Error building package python3-3.8.5

[Günter Rote]

************************************************************************
Error building package python3-3.8.5
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
  /home/rote/Dokumente/sage/logs/pkgs/python3-3.8.5.log
Describe your computer, operating system, etc.


======

I downloaded today the Branch "develop"
I am running under
Ubuntu 18.04

Could not make sage.

(I have python 3.8.0 installed anyway, but sage wants to install its own more recent version, apparently.) 

[Matthias Koeppe]

On Saturday, January 2, 2021 at 9:45:58 AM UTC-8 roteg...@gmail.com wrote:

Error building package python3-3.8.5
[...]

I downloaded today the Branch "develop"
I am running under
Ubuntu 18.04

Could not make sage.

From the log:

*** WARNING: renaming "readline" since importing it failed: /home/rote/Dokumente/sage/local/lib/libreadline.so.8: undefined symbol: UP Python build finished successfully! The necessary bits to build these optional modules were not found: _dbm _gdbm _tkinter To find the necessary bits, look in setup.py in detect_modules() for the module's name. The following modules found by detect_modules() in setup.py, have been built by the Makefile instead, as configured by the Setup files: _abc atexit pwd time Following modules built successfully but were removed because they could not be imported: readline running build_scripts creating build/scripts-3.8 copying and adjusting /home/rote/Dokumente/sage/local/var/tmp/sage/build/python3-3.8.5/src/Tools/scripts/pydoc3 -> build/scripts-3.8 copying and adjusting /home/rote/Dokumente/sage/local/var/tmp/sage/build/python3-3.8.5/src/Tools/scripts/idle3 -> build/scripts-3.8 copying and adjusting /home/rote/Dokumente/sage/local/var/tmp/sage/build/python3-3.8.5/src/Tools/scripts/2to3 -> build/scripts-3.8 changing mode of build/scripts-3.8/pydoc3 from 644 to 755 changing mode of build/scripts-3.8/idle3 from 644 to 755 changing mode of build/scripts-3.8/2to3 from 644 to 755 renaming build/scripts-3.8/pydoc3 to build/scripts-3.8/pydoc3.8 renaming build/scripts-3.8/idle3 to build/scripts-3.8/idle3.8 renaming build/scripts-3.8/2to3 to build/scripts-3.8/2to3-3.8 Testing importing of various modules... ctypes module imported OK math module imported OK hashlib module imported OK crypt module imported OK Traceback (most recent call last): File "<string>", line 1, in <module> ModuleNotFoundError: No module named 'readline' readline module failed to import socket module imported OK zlib module imported OK sqlite3 module imported OK Error: One or more modules failed to import.  

This might be a problem with ncurses.

(I have python 3.8.0 installed anyway, but sage wants to install its own more recent version, apparently.) 

Please post config.log, which will also explain why system python 3.8 was not accepted by Sage.

 

[Günter Rote]

My mistake: I installed Python 3.8 after running configure

The build is running now smoothly. (so far)

[Günter Rote]

I am posting config.log.

(I had linked /usr/bin/python3 to /usr/bin/python3.8, and then the sage build went through without problems.

But then I ran into a different problem: I could not open a terminal window. After a frightening hour, I

discovered the reason: /usr/bin/gnome-terminal could not find some library on line 8:

#!/usr/bin/python3

import string

import subprocess

import sys

import random

from argparse import ArgumentParser, SUPPRESS

from gi.repository import GLib, Gio

...

Now I have switched back /usr/bin/python3 to /usr/bin/python3.6, but now sage won't build any more.

Matthias Koeppe schrieb am Samstag, 2. Januar 2021 um 19:55:15 UTC+1:

[Dima Pasechnik]

There is a way to configure Sage to use any Python3, e.g. to use
python3.8 (assuming this is how your Python 3.8 executable
is called)

./configure --with-python=python3.8

(and then of course you'd have to rebuild all the python packages of Sage)

Needless to say, modifying /usr/bin/python3 is not a good idea - as
you discovered.

