|x| < 1$.

admin:3         | Integral #2: why is f(x) = x * sqrt(1-x^2), (x in [-1,1]) easier?

admin:4         | Oval body & `tail' of @rana-aerea

admin:5         | Calculus of log|x|, x > 0.

admin:6         | mycalc

admin:7         | mycalc

```


The other command upgrades the notebook.

For example,

"sage --notebook=export ----ipynb mycalc-a admin:6"

converts the notebook with title "mycalc" with the unique id "admin:6".

It is possible some notebooks of yours have unique id of the form "guest:0"

or some other "user name". I guess 

"sage --notebook=export ----ipynb guestnotebook guest:0"

also works.

Anita Rojas

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Apr 5, 2020, 11:40:02 AM4/5/20
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Thanks, but I installed 8.9 and it did not work. Back again to point 0.
I did the line "sudo....disable" but I still get:

“python2.7” no se puede abrir porque no se puede verificar el desarrollador.


(meaning that python2.7 can not open because it could be a malware)


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Anita Rojas

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Apr 5, 2020, 11:58:40 AM4/5/20
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Thanks. I did it and I got no ID. The message was:
---------------

anirojas@MacBook-de-Anita ~ % /Applications/SageMath/sage --notebook=export --list

Unique ID       | Notebook Name

-------------------------------------------------------------------------------

Traceback (most recent call last):

  File "/Applications/SageMath/local/bin/sagenb-export", line 11, in <module>

    load_entry_point('sagenb-export==3.3', 'console_scripts', 'sagenb-export')()

  File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/cmdline.py", line 49, in main

    action_list(dot_sage)

  File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py", line 14, in action_list

    for notebook in NotebookSageNB.all_iter(dot_sage)

  File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py", line 14, in <genexpr>

    for notebook in NotebookSageNB.all_iter(dot_sage)

  File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/sagenb_reader.py", line 217, in sort_key

    return (self.conf['owner'], self.conf['id_number'])

KeyError: 'owner'


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Anita Rojas

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Apr 5, 2020, 2:14:47 PM4/5/20
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Thanks a lot for your support and patience but I gave up. I can not succeed. There are too many difficulties that I am not going to be able of solving: My older routines lost, my files with computations and examples. I do not know how to recover them. Perhaps I will try again in next future, with less anxiety and more energy.
Thanks again.
Best regards

On Sat, Apr 4, 2020 at 12:13 AM Dima Pasechnik <dim...@gmail.com> wrote:
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rana-aere

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Apr 6, 2020, 10:59:55 AM4/6/20
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I am sorry for I might have given you extra work, which produced nothing.
I agree it is not a good time to use SageMath on Catalina.


2020年4月6日月曜日 3時14分47秒 UTC+9 Anita Rojas:
Thanks a lot for your support and patience but I gave up. I can not succeed. There are too many difficulties that I am not going to be able of solving: My older routines lost, my files with computations and examples. I do not know how to recover them. Perhaps I will try again in next future, with less anxiety and more energy.
Thanks again.
Best regards

On Sat, Apr 4, 2020 at 12:13 AM Dima Pasechnik <dim...@gmail.com> wrote:


On Sat, 4 Apr 2020, 11:11 Anita Rojas, <roja...@gmail.com> wrote:

Hi! I am far away of being a OSX guru, but I managed to get my SAGE working. 

It use to work properly but now I got the following message:


Error: Tried to use Sage's Python which was not yet installed.

If this was called from an spkg-install script for another 

package you should add $(PYTHON) as a dependency in 

build/pkgs/<pkg>/dependencies


I looked for solutions but I could not find answers. I would appreciate help.


Probably a MacOS update broke your Sage installation.

If so, reinstalling might be the only  known way to fix this.


Best,

Anita

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Anita Rojas

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Apr 6, 2020, 12:07:36 PM4/6/20
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Not at all, please! Thanks for your support. I will come back to these line of messages once again in (hopefully) near future.
Best,
Anita

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rana-aere

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Apr 6, 2020, 2:37:31 PM4/6/20
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Dear Dima,

I found something strange in this error message.
