question on Python version when installing 9.6 beta 7

[Nasser M. Abbasi]

Basic question:

I Downloaded beta 7 source code. When I do ./configure, it tells me that it wants to install Python 3-3.1.0.3 since no suitable one found.

However, I have Python 3.10.4 installed.  

So why is it building [python3-3.10.3] ?

>which python
/bin/python
>python --version
Python 3.10.4
>

I am on Ubuntu 20.04

I hope this Python it is building will not interfere with my own Python after installation of sagemath when it is done building?

--Nasser

[Dima Pasechnik]

On Thu, Apr 7, 2022 at 6:17 AM 'Nasser M. Abbasi' via sage-devel
<sage-...@googlegroups.com> wrote:
>
> Basic question:
>
> I Downloaded beta 7 source code. When I do ./configure, it tells me that it wants to install Python 3-3.1.0.3 since no suitable one found.
>
> However, I have Python 3.10.4 installed.
> So why is it building [python3-3.10.3] ?
>
> >which python
> /bin/python
> >python --version
> Python 3.10.4

the tests in ./configure are for python3, not python

What's the output of

which python3

?

> >
>
> I am on Ubuntu 20.04
>
> I hope this Python it is building will not interfere with my own Python after installation of sagemath when it is done building?
>
> --Nasser
>
>
>
>

> --
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[Dima Pasechnik]

On Thu, Apr 7, 2022 at 9:01 AM Dima Pasechnik <dim...@gmail.com> wrote:
>
> On Thu, Apr 7, 2022 at 6:17 AM 'Nasser M. Abbasi' via sage-devel
> <sage-...@googlegroups.com> wrote:
> >
> > Basic question:
> >
> > I Downloaded beta 7 source code. When I do ./configure, it tells me that it wants to install Python 3-3.1.0.3 since no suitable one found.
> >
> > However, I have Python 3.10.4 installed.
> > So why is it building [python3-3.10.3] ?
> >
> > >which python
> > /bin/python
> > >python --version
> > Python 3.10.4
>
> the tests in ./configure are for python3, not python
>
> What's the output of
>
> which python3
>
> ?

also, check

python3 --version


In any case, if you're still stuck, please post the top-level config.log

[Nasser M. Abbasi]

Here is the information you asked for

>which python3
/bin/python3

>python3 --version
Python 3.10.4

>which python
/bin/python

>python --version
Python 3.10.4
>

[Dima Pasechnik]

On Thu, Apr 7, 2022 at 4:41 PM 'Nasser M. Abbasi' via sage-devel
<sage-...@googlegroups.com> wrote:
>
> Here is the information you asked for
>
> >which python3
> /bin/python3
>
> >python3 --version
> Python 3.10.4
>
> >which python
> /bin/python
>
> >python --version
> Python 3.10.4
> >
>

Thanks.
How about config.log?
I suppose your python3 is rejected as it does not have all the
required by Sage modules
installed. (Or its other dependencies are not fully installed)

At the end of the run of ./configure there is a message printed with
recommendations
what you should install system-wide.
In particular, you should run

sudo apt-get libffi-dev libbz2-dev bzip2 xz-utils liblzma-dev

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/2ff27a53-69e6-4be2-bee1-24604ca9e651n%40googlegroups.com.

[Nasser M. Abbasi]

looking at config.log, it rejected the python version Python 3.10.4 I had because of this

## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:31945: checking whether any of bzip2 liblzma libffi is installed as or will be installed as SPKG
configure:31954: result: no
configure:31958: checking for python3 >= 3.7.0, < 3.11.0 with modules sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl
configure:32625: result:
configure:32649: checking ... whether /bin/python3 is good
CC=gcc CXX=g++ -std=gnu++11 conftest_venv/bin/python3 conftest.py --verbose build --build-base=conftest.dir
/mnt/g/nabbasi/data/CDROM/sagemath/sage-9.6.beta7/conftest.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.core import setup
running build
running build_ext
building 'config_check_distutils' extension
creating conftest.dir
creating conftest.dir/temp.linux-x86_64-3.10
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/mnt/g/nabbasi/data/CDROM/sagemath/sage-9.6.beta7/conftest_venv/include -I/usr/include/python3.10 -c conftest.c -o conftest.dir/temp.linux-x86_64-3.10/conftest.o
conftest.c:75:10: fatal error: Python.h: No such file or directory
75 | #include <Python.h>
| ^~~~~~~~~~
compilation terminated.
error: command '/bin/gcc' failed with exit code 1
configure:33213: result: no, the version is in the supported range, and the modules can be imported, but distutils cannot build a C extension
configure:32649: checking ... whether /usr/bin/python3 is good
CC=gcc CXX=g++ -std=gnu++11 conftest_venv/bin/python3 conftest.py --verbose build --build-base=conftest.dir
/mnt/g/nabbasi/data/CDROM/sagemath/sage-9.6.beta7/conftest.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.core import setup
running build
running build_ext
building 'config_check_distutils' extension
creating conftest.dir
creating conftest.dir/temp.linux-x86_64-3.10
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/mnt/g/nabbasi/data/CDROM/sagemath/sage-9.6.beta7/conftest_venv/include -I/usr/include/python3.10 -c conftest.c -o conftest.dir/temp.linux-x86_64-3.10/conftest.o
conftest.c:75:10: fatal error: Python.h: No such file or directory
75 | #include <Python.h>
| ^~~~~~~~~~
compilation terminated.
error: command '/bin/gcc' failed with exit code 1
configure:33213: result: no, the version is in the supported range, and the modules can be imported, but distutils cannot build a C extension
configure:33271: result:
configure:33275: to try to use a different system python, use ./configure --with-python=/path/to/python
configure:33302: no suitable system package found for SPKG python3

[Vincent Delecroix]

You could install the python3-dev Ubuntu package to fix the issue.

>> https://groups.google.com/d/msgid/sage-devel/2ff27a53-69e6-4be2-bee1-24604ca9e651n%40googlegroups.com
>> .
>>
>

[Dima Pasechnik]

On Fri, Apr 8, 2022 at 2:39 PM Vincent Delecroix

<20100.d...@gmail.com> wrote:
>
> You could install the python3-dev Ubuntu package to fix the issue.

Yes, this is needed for Python headers, but still

sudo apt-get libffi-dev libbz2-dev bzip2 xz-utils liblzma-dev openssl libssl-dev

might be needed too.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/927a0aef-88e5-33a9-48b0-eccecf28a275%40gmail.com.

[ph h]

Dear All,

In following this thread, it was found out, on this WSL system:

~/sage-9.6$ python --version

Command 'python' not found, did you mean:

  command 'python3' from deb python3
  command 'python' from deb python-is-python3

~/sage-9.6$ python3 --version
Python 3.8.10

~/sage-9.6$ python3.10 --version
Python 3.10.4

~/sage-9.6$ ls -l /usr/bin/*python*

lrwxrwxrwx 1 root root      60 Feb 17  2020 /usr/bin/depythontex -> ../share/texlive/texmf-dist/scripts/pythontex/depythontex.py
lrwxrwxrwx 1 root root       9 Mar 13  2020 /usr/bin/python3 -> python3.8
lrwxrwxrwx 1 root root      16 Mar 13  2020 /usr/bin/python3-config -> python3.8-config
-rwxr-xr-x 1 root root 5548344 Mar 24 12:12 /usr/bin/python3.10
lrwxrwxrwx 1 root root      34 Mar 24 12:12 /usr/bin/python3.10-config -> x86_64-linux-gnu-python3.10-config
-rwxr-xr-x 1 root root 5490448 Mar 15 08:22 /usr/bin/python3.8
lrwxrwxrwx 1 root root      33 Mar 15 08:22 /usr/bin/python3.8-config -> x86_64-linux-gnu-python3.8-config
lrwxrwxrwx 1 root root      58 Feb 17  2020 /usr/bin/pythontex -> ../share/texlive/texmf-dist/scripts/pythontex/pythontex.py
lrwxrwxrwx 1 root root      33 Mar 13  2020 /usr/bin/x86_64-linux-gnu-python3-config -> x86_64-linux-gnu-python3.8-config
-rwxr-xr-x 1 root root    3246 Mar 24 12:12 /usr/bin/x86_64-linux-gnu-python3.10-config
-rwxr-xr-x 1 root root    3241 Mar 15 08:22 /usr/bin/x86_64-linux-gnu-python3.8-config

