Cannot compile in Sagemath 9.8beta7 in Fedora 37

[enriqueartal]

I got error with make snappy in Sagemath 9.8beta7, with python3-3.1.11:

[snappy]       
error: Command "gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Ikernel/headers -Ikernel/unix_kit -Ikernel/addl_code -Ikernel/real_type -I/usr/local/sage-310/local/var/lib/sage/venv-python3.11/include -I/usr/include/python3.11 -c cython/SnapPy.c -o build/temp.linux-x86_64-cpython-311/cython/SnapPy.o" failed with exit status 1

[NathanDunfield]

Thanks for the report. Could you upload a complete log of the output prior to the error? We'll need more to go on to figure this out.

[enriqueartal]

snappy.log

Here is the log; I tried also with the git version; would that log also useful?

[enriqueartal]

It seems to be independent of sagemath, essentially the same error happens with pip, both with 3.0.3 or the from github repo

[NathanDunfield]

What version of Cython do you have? Since Python 3.11 is relatively new, you need a recent Cython to be able to build snappy.

[enriqueartal]

The version is 0.29.32, last one in Fedora 37

[NathanDunfield]

Thanks for the clarification. Your error messages look a lot like these from cython/cython#4500. But that issue was fixed in cython/cython#4584 and we have successfully built SnapPy with Cython 0.29.32 and Python 3.11 on Linux, namely the pypa docker image.

Does the below wheel work for you? That might be the easiest solution here:

snappy-3.1rc1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.gz

[enriqueartal]

I tried to install the above file (after gunzip) via pip install name_of_the_file
I got a similar error:

gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Iplanarity_src/c/ -I/usr/include/python3.11 -c planarity_src/c/stack.c -o build/temp.linux-x86_64-cpython-311/planarity_src/c/stack.o
      gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Iplanarity_src/c/ -I/usr/include/python3.11 -c planarity_src/planarity.c -o build/temp.linux-x86_64-cpython-311/planarity_src/planarity.o
      planarity_src/planarity.c:216:12: error fatal: longintrepr.h: No existe el fichero o el directorio
        216 |   #include "longintrepr.h"

Nevertheless I found /usr/include/python3.11/cpython/longintrepr.h in my system.

[NathanDunfield]

That error is from it trying to build the dependency spherogram from the source tarball (no compilation will is needed to install the snappy wheel itself) on pypi. That tarball includes Cython-generated C code that is incompatible with Python 3.11. I think you need to clone https://github.com/3-manifolds/Spherogram and then do pip install . in the resulting directory. Then try installing the snappy wheel again.

[enriqueartal]

It did not work straightforward because I did not send the whole log; doing the same thing with low-index (cloning and installing). BTW, I do not know how to start snappy from the command line! But I can work inside inside sagemath which was the goal. Thanks!

[NathanDunfield]

You can start the app with python3 -m snappy.app assuming the Fedora package python3-tkinter is installed.

[dimpase]

Why does spherogram include Cython-generated files? Isn't Cython standard enough so that you don't have to do this?

[dimpase]

Should spherogram be a separate package on in SageMath?

[NathanDunfield]

Why does spherogram include Cython-generated files?

Because this is the practice that has always been recommended by the Cython docs. I believe the issue is many machines lack Cython or at least a sufficiently up-to-date version. Withpyproject.toml, you can now specify separate build-time requirements (like Cython), but that's a new development and snappy hasn't switched over to it entirely.

I think the real issue here is that we have yet to do a formal release of SnapPy that supports Python 3.11. I hope to do so in the next few weeks.

[dimpase]

I don't understand - pip install Cython isn't such a big deal. (I think it's a bad, outdated, advice on Cython side, too - probably from pre-pip times?)

[dimpase]

Please see cython/cython#5089 - while Cython devs still sit on the fence regarding the issue, please feel free to voice your opinion there.