HTH
Dima

> --
> You received this message because you are subscribed to the Google Groups "sage-devel" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/b0395701-5f00-4f34-ba4b-99c0cc7e973an%40googlegroups.com.

[Matthias Koeppe]

On Sunday, January 3, 2021 at 2:12:14 AM UTC-8 roteg...@gmail.com wrote:

I am posting config.log.

From the log:

....

configure:31101: no suitable system package found for SPKG xz 

...

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

configure:31215: checking whether any of libpng bzip2 xz libffi is installed as or will be installed as SPKG 

configure:31219: result: yes; install python3 as well configure:31854: no suitable system package found for SPKG python3 

...

To get Sage to accept system python3 (see Dima's message for how to select the version you want to use), xz is needed too.

At the end of ./configure you will see a list of system packages that can be installed - which includes the package providing xz.

[brettpim]

I am having a similar problem.  I have pulled the master branch from git and I when run

# ./configure

it finishes with

configure: notice: the following SPKGs did not find equivalent system packages: boost cbc coxeter3 gp2c isl libnauty libsemigroups pari_elldata pari_galpol pari_nftables pari_seadata python3 tox
checking for the package system in use... debian
configure: hint: installing the following system packages is recommended and may avoid building some of the above SPKGs from source:
configure:   $ sudo apt-get update
  $ sudo apt-get install libboost-dev coinor-cbc coinor-libcbc-dev pari-gp2c libisl-dev libnauty-dev python3 libpython3-dev python3-distutils

but all these APT packages are already installed:

# apt-get install libboost-dev coinor-cbc coinor-libcbc-dev pari-gp2c libisl-dev libnauty-dev python3 libpython3-dev python3-distutils
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'libnauty2-dev' instead of 'libnauty-dev'
libboost-dev is already the newest version (1.71.0.0ubuntu2).
libisl-dev is already the newest version (0.22.1-1).
libpython3-dev is already the newest version (3.8.2-0ubuntu2).
python3 is already the newest version (3.8.2-0ubuntu2).
coinor-cbc is already the newest version (2.10.3+repack1-1build1).
coinor-libcbc-dev is already the newest version (2.10.3+repack1-1build1).
libnauty2-dev is already the newest version (2.6r10+ds-1ubuntu1).
pari-gp2c is already the newest version (0.0.11pl2-3).
python3-distutils is already the newest version (3.8.5-1~20.04.1).
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.

I don;t know what I need to get ./configure to recognize my python3. The 'xz' package Matthias refers to is installed:

configure:30241: checking for xz >= 4.999.0
configure:30320: result: /usr/bin/xz
configure:30329: will use system package and not install SPKG xz

config.log attached

[Dima Pasechnik]

from your config.log:

## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:30455: checking whether any of sqlite libpng bzip2 xz libffi

is installed as or will be installed as SPKG

configure:30459: result: yes; install python3 as well

As you see, xz is only one piece of the puzzle, you also need e.g.
sqlite, which is

## Checking whether SageMath should install SPKG sqlite... ##
## ------------------------------------------------------- ##
configure:30003: sqlite has already been installed by SageMath

same with png:

## Checking whether SageMath should install SPKG sqlite... ##
## ------------------------------------------------------- ##
configure:30003: sqlite has already been installed by SageMath

... etc. Having a system python (which should have all these modules) and
the corresponding libs installed in Sage is a problem, that's why it's rejected.

You need to unistall them all:

make sqlite-clean libpng-clean bzip2-clean xz-clean libffi-clean

and then run

./configure --with-python=python3.8

again

HTH
Dima

>
> configure:30241: checking for xz >= 4.999.0
> configure:30320: result: /usr/bin/xz
> configure:30329: will use system package and not install SPKG xz
>
>
> config.log attached
>
>

> --
> You received this message because you are subscribed to the Google Groups "sage-devel" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/5ae392d5-88b2-4016-8e03-702de8327336n%40googlegroups.com.