Is it necessary to link python or  python3 to python3.10 so that sage will use python3.10.4 

Thank you for your help

Regards,

phiho

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq3yZSG%3Dtbm7ha5v-e76fO6dYUYJEiBsqS83Zn5cw-waEA%40mail.gmail.com.

[ph h]

Hi,

> Yes, this is needed for Python headers, but still
> sudo apt-get libffi-dev libbz2-dev bzip2 xz-utils liblzma-dev openssl libssl-dev

~/sage-9.6$ sudo apt-get libffi-dev libbz2-dev bzip2 xz-utils liblzma-dev openssl libssl-dev
E: Invalid operation libffi-dev

Is something missing on this WSL system?

Thank you for your help.

Regards,

phiho

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq3yZSG%3Dtbm7ha5v-e76fO6dYUYJEiBsqS83Zn5cw-waEA%40mail.gmail.com.

[Dima Pasechnik]

On Fri, 8 Apr 2022, 22:06 ph h, <hohoa...@gmail.com> wrote:

Hi,

> Yes, this is needed for Python headers, but still
> sudo apt-get libffi-dev libbz2-dev bzip2 xz-utils liblzma-dev openssl libssl-dev

~/sage-9.6$ sudo apt-get libffi-dev libbz2-dev bzip2 xz-utils liblzma-dev openssl libssl-dev
E: Invalid operation libffi-dev

Is something missing on this WSL system?

sorry, it should be 

sudo apt-get install libffi-dev ....

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CALZQg1bPreaipTULxBzsTAcLr9_yr4WajiTFotvYqEQuwY-fcQ%40mail.gmail.com.

[ph h]

Hi,

> sudo apt-get install libffi-dev ....

Thanks, that works.

phiho

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq31RNNWgCBY_7pT7pzqhmT8CCzTBG%3DMWTzT%2BF5YH%3DVpmg%40mail.gmail.com.

[ph h]

>> sudo apt-get install libffi-dev ....

> Thanks, that works.

But ...

$ python --version

Python 3.10.4

$ python3 --version
Python 3.10.4

$ sudo apt-get install python3.10-dev

Reading package lists... Done
Building dependency tree
Reading state information... Done
python3.10-dev is already the newest version (3.10.4-1+focal1).

0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ sudo apt-get install libffi-dev libbz2-dev bzip2 xz-utils liblzma-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
bzip2 is already the newest version (1.0.8-2).
libbz2-dev is already the newest version (1.0.8-2).
libffi-dev is already the newest version (3.3-4).
liblzma-dev is already the newest version (5.2.4-1ubuntu1).
xz-utils is already the newest version (5.2.4-1ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ ls -l logs/pkgs | grep ython

-rw-rw-rw- 1 hph hph  109867 Apr  8 19:33 cython-0.29.28.log
-rw-rw-rw- 1 hph hph 1930797 Apr  8 19:24 python3-3.10.3.log

From config.log:

## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##

configure:31722: checking whether any of bzip2 liblzma libffi is installed as or will be installed as SPKG
configure:31731: result: no
configure:31735: checking for python3 >= 3.7.0, < 3.11.0 with modules sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl
configure:32402: result:
configure:32426: checking ... whether /usr/bin/python3 is good
configure:32997: result: no, the version is in the supported range but cannot import one of the required modules: sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl
configure:32426: checking ... whether /bin/python3 is good
configure:32997: result: no, the version is in the supported range but cannot import one of the required modules: sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl
configure:33048: result:
configure:33052: to try to use a different system python, use ./configure --with-python=/path/to/python
configure:33079: no suitable system package found for SPKG python3
#

Please advise what else needs to be done to fix this issue.