--------
anirojas@MacBook-de-Anita ~ % /Applications/SageMath/sage --notebook=export --list

File "/Applications/SageMath/local/bin/sagenb-export"

File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/cmdline.py",

File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py",

File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py",

File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/sagenb_reader.py"


On MacOS, normally, we see

---------

/Applications/SageMath-9.0.app/sage --notebook=export --list

/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/sagenb_export/...



I do not understand why "Contents/Resources/sage/" disappeared.

More strangely, functions defined in these files are actually executed.

Is it possible some problem in setting PATH leads to python3 bundled with Catalina controls

Sagemath instead of python3.7 included in Sagemath?


I do not have Catalina installed. So, I cannot verify anything on it.

I only heard Catalina now has python3 not python2.

The default shell changed to zsh instead of bash.

Dima Pasechnik

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Apr 6, 2020, 10:03:07 PM4/6/20
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On Tue, Apr 7, 2020 at 2:37 AM rana-aere <rana-...@air.nifty.jp> wrote:
>
> Dear Dima,
>
> I found something strange in this error message.
> --------
> anirojas@MacBook-de-Anita ~ % /Applications/SageMath/sage --notebook=export --list
>
> File "/Applications/SageMath/local/bin/sagenb-export"
>
> File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/cmdline.py",
>
> File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py",
>
> File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py",
>
> File "/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/sagenb_reader.py"
>
>
> On MacOS, normally, we see
>
> ---------
>
> /Applications/SageMath-9.0.app/sage --notebook=export --list
>
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/sagenb_export/...
>
This might be due to a different binary Sage package installed (.app
vs non-app, packaged as a tar file)

>
>
> I do not understand why "Contents/Resources/sage/" disappeared.
>
> More strangely, functions defined in these files are actually executed.
>
> Is it possible some problem in setting PATH leads to python3 bundled with Catalina controls
>
> Sagemath instead of python3.7 included in Sagemath?
>
the recent Sage 9.1 betas have ability to use system Python3 rarher
than build Python.
But then there would not be "SageMath" in some paths at all.


>
> I do not have Catalina installed. So, I cannot verify anything on it.
>
> I only heard Catalina now has python3 not python2.
>
> The default shell changed to zsh instead of bash.
>
> --
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Anita Rojas

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Apr 7, 2020, 2:19:09 PM4/7/20
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Hi. Thanks. Sage 9.0 is working on my mac, still with some issues.

I have to run in a terminal:
 

sudo spctl --master-disable

~/Applications/SageMath/sage -n jupyter

(without "sudo..." it does not open because some archives can not be checked)

My older routines don't work. They use GAP and I got the message:

“gap-bin” no se puede abrir porque no se puede verificar el desarrollador.
macOS no puede verificar si esta app está libre de software malicioso.

(Same as before: gap-bin can not be executed because it can not be verified and it could be a malware)

I can not even use the line G=SmallGroup(2,1)

I thought it was a problem of security and I gave full access to disk to sage, I work under this "sudo....disable", but still..

Well. Thanks again for all your support. I am sure the main problem is that I am barely qualified in anything more than a user level of mac.

Best,
Anita


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slelievre

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Apr 8, 2020, 1:25:03 PM4/8/20
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Have you tried running


    THING="~/Applications/SageMath/"

    xattr -rd com.apple.quarantine $THING

Anita Rojas

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Apr 8, 2020, 3:02:33 PM4/8/20
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This worked! Thanks
Now I have troubles calling gap. I used to do

sage:  libgap.eval('LoadPackage("kbmag")')


but now I got 


fail



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slelievre

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Apr 8, 2020, 5:43:12 PM4/8/20
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Wed 2020-04-08 19:02:33 UTC, Anita Rojas:
>
> Now I have trouble calling GAP. I used to do
>
>     sage: libgap.eval('LoadPackage("kbmag")')
>
> but now I got 
>
>     fail

The following says the `kbmag` GAP package cannot be loaded.

    sage: libgap.eval('LoadPackage("kbmag")')
    fail

It fails to load because it is not installed in Sage's GAP.

Thankfully, installing packages has become a pleasant task
thanks to Michael Torpey's `PackageManager` GAP package.