[Samuel Lelievre]

In your `config.log`, the report for checking

whether to install the `python3` SPGK reads:

```

## -------------------------------------------------------- ##

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

## -------------------------------------------------------- ##

configure:30455: checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG

configure:30459: result: yes; install python3 as well

configure:31094: no suitable system package found for SPKG python3

```

So the decision for `python3` depends, here, not on whether

a suitable system `python3` exists, but on the status for

`sqlite`, `libpng`, `bzip2`, `xz`, `libffi`.

Here are the corresponding checks in `config.log`:

```

## ------------------------------------------------------- ##

## Checking whether SageMath should install SPKG sqlite... ##

## ------------------------------------------------------- ##

configure:30003: sqlite has already been installed by SageMath

```

```

## ------------------------------------------------------- ##

## Checking whether SageMath should install SPKG libpng... ##

## ------------------------------------------------------- ##

configure:14052: libpng has already been installed by SageMath

```

```

## ------------------------------------------------------ ##

## Checking whether SageMath should install SPKG bzip2... ##

## ------------------------------------------------------ ##

configure:14668: bzip2 has already been installed by SageMath

```

```

## --------------------------------------------------- ##

## Checking whether SageMath should install SPKG xz... ##

## --------------------------------------------------- ##

configure:30190: checking for lzma_raw_decoder in -llzma

configure:30215: g++ -std=gnu++11 -std=gnu++11 -o conftest -g -O2  -Wl,-rpath-link,/home/brett/Projects/SAGE/sage/local/lib -L/home/brett/Projects/SAGE/sage/local/lib -Wl,-rpath,/home/brett/Projects/SAGE/sage/local/lib  conftest.cpp -llzma  -lm  >&5

configure:30215: $? = 0

configure:30224: result: yes

configure:30232: checking lzma.h usability

configure:30232: g++ -std=gnu++11 -std=gnu++11 -c -g -O2  conftest.cpp >&5

configure:30232: $? = 0

configure:30232: result: yes

configure:30232: checking lzma.h presence

configure:30232: g++ -std=gnu++11 -E -std=gnu++11  conftest.cpp

configure:30232: $? = 0

configure:30232: result: yes

configure:30232: checking for lzma.h

configure:30232: result: yes

configure:30241: checking for xz >= 4.999.0

configure:30320: result: /usr/bin/xz

configure:30329: will use system package and not install SPKG xz

```

```

## ------------------------------------------------------- ##

## Checking whether SageMath should install SPKG libffi... ##

## ------------------------------------------------------- ##

configure:23725: checking for LIBFFI

configure:23732: $PKG_CONFIG --exists --print-errors "libffi"

configure:23735: $? = 0

configure:23749: $PKG_CONFIG --exists --print-errors "libffi"

configure:23752: $? = 0

configure:23938: result: yes

configure:23946: will use system package and not install SPKG libffi

```

The `configure` script concludes that it can use system packages

for `xz` and `libffi`; and that `sqlite`, `libpng` and `bzip2`

have already been installed by SageMath, so there is no point

in checking for the existence of corresponding system packages.

The final recommendations emitted by `configure` are slightly off:

it recommends installing every package for which the decision

reached during the checks was not to use the sytem package.

But sometimes, what led to that decision was not the absence

of a suitable system package, but other factors.

Improving that is tracked at

- Sage Trac ticket 29586

  Improve configure's recommendations

  https://trac.sagemath.org/ticket/29586

If you want Sage to use your system's Python3, maybe you can

uninstall the `sqlite`, `libpng` and `bzip2` SPKGs:

```

$ make sqlite-clean

$ make libpng-clean

$ make bzip2-clean

```

and run `configure` again.

If you want to make sure to use as many system packages

as possible, you might want to uninstall more things with:

```

$ make distclean

```

and run `configure` again.

 

[brettpim]

Thanks Dima and Samuel.

I did as you suggested and I am a hour into the compile and no errors yet so it is looking good.

brett