Thank you for your help.

Regards,

phiho

[Dima Pasechnik]

which of these modules is not there?

start python3 and try running
>>> import sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CALZQg1Z%2B7sBFeihZyC7r82c0-FK3UvpDiscH4-dE52k7%3DYxvZA%40mail.gmail.com.

[ph h]

$ python
Python 3.10.4 (main, Mar 24 2022, 16:12:56) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

>>> import sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl

<stdin>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'distutils.core'
>>>

It looks like 'distutils.core' has been deprecated (and removed from python3.10-dev?)

> Use setuptools or check PEP 632 for potential alternatives

Should 'setuptools' be installed so that sage will use python-3.10.4 on the system?

Thanks for your help

Regards,

phiho

Regards,

phiho

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq3M%3DwbGuprLQAa6xpL%2BggTmJtEw0GQBXhC9WsrTUc1A0w%40mail.gmail.com.

[Matthias Koeppe]

configure informs you about the system packages that should be installed. 

It's on the last screen of the configure output.

[Dima Pasechnik]

On Sat, Apr 9, 2022 at 4:50 PM ph h <hohoa...@gmail.com> wrote:
>
> $ python
> Python 3.10.4 (main, Mar 24 2022, 16:12:56) [GCC 9.4.0] on linux
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl
> <stdin>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ModuleNotFoundError: No module named 'distutils.core'
> >>>
>
> It looks like 'distutils.core' has been deprecated (and removed from python3.10-dev?)

it's deprecated, but still available for python3.10.4
It will be removed in 3.12.

A number of Sage packages still uses distutils, as far as I know.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CALZQg1YkBx2rAc%3D079GieSDCyFwb%3DvN-z0JO_Bj%2B6SWhtP7WoA%40mail.gmail.com.

[ph h]

Hi,

In that case, maybe 'configure' should try to re-install  'distutils.core' and use the python3-3.10.x (or  python3-3.11.x later on) available on the system instead of rebuilding the whole python3?

Your help and patience is much appreciated.

Regards,

phiho

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq2RYC7zfqhHRd2v4U6nsK%3DZGYmOt75ysSE1O%2BY5cCwtkw%40mail.gmail.com.

[ph h]

> configure informs you about the system packages that should be installed. 

> It's on the last screen of the configure output.

Would it be too late to fix the issues related to python3-1.0.4 after 'configure' was run?

Any way, this is the last screen of configure output:

config.status: creating convenience symlink venv -> local/var/lib/sage/venv-python3.10
configure:

    notice: the following SPKGs did not find equivalent system packages:

        arb cddlib ecl eclib flint fplll gc giac lcalc libhomfly linbox lrcalc pari pari_galdata pari_seadata_small primecount primesieve qhull singular   4ti2 _recommended coxeter3 gp2c igraph libsemigroups lrslib pari_elldata pari_galpol pari_nftables pari_seadata polymake

checking for the package system in use... (ignoring conda because no environment is active) debian
configure:

    hint: installing the following system packages, if not
    already present, is recommended and may avoid having to
    build them (though some may have to be built anyway):

      $ sudo apt-get update
      $ sudo apt-get install  libflint-arb-dev libcdd-dev libcdd-tools ecl libec-dev eclib-tools libflint-dev libfplll-dev libgc-dev libgiac-dev xcas lcalc liblfunction-dev libhomfly-dev liblinbox-dev liblrcalc-dev pari-gp2c libpari-dev pari-doc pari-elldata pari-galdata pari-galpol pari-seadata libprimesieve-dev libqhull-dev singular singular-doc libsingular4-dev

configure:

    hint: installing the following system packages, if not
    already present, may provide additional optional features:

      $ sudo apt-get update
      $ sudo apt-get install  4ti2 default-jdk libavdevice-dev pari-gp2c libigraph-dev lrslib polymake libpolymake-dev

configure:

    hint: After installation, re-run configure using:

      $ ./config.status --recheck && ./config.status

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[Nasser M. Abbasi]

This might be useful:

" You can also use --with-python=/path/to/python3_binary to tell Sage to use /path/to/python3_binary to set up the venv. 

