Problems installing Sage in Ubuntu 24

[Javier Gomez Serrano]

Hi:

I've been having some trouble installing Sage in Ubuntu. I was following the instructions from here:

https://sagemanifolds.obspm.fr/install_ubuntu.html

but I struggle installing contourpy-1.1.1, scipy-1.12.0 and sagelib-10.4.

I've tried reinstalling scipy with no luck.
I attach the logs (the sagelib log seems to be too large to be attached).

Thanks a lot for your time
Best,
Javi

[Dima Pasechnik]

On Fri, Nov 8, 2024 at 11:49 AM Javier Gomez Serrano
<javier_gom...@brown.edu> wrote:
>
> Hi:
>
> I've been having some trouble installing Sage in Ubuntu. I was following the instructions from here:
>
> https://sagemanifolds.obspm.fr/install_ubuntu.html
>
> but I struggle installing contourpy-1.1.1, scipy-1.12.0 and sagelib-10.4.

You have an (old?) version of pybind11 installed in /usr/local/ (cf
/usr/local/include/pybind11/)
which gets picked up.

One way out is to install an up to date pybind11 there.

>
> I've tried reinstalling scipy with no luck.
> I attach the logs (the sagelib log seems to be too large to be attached).
>
> Thanks a lot for your time
> Best,
> Javi
>

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[Javier Gomez Serrano]

Thanks!
When using dpkg, pybind11 didn't prompt to that folder.
I tried to uninstall pybind11 and reinstall Sage and it didn't work.
Then I tried to move the folder. The installation still gets stuck. This is the end of the output:

```Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package: contourpy-1.1.1
last build time: Nov 9 09:59
log file: /home/javi/Work/Sage_v2/sage/logs/pkgs/contourpy-1.1.1.log

* package: scipy-1.12.0
last build time: Nov 9 10:08
log file: /home/javi/Work/Sage_v2/sage/logs/pkgs/scipy-1.12.0.log

* package: sagelib-10.4
last build time: Nov 9 10:41
log file: /home/javi/Work/Sage_v2/sage/logs/pkgs/sagelib-10.4.log

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

real 0m12.750s user 0m30.931s sys 0m5.747s
make[1]: *** [Makefile:40: all-start] Error 1
make[1]: Leaving directory '/home/javi/Work/Sage_v2/sage'
```
It is now failing installing sagelib (I did the folder move between 10:08 and 10:41). The log is too big to be posted. Here's the end of it:

************************************************************************
Setting up build directory /home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/sagelib-10.4
Host system: Linux Javi-TPX1 6.8.0-48-generic #48-Ubuntu SMP PREEMPT_DYNAMIC Fri Sep 27 14:04:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
C compiler: gcc, Using built-in specs., COLLECT_GCC=gcc, COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/13/lto-wrapper, OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa, OFFLOAD_TARGET_DEFAULT=1, Target: x86_64-linux-gnu, Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-23ubuntu4' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu, Thread model: posix, Supported LTO compression algorithms: zlib zstd, gcc version 13.2.0 (Ubuntu 13.2.0-23ubuntu4)
No stamp file for package 'sagelib' in /home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/var/lib/sage/installed
No spkg-legacy-uninstall script; nothing to do
[spkg-install] Installing sagelib-10.4 (editable mode)
[spkg-install] Using pip 24.0 from /home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pip (python 3.12)
[spkg-install] Obtaining file:///home/javi/Work/Sage_v2/sage/src
[spkg-install]   Checking if build backend supports build_editable: started
[spkg-install]   Running command Checking if build backend supports build_editable
[spkg-install]   Checking if build backend supports build_editable: finished with status 'done'
[spkg-install]   Preparing metadata (pyproject.toml): started
[spkg-install]   Running command Preparing metadata (pyproject.toml)
[spkg-install]   Traceback (most recent call last):
[spkg-install]     File "/home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
[spkg-install]       main()
[spkg-install]     File "/home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
[spkg-install]       json_out['return_val'] = hook(**hook_input['kwargs'])
[spkg-install]                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[spkg-install]     File "/home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
[spkg-install]       return hook(metadata_directory, config_settings)
[spkg-install]              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[spkg-install]     File "/home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel
[spkg-install]       self.run_setup()
[spkg-install]     File "/home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/build_meta.py", line 311, in run_setup
[spkg-install]       exec(code, locals())
[spkg-install]     File "<string>", line 21, in <module>
[spkg-install]   ImportError: cannot import name 'is_package_installed_and_updated' from 'sage.misc.package' (/usr/lib/python3/dist-packages/sage/misc/package.py)
[spkg-install]   error: subprocess-exited-with-error
[spkg-install]  
[spkg-install]   × Preparing metadata (pyproject.toml) did not run successfully.
[spkg-install]   │ exit code: 1
[spkg-install]   ╰─> See above for output.
[spkg-install]  
[spkg-install]   note: This error originates from a subprocess, and is likely not a problem with pip.
[spkg-install]   full command: /home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/bin/python3 /home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmps_4twkoo
[spkg-install]   cwd: /home/javi/Work/Sage_v2/sage/src
[spkg-install]   Preparing metadata (pyproject.toml): finished with status 'error'
[spkg-install] error: metadata-generation-failed
[spkg-install]
[spkg-install] × Encountered error while generating package metadata.
[spkg-install] ╰─> See above for output.
[spkg-install]
[spkg-install] note: This is an issue with the package mentioned above, not pip.
[spkg-install] hint: See above for details.
[spkg-install] ************************************************************************************************************************
[spkg-install] Error installing sagelib-10.4
[spkg-install] ************************************************************************************************************************
************************************************************************
Error installing package sagelib-10.4
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log files
  /home/javi/Work/Sage_v2/sage/logs/pkgs/sagelib-10.4.log
and
  /home/javi/Work/Sage_v2/sage/config.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/sagelib-10.4 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/home/javi/Work/Sage_v2/sage/local/var/lib/sage/venv-python3.12/var/tmp/sage/build/sagelib-10.4' && '/home/javi/Work/Sage_v2/sage/sage' --buildsh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

Thanks!
Javi

[Dima Pasechnik]

> [spkg-install]   ImportError: cannot import > name 'is_package_installed_and_updated' from 'sage.misc.package' (/usr/lib/python3/dist-packages/sage/misc/package.py)

This appears to indicate that you have a dpkg-installed (old) version of Sage, which conflicts with the one you are installing.

[Javier Gomez Serrano]

Removing the old version and reinstalling worked. Thank you so much!!!!

Best,
Javi