Load the `PackageManager` GAP package, whose job
is to help you install further packages:

    sage: libgap.eval('LoadPackage("PackageManager")')
    true

and let it install `kbmag` with this command:

    sage: libgap.eval('InstallPackage("kbmag")')
    true

Now loading `kbmag` works:

    sage: libgap.eval('LoadPackage("kbmag")')
    true

The `kbmag` package is now loaded, ready to
try and make rewriting systems confluent.

Further reading:

- kbmag GAP package
  Knuth-Bendix on Monoids and Automatic Groups
  by Derek Holt

- PackageManager GAP package --- GAP Package Manager
  Easily download and install GAP packages
  by Michael Torpey

Anita Rojas

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Apr 8, 2020, 7:33:09 PM4/8/20
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Thanks a lot. But I also got:

sage: libgap.eval('LoadPackage("PackageManager")')

fail


 Should I add (or install) some gap package inside SageMath folder?

Sorry

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Samuel Lelièvre

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Apr 8, 2020, 7:37:55 PM4/8/20
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Forgot one step. Run this:

sage -i gap_packages
After that, the steps indicated earlier should work.

Anita Rojas

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Apr 9, 2020, 9:43:35 AM4/9/20
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Thanks. It did work! It has recovered almost all his previous capabilities. 
Although, I still do not know how to add the SmallGroup Data base directly to sage. 

Currently it is working by doing, for instance: 
g=gap.SmallGroup(6,2)

And before this Catalina's upgrade I used to write just
g=SmallGroup(6,2)

I am deeply grateful to everyone who helped me, and to SAGE developers.

Best,

(I hope MacOS does not mess with my running softwares again...)

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Dima Pasechnik

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Apr 9, 2020, 10:20:09 AM4/9/20
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On Thu, Apr 9, 2020 at 9:43 PM Anita Rojas <roja...@gmail.com> wrote:
>
> Thanks. It did work! It has recovered almost all his previous capabilities.
> Although, I still do not know how to add the SmallGroup Data base directly to sage.
>
> Currently it is working by doing, for instance:
> g=gap.SmallGroup(6,2)
>
> And before this Catalina's upgrade I used to write just
> g=SmallGroup(6,2)

I believe this has been removed many Sage versions ago. You can still
just define it yourself:

sage: def SmallGroup(*args):
....: return libgap.SmallGroup(*args)
sage: SmallGroup(6,2)
<pc group of size 6 with 2 generators>

(PS. don't use gap.* prefix, use libgap.* prefix, as above, as gap.*
functions are deprecated - libgap.*
provides a much faster adn more reliable interface)



>
> I am deeply grateful to everyone who helped me, and to SAGE developers.
>
> Best,
>
> (I hope MacOS does not mess with my running softwares again...)
>
> On Wed, Apr 8, 2020 at 7:37 PM Samuel Lelièvre <samuel....@gmail.com> wrote:
>>
>> Forgot one step. Run this:
>>
>> sage -i gap_packages
>> After that, the steps indicated earlier should work.
>>
>> --
>> You received this message because you are subscribed to a topic in the Google Groups "sage-support" group.
>> To unsubscribe from this topic, visit https://groups.google.com/d/topic/sage-support/NletjrinNhM/unsubscribe.
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>> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAEcArF18yaZKbDR-W23%2BSn21mZUSf9uB8MWc6sm1c0Wr7EOcDA%40mail.gmail.com.
>
>
>
> --
> Anita M. Rojas
> Departamento de Matemáticas
> Facultad de Ciencias
> Universidad de Chile
>
> https://sites.google.com/a/u.uchile.cl/mat-ciencias-prof-anita-rojas/
>
> --
> You received this message because you are subscribed to the Google Groups "sage-support" group.
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Anita Rojas

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Mar 14, 2021, 3:24:48 PMMar 14
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Dear Developers, I hope you are well. Here I am struggling with the installation of Sage9.1 (I gave up on Sage9.2) in my new Imac.

I succeeded up to some point with Sage9.1 but when running sage -n jupyter
It opens Chrome and the right page but when I try to open a Sage9.1 Notebook it says:

Creating Notebook Failed

An error occurred while creating a new notebook.
Unexpected error while saving file: Untitled.ipynb [Errno 30] Read-only file system: '/Untitled.ipynb'
I have tried all your instructions from last time unsuccessfully. 