Note that setting up venv requires a number of Python modules to be available within the Python in question. Currently, for Sage 9.2, these modules are as follows: sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core - they will be checked for by configure."

From https://doc.sagemath.org/pdf/en/installation/installation.pdf  on page 15. 

I will try the above when Beta 8 is out and see.

[Nasser M. Abbasi]

Finally, this made it use install python

sudo apt-get install libpython3.10-dev
./configure --enable-fricas --with-python=/bin/python3

gives

Checking whether SageMath should install SPKG python3...

checking whether any of bzip2 liblzma libffi is installed as or will be installed as SPKG... no
checking for python3 >= 3.7.0, < 3.11.0 with modules sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl...
checking for /bin/python3... /bin/python3
checking ... whether /bin/python3 is good... <string>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
yes
checking for python3 >= 3.7.0, < 3.11.0 with modules sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core, ssl... /bin/python3
configure: will use system package and not install SPKG python3
checking whether /bin/python3 is configured to build multiarch extensions... no
checking whether "-march=native" works with the C/C++ compilers configured for building extensions for /bin/python3... yes
checking whether OpenMP works with the C/C++ compilers configured for building extensions for /bin/python3... yes

[ph h]

Hi,

> sudo apt-get install libpython3.10-dev
> ./configure --enable-fricas --with-python=/bin/python3

Would you please verify if you have  'distutils.core' on your system and did the make complete successfully?

Regards,

phiho

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/f88aaefd-a5a5-44c9-b741-1908dfdaeac3n%40googlegroups.com.

[Nasser M. Abbasi]

How to check for this   'distutils.core'  ?

YES. the build completed successfully. Using    RC0 just released.

====================

[sagetex-3.5] Successfully installed sagetex-3.5
[sagetex-3.5] Deleting temporary build directory
[sagetex-3.5] /home/me/sagemath/sage-9.6.rc0/local/var/lib/sage/venv-python3.10/var/tmp/sage/build/sagetex-3.5
[sagetex-3.5] Finished installing sagetex-3.5
make[2]: Leaving directory '/home/me/sagemath/sage-9.6.rc0/build/make'

real    116m35.126s
user    109m40.552s
sys     6m39.450s
Sage build/upgrade complete!
make[1]: Leaving directory '/home/me/sagemath/sage-9.6.rc0'
>

>ls -lrt config.log
-rw-r--r-- 1 me me 334247 Apr 10 15:12 config.log
>which sage
/home/me/sagemath/sage-9.6.rc0/sage
>sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.6.rc0, Release Date: 2022-04-10                 │
│ Using Python 3.10.4. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage:

===========================

Here is my config.log file you can look to see if you find what you want.

https://12000.org/tmp/sagemath_rc0/config.log

--Nasser

[ph h]

Hi,

> How to check for this   'distutils.core'  ?

$ python
Python 3.10.4 (main, Mar 24 2022, 16:12:56) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

>>> import distutils.core

<stdin>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
>>>

Regards,

phiho

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[Nasser M. Abbasi]

I get the same exact thing as you show. but this had no effect on sagemath build accepting my external python.

>python
Python 3.10.4 (main, Mar 24 2022, 16:12:56) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import distutils.core
<stdin>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
>>>

I made sure also this time to do all apt install commands the ./configure suggested at the end.  The trick seems to be to install 

       sudo apt-get install libpython3.10-dev

Before hand. 

Linux Ubuntu 20.04 under windows 10  WSL 2 subsystem.

[ph h]

Hi,

That is OK, your system already has 'distutils.core' which sage needs.

Thanks for your verification.

Regards,

phiho

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