# Apparently Sage lost Python

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### Anita Rojas

Apr 3, 2020, 11:11:03 PM4/3/20
to sage-support

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 unread, Apr 3, 2020, 11:13:49 PM4/3/20 to sage-support Probably a MacOS update broke your Sage installation. If so, reinstalling might be the only known way to fix this. Best, Anita -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/e7c84768-c030-425a-b78b-aa1a378e757e%40googlegroups.com. ### Anita Rojas unread, Apr 3, 2020, 11:47:53 PM4/3/20 to sage-s...@googlegroups.com 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 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq0h61z4n-xV2yT6-CB_-izF5ZkOtF%3DXUu%2Bq_h%2BDekYCZw%40mail.gmail.com. -- Anita M. Rojas Departamento de Matemáticas Facultad de Ciencias Universidad de Chile ### Dima Pasechnik unread, Apr 3, 2020, 11:54:48 PM4/3/20 to sage-support 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 unread, Apr 4, 2020, 12:25:46 AM4/4/20 to sage-s...@googlegroups.com 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 unread, Apr 4, 2020, 1:12:13 AM4/4/20 to sage-support 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 unread, Apr 4, 2020, 9:10:35 AM4/4/20 to sage-s...@googlegroups.com Thanks. Still not working :( Now I got: 500 : Internal Server Error in Chrome browser. What should I do? Sorry and deep thanks. ### Dima Pasechnik unread, Apr 4, 2020, 12:41:23 PM4/4/20 to sage-support 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

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

Apr 4, 2020, 1:34:11 PM4/4/20
to sage-support
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 unread, Apr 5, 2020, 10:17:02 AM4/5/20 to sage-s...@googlegroups.com 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 unread, Apr 5, 2020, 10:31:56 AM4/5/20 to sage-support 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 unread, Apr 5, 2020, 11:08:28 AM4/5/20 to sage-s...@googlegroups.com 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] [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: ----------------- My browser opens with: I am downloading sage 8.8 (sorry!) Thanks again ### Anita Rojas unread, Apr 5, 2020, 11:13:58 AM4/5/20 to sage-s...@googlegroups.com 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 -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### rana-aere unread, Apr 5, 2020, 11:16:06 AM4/5/20 to sage-support 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 unread, Apr 5, 2020, 11:16:13 AM4/5/20 to sage-support 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 unread, Apr 5, 2020, 11:31:24 AM4/5/20 to sage-support 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 unread, Apr 5, 2020, 11:40:02 AM4/5/20 to sage-s...@googlegroups.com 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) -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### Anita Rojas unread, Apr 5, 2020, 11:58:40 AM4/5/20 to sage-s...@googlegroups.com 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' -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### Anita Rojas unread, Apr 5, 2020, 2:14:47 PM4/5/20 to sage-s...@googlegroups.com 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: 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq0h61z4n-xV2yT6-CB_-izF5ZkOtF%3DXUu%2Bq_h%2BDekYCZw%40mail.gmail.com. ### rana-aere unread, Apr 6, 2020, 10:59:55 AM4/6/20 to sage-support 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

Apr 6, 2020, 12:07:36 PM4/6/20
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

Apr 6, 2020, 2:37:31 PM4/6/20
to sage-support
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",

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

Apr 6, 2020, 10:03:07 PM4/6/20
to sage-support
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",
>
>
>
> 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.
>
> --
> You received this message because you are subscribed to the Google Groups "sage-support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.

### Anita Rojas

Apr 7, 2020, 2:19:09 PM4/7/20
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

Apr 8, 2020, 1:25:03 PM4/8/20
to sage-support
Have you tried running

THING="~/Applications/SageMath/"

xattr -rd com.apple.quarantine $THING ### Anita Rojas unread, Apr 8, 2020, 3:02:33 PM4/8/20 to sage-s...@googlegroups.com This worked! Thanks Now I have troubles calling gap. I used to do sage: libgap.eval('LoadPackage("kbmag")') but now I got fail -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### slelievre unread, Apr 8, 2020, 5:43:12 PM4/8/20 to sage-support 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 unread, Apr 8, 2020, 7:33:09 PM4/8/20 to sage-s...@googlegroups.com 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 -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### Samuel Lelièvre unread, Apr 8, 2020, 7:37:55 PM4/8/20 to Sage-support Forgot one step. Run this: sage -i gap_packages After that, the steps indicated earlier should work. ### Anita Rojas unread, Apr 9, 2020, 9:43:35 AM4/9/20 to sage-s...@googlegroups.com 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...) -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### Dima Pasechnik unread, Apr 9, 2020, 10:20:09 AM4/9/20 to sage-support 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. >> To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. >> 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. > To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAFV-Ve0Ow0fEL_ZprWX-RYtogAM22iPZrjfPvM4_eUUEu%2BHBjg%40mail.gmail.com. ### Anita Rojas unread, Mar 14, 2021, 3:24:48 PMMar 14 to sage-s...@googlegroups.com 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: -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### Anita Rojas unread, Mar 14, 2021, 5:35:50 PMMar 14 to sage-s...@googlegroups.com 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 unread, 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 You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAFV-Ve0Vth40NuwGiLcK0KHDD_RfMn-FKPa13gaDLvbYPyAo2Q%40mail.gmail.com. -- .~. /V\ Jan Groenewald /( )\ www.aims.ac.za ^^-^^ ### Samuel Lelièvre unread, 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 unread, Mar 18, 2021, 10:45:12 AMMar 18 to sage-s...@googlegroups.com 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 -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### Nathan Dunfield unread, Mar 18, 2021, 3:14:11 PMMar 18 to sage-support 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 unread, Mar 18, 2021, 3:27:16 PMMar 18 to sage-s...@googlegroups.com 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 unread, 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. > To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/42cdf878-6cdc-4aaa-a462-2abe3017901bn%40googlegroups.com. ### Isuru Fernando unread, Mar 18, 2021, 3:39:51 PMMar 18 to sage-s...@googlegroups.com > (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 unread, Mar 18, 2021, 3:50:44 PMMar 18 to sage-s...@googlegroups.com 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 unread, Mar 18, 2021, 4:07:24 PMMar 18 to sage-s...@googlegroups.com 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 unread, Mar 18, 2021, 4:41:44 PMMar 18 to sage-support 1. The version at: This would be great news - thanks to anyone who is working on this! ### Dima Pasechnik unread, 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 unread, 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: -- 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. To unsubscribe from this group and all its topics, send an email to sage-support...@googlegroups.com. ### 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

(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
...
true
gap> InstallPackage("kbmag");
true
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.