I would really appreciate some help. Thanks in advance.

Best regards,
Anita
(Ah! I have macOS BigSur 11.2.3 on a  3,1 GHz Intel Core i5 de seis núcleos)


On Wed, Apr 8, 2020 at 7:37 PM Samuel Lelièvre <samuel....@gmail.com> wrote:
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Anita Rojas

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Mar 14, 2021, 5:35:50 PMMar 14
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Sorry! Me again. I got further: I manage to start sage -n jupyter. I did some trigonometric graphs
but my gap-routines didn't work. So I run in a terminal:

/Application/ XXX /sage -i gap_packages


and then I got backwards to this:

**********************************************************************


Oops, Sage crashed. We do our best to make it stable, but...


A crash report was automatically generated with the following information:

  - A verbatim copy of the crash traceback.

  - A copy of your input history during this session.

  - Data on your current Sage configuration.


It was left in the file named:

'/Users/anitaimac/.sage/ipython-5.0.0/Sage_crash_report.txt'

If you can email this file to the developers, the information in it will help

them in understanding and correcting the problem.


You can mail it to: sage-support at sage-s...@googlegroups.com

with the subject 'Sage Crash Report'.


If you want to do it now, the following command will work (under Unix):

mail -s 'Sage Crash Report' sage-s...@googlegroups.com < /Users/anitaimac/.sage/ipython-5.0.0/Sage_crash_report.txt


In your email, please also include information about:

- The operating system under which the crash happened: Linux, macOS, Windows,

  other, and which exact version (for example: Ubuntu 16.04.3, macOS 10.13.2,

  Windows 10 Pro), and whether it is 32-bit or 64-bit;

- How Sage was installed: using pip or conda, from GitHub, as part of

  a Docker container, or other, providing more detail if possible;

- How to reproduce the crash: what exact sequence of instructions can one

  input to get the same crash? Ideally, find a minimal yet complete sequence

  of instructions that yields the crash.


To ensure accurate tracking of this issue, please file a report about it at:

http://trac.sagemath.org


Hit <Enter> to quit (your terminal may close):


---


Now nothing works. I tried sage 9.1 and 9.2, and also sage.app 9.1. Nothing. 

I'll stop here and wait for your help... Thanks.

Jan Groenewald

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Mar 15, 2021, 4:57:50 AMMar 15
to sage-support
Hi

Your initial error said Read Only Filesystem.

This is probably not related to sage. Perhaps your filesystem filled up or there is another problem?

Regards,
Jan

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--
  .~.
  /V\     Jan Groenewald
 /( )\    www.aims.ac.za
 ^^-^^

Samuel Lelièvre

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Mar 18, 2021, 7:50:37 AMMar 18
to Sage-support
¡Hola Anita!

You could try the new macOS app, currently in beta testing at:

https://github.com/3-manifolds/Sage_macOS/releases/
Let us know if it solves your problems. --Samuel

Anita Rojas

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Mar 18, 2021, 10:45:12 AMMar 18
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Dear Samuel,
thank you very much for your help. I installed the version you told me. It worked in the basics, so thanks!
But I still have some problems. I write them here, hoping you can help me. Thanks in advance!
1. I double click on SageMath icon, and it opens in a Terminal. I do not know how to open it as a Sage notebook in
jupyter. In my macbook I run sage -n jupyter.
2. I have some routines using the underlying GAP. They do not work here. I tried (and fail) the following:
sage:  libgap.eval('LoadPackage("kbmag")')                                      
fail

Thank you very much for all your help and support.
With best regards,
Anita


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Nathan Dunfield

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Mar 18, 2021, 3:14:11 PMMar 18
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Anita, 

1. The version at:


was just updated last night.  Now double-clicking the icon should produce a window which offers a choice of terminal or Jupyter.

2. I don't think kbmag comes with Sage, or at least your command failed on three different versions of Sage I tried (one Mac, two Linux).  So I assume this is a file in one of your own directories that you are trying to load.  If so, probably the file is not in the directory where Sage starts (which is /Users/anita or similar).

Best,

Nathan

Anita Rojas

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Mar 18, 2021, 3:27:16 PMMar 18
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Nathan, thank you very much for your answer. I have some comments:

1. There is something wrong with Jupyter in my Mac. I do not know what it is. I manage to run it but
it can not upload files (that do upload in the Terminal version of Sage). So if I can make the Terminal
version of Sage work, it would be great.

2. Regarding the gap issue (kbmag) In my old version of Sage I run the following commands in order to work:

In a terminal:

/Applications/SageMath/sage -i gap_packages

Then in sage:
libgap.eval(‘LoadPackage(“PackageManager")')
libgap.eval('InstallPackage("kbmag")')

Now loading `kbmag` works:


    sage: libgap.eval('LoadPackage("kbmag")')
    true

But sadly the first step (sage -i gap_packages) does not work now. That is why, I think, everything fails after that.
Moreover, after that line, my sage does not start anymore and I have to reinstall it.

I hope I have explained my problem clearly. I definitely can use some help.
Best,
Anita


Dima Pasechnik

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Mar 18, 2021, 3:35:02 PMMar 18
to sage-support
On Thu, Mar 18, 2021 at 7:14 PM Nathan Dunfield <nat...@dunfield.info> wrote:
>
> Anita,
>
> 1. The version at:
>
> https://github.com/3-manifolds/Sage_macOS/releases/tag/v1.0-beta
>
> was just updated last night. Now double-clicking the icon should produce a window which offers a choice of terminal or Jupyter.
>
> 2. I don't think kbmag comes with Sage, or at least your command failed on three different versions of Sage I tried (one Mac, two Linux). So I assume this is a file in one of your own directories that you are trying to load. If so, probably the file is not in the directory where Sage starts (which is /Users/anita or similar).

kbmag is a part of Sage's optional package gap-packages

One can certainly get it, but it might entail building Sage from source.
(Not sure whether with Conda one would get it, or it's not in Conda)

Dima
> You received this message because you are subscribed to the Google Groups "sage-support" group.
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Isuru Fernando

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Mar 18, 2021, 3:39:51 PMMar 18
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>  (Not sure whether with Conda one would get it, or it's not in Conda)

It's not in conda. We have almost all the gap packages except for a few problematic ones. (compile failures)
`kbmag` is one of them. https://github.com/conda-forge/gap-feedstock/blob/19ff5a3e3365bd1ef9ed9bd9315f0596d9e7de21/recipe/build.sh#L44-L48

Isuru

Anita Rojas

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Mar 18, 2021, 3:50:44 PMMar 18
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Thanks! But I installed Sage 9.0 (which works perfectly in my Macbook) and I can not make these gap packages 
work too...Although I run the same lines I run in my Macbook.
I do not understand. Thanks for the support!
Anita

Anita Rojas

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Mar 18, 2021, 4:07:24 PMMar 18
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This is the error message I got when running:
 /Applications/SageMath/sage -i gap_packages

In Sage 9.0 (line which worked before...)

[gap_packages-4.10.2.p1] ************************************************************************

make[1]: *** [/Applications/SageMath/local/var/lib/sage/installed/gap_packages-4.10.2.p1] Error 1


real 2m15.572s

user 1m51.981s

sys 0m20.152s

***************************************************************

Error building Sage.


The following package(s) may have failed to build (not necessarily

during this run of 'make gap_packages'):


* package: gap_packages-4.10.2.p1

  log file: /Applications/SageMath/logs/pkgs/gap_packages-4.10.2.p1.log

  build directory: /Applications/SageMath/local/var/tmp/sage/build/gap_packages-4.10.2.p1


The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.


make: *** [gap_packages] Error 1



--

kcrisman

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Mar 18, 2021, 4:41:44 PMMar 18
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This would be great news - thanks to anyone who is working on this! 

Dima Pasechnik

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Mar 18, 2021, 5:24:45 PMMar 18
to sage-support
On Thu, Mar 18, 2021 at 7:39 PM Isuru Fernando <isu...@gmail.com> wrote:
>
> > (Not sure whether with Conda one would get it, or it's not in Conda)
>
> It's not in conda. We have almost all the gap packages except for a few problematic ones. (compile failures)
> `kbmag` is one of them. https://github.com/conda-forge/gap-feedstock/blob/19ff5a3e3365bd1ef9ed9bd9315f0596d9e7de21/recipe/build.sh#L44-L48

it's not clear to me why these have to be disabled. (I understand
about xgap and polymakeinterface, but the rest
looks fine, they are just not very clean mostly C code packages - and
they have been updated recently, they
build on everything Sage builds)

Any pointers on reproducing these failures?
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CA%2B01voNEe4tq55jorMS_bZKSVLq3yTXwVj1S%3DkA9pZCyYcHrJQ%40mail.gmail.com.

Anita Rojas

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May 27, 2021, 9:00:03 PMMay 27
to sage-s...@googlegroups.com
Hello. I hope you are OK. Here I am back trying to get sage working in my new mac 
(with Big Sur 11.2.3). Sage still works in the old one (fortunately).

Now I have a problem with the package kbmag from gap.

When working I got the error I pasted at the end of this email.
I have tried the following to solve it (which works in my old computer), unsuccesfully:

1. In a Terminal:

sage -i gap_packages


and got: make: *** No rule to make target `all-toolchain'.  Stop.


2. In sage:


libgap.eval('LoadPackage("PackageManager")')


and got: fail


3. In sage:


libgap.eval('InstallPackage("kbmag")')


and got:

---------------------------------------------------------------------------
GAPError                                  Traceback (most recent call last)
<ipython-input-20-e51e2455bf67> in <module>
----> 1 libgap.eval('InstallPackage("kbmag")')

/var/tmp/sage-jc4b6yulaujayb9sr94ia88eourzeqip0oidmas3/local/lib/python3.8/site-packages/sage/libs/gap/libgap.pyx in sage.libs.gap.libgap.Gap.eval (build/cythonized/sage/libs/gap/libgap.c:4254)()
    398 
    399         initialize()
--> 400         elem = make_any_gap_element(self, gap_eval(gap_command))
    401 
    402         # If the element is NULL just return None instead

/var/tmp/sage-jc4b6yulaujayb9sr94ia88eourzeqip0oidmas3/local/lib/python3.8/site-packages/sage/libs/gap/util.pyx in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:6077)()
    396     try:
    397         GAP_Enter()
--> 398         result = GAP_EvalString(cmd)
    399         # We can assume that the result object is a GAP PList (plain list)
    400         # and we should use functions for PLists directly for now; see

GAPError: Error, Variable: 'InstallPackage' must have a value



And finally the Error in my computations:


---------------------------------------------------------------------------
GAPError                                  Traceback (most recent call last)
/var/tmp/sage-jc4b6yulaujayb9sr94ia88eourzeqip0oidmas3/local/lib/python3.8/site-packages/sage/libs/gap/element.pyx in sage.libs.gap.element.GapElement.__getattr__ (build/cythonized/sage/libs/gap/element.c:8322)()
    735             proxy = make_GapElement_MethodProxy\
--> 736                 (self.parent(), gap_eval(name), self)
    737         except GAPError:

/var/tmp/sage-jc4b6yulaujayb9sr94ia88eourzeqip0oidmas3/local/lib/python3.8/site-packages/sage/libs/gap/util.pyx in sage.libs.gap.util.gap_eval (build/cythonized/sage/libs/gap/util.c:6077)()
    397         GAP_Enter()
--> 398         result = GAP_EvalString(cmd)
    399         # We can assume that the result object is a GAP PList (plain list)

GAPError: Error, Variable: 'KBMAGRewritingSystem' must have a value

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
<ipython-input-11-23587a78dfd9> in <module>
----> 1 P=Poly(G,[Integer(7),Integer(3),Integer(2)])

<string> in __init__(self, G, x, seed, alphabet, compute)

<string> in __process_group(self, seed)

<string> in __init__(self, fund_poly, g, label, w)

<string> in word_reducer(self)

<string> in kbword_reducer(F)

/var/tmp/sage-jc4b6yulaujayb9sr94ia88eourzeqip0oidmas3/local/lib/python3.8/site-packages/sage/libs/gap/element.pyx in sage.libs.gap.element.GapElement.__getattr__ (build/cythonized/sage/libs/gap/element.c:8401)()
    736                 (self.parent(), gap_eval(name), self)
    737         except GAPError:
--> 738             raise AttributeError(f"'{name}' is not defined in GAP")
    739         if not proxy.is_function():
    740             raise AttributeError(f"'{name}' does not define a GAP function")

AttributeError: 'KBMAGRewritingSystem' is not defined in GAP

Thanks in advance.
Best regards,
Anita

On Thu, Mar 18, 2021 at 8:50 AM Samuel Lelièvre <samuel....@gmail.com> wrote:
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slelievre

unread,
May 31, 2021, 1:10:18 PMMay 31
to sage-support
The Sage shipped by the SageMath macOS app
can run Sage and install many extra packages,
but does not ship build tools that are necessary
for installing certain extra packages.

So you might want to install a fuller Sage.

Some suggested steps follow. Lines that start
with a dollar sign and space are commands to run
in a terminal (without the initial dollar sign).

A.  Visit the SageMath macOS download page:

B.  Select a mirror close to you

C.  Click "intel"

D.  Get the latest version for your system,
    for instance if you have macOS 11, get:
    `sage-9.3-OSX_11.2.3-x86_64.tar.bz2`

E.  Move the dowloaded `.tar.bz2` file to the location
    of your choice, for instance `/Applications`

F.  Extract it, either by a double click or with
    ```
    $ cd /Applications
    $ tar xf sage-9.3-OSX_11.2.3-x86_64.tar.bz2
    ```
    and get a folder called SageMath.

G.  Clear any extended attributes macOS might
    have put on the files in that folder with
    ```
    $ xattr -cr /Applications/SageMath
    ```

H.  Create a symlink to the Sage executable,
    placing it somewhere in your path, for example:
    ```
    $ ln -sf /Applications/SageMath/sage /usr/local/bin
    ```
    If there is a permission problem, use sudo:
    ```
    $ sudo ln -sf /Applications/SageMath/sage /usr/local/bin
    ```
    (enter your admin password for that Mac when prompted).
    (Note that if the version without sudo failed, you can
    avoid re-typing or copy-pasting the whole ln command:
    use "up-arrow" to get the last command, hit Ctrl-A
    to move to the start of the line, then type `sudo`,
    hit Space, hit Enter.)

I.  Now you can start Sage from any location
    ```
    $ which sage
    /usr/local/bin/sage
    $ ls -halF $(which sage)
    ...
    $ sage --version
    ...
    $ sage
    ...
    ```
    Hit Ctrl-D, or type `quit` and hit Enter, to quit.

    To launch Jupyter, you can run
    ```
    $ sage -n jupyter
    ```

J.  Install any extra packages you like, e.g.
    ```
    $ sage -i fricas
    $ sage -i gap_packages
    $ sage -i jupyterlab_widgets
    $ sage --pip install RISE
    $ sage --pip install jupytext
    ```

K.  To install extra GAP packages, e.g. `kbmag`,
    one way is to use the GAP package `PackageManager`.
    
    This can be done in GAP. Here we start Sage's GAP
    and work there (don't forget the semicolons!):
    ```
    $ sage --gap
    ...
    gap> LoadPackage("PackageManager");
    true
    gap> InstallPackage("kbmag");
    true
    gap> LoadPackage("kbmag");
    true
    ```
    To quit GAP, either hit Ctrl-D or type `quit;` and hit Enter.

    Or this can be done in Sage using `libgap`:
    ```
    $ sage -q
    sage: libgap.eval('LoadPackage("PackageManager")')
    true
    sage: libgap.eval('InstallPackage("kbmag")')
    true
    sage: libgap.eval('LoadPackage("kbmag")')
    true
    ```

    Note: kbmag is installed once and for all. Next time
    you start GAP or Sage, you can directly load it.

L.  If you want to make the SageMath Jupyter kernel
    available to a system-wide Jupyter installation:
    ```
    $ ORIG=/Applications/SageMath/local/share/jupyter/kernels
    $ DEST=~/Library/Jupyter/kernels
    $ ln -sf $ORIG/sagemath $DEST
    ```

M.  If you want the ability to double-click `.ipynb` files
    to open them, install nteract from

Hope this helps. Let us know if you got things working.

slelievre

unread,
Jun 8, 2021, 6:37:04 PM (7 days ago) Jun 8