installing the freesasa python module with gcc 12 and gcc 13

[vcojocaru]

Dear all,

I am trying to install the freesasa python module on an updated openSUSE Tumbleweed distribution (gcc 13 and gcc 12). I did the following steps: (i) created a virtual environment with virtualenv with either python 3.9, 3.10, and 3.11; (ii) use pip install freesasa whitin that environment. In all cases (both gcc versions, all 3 python versions) I get the error below when building.

I'd appreciate any insight on how to fix this.

Thanks
Vlad

---- error message ---

Collecting freesasa
Using cached freesasa-2.2.0.post3.tar.gz (223 kB)
Preparing metadata (setup.py) ... done
Building wheels for collected packages: freesasa
Building wheel for freesasa (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [72 lines of output]
Define environment variable USE_CYTHON to build from Cython source
/apps/haddock/3.0/2023-11-15/.venv-python3.9/lib/python3.9/site-packages/setuptools/init.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

          ********************************************************************************
          Requirements should be satisfied by a PEP 517 installer.
          If you are using pip, you can try `pip install --use-pep517`.
          ********************************************************************************
  
  !!
    dist.fetch_build_eggs(dist.setup_requires)
  running bdist_wheel
  running build
  running build_ext
  building 'freesasa' extension
  creating build
  creating build/temp.linux-x86_64-cpython-39
  creating build/temp.linux-x86_64-cpython-39/lib
  creating build/temp.linux-x86_64-cpython-39/lib/src
  creating build/temp.linux-x86_64-cpython-39/src
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/apps/haddock/3.0/2023-11-15/.venv-python3.9/include -I/usr/include/python3.9 -c lib/src/classifier.c -o build/temp.linux-x86_64-cpython-39/lib/src/classifier.o -DHAVE_CONFIG_H -std=gnu99
  lib/src/classifier.c: In function ‘freesasa_atom_is_backbone’:
  lib/src/classifier.c:990:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
    990 |     for (i = 0; i < sizeof(bb)/sizeof(const char*); ++i) {
        |                   ^
  lib/src/classifier.c: In function ‘freesasa_classifier_add_type’:
  lib/src/classifier.c:411:21: warning: pointer ‘tn’ may be used after ‘realloc’ [-Wuse-after-free]
    411 |         types->name = tn;
        |         ~~~~~~~~~~~~^~~~
  lib/src/classifier.c:410:24: note: call to ‘realloc’ here
    410 |     if ((types->name = realloc(tn, sizeof(char*)*n)) == NULL) {
        |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  lib/src/classifier.c:416:28: warning: pointer ‘tr’ may be used after ‘realloc’ [-Wuse-after-free]
    416 |         types->type_radius = tr;
        |         ~~~~~~~~~~~~~~~~~~~^~~~
  lib/src/classifier.c:415:31: note: call to ‘realloc’ here
    415 |     if ((types->type_radius = realloc(tr, sizeof(double)*n)) == NULL) {
        |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  lib/src/classifier.c:421:27: warning: pointer ‘tc’ may be used after ‘realloc’ [-Wuse-after-free]
    421 |         types->type_class = tc;
        |         ~~~~~~~~~~~~~~~~~~^~~~
  lib/src/classifier.c:420:30: note: call to ‘realloc’ here
    420 |     if ((types->type_class = realloc(tc, sizeof(int) * n)) == NULL) {
        |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  lib/src/classifier.c: In function ‘freesasa_classifier_add_residue’:
  lib/src/classifier.c:561:25: warning: pointer ‘rn’ may be used after ‘realloc’ [-Wuse-after-free]
    561 |         c->residue_name = rn;
        |         ~~~~~~~~~~~~~~~~^~~~
  lib/src/classifier.c:560:28: note: call to ‘realloc’ here
    560 |     if ((c->residue_name = realloc(rn, sizeof(char*) * res)) == NULL) {
        |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  lib/src/classifier.c:566:20: warning: pointer ‘cr’ may be used after ‘realloc’ [-Wuse-after-free]
    566 |         c->residue = cr;
        |         ~~~~~~~~~~~^~~~
  lib/src/classifier.c:565:23: note: call to ‘realloc’ here
    565 |     if ((c->residue = realloc(cr, sizeof(struct classifier_residue *) * res)) == NULL) {
        |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  lib/src/classifier.c: In function ‘next_line’:
  lib/src/classifier.c:187:5: warning: ‘__builtin_strncpy’ output may be truncated copying 256 bytes from a string of length 256 [-Wstringop-truncation]
    187 |     strncpy(line, first, MAX_LINE_LEN);
        |     ^
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/apps/haddock/3.0/2023-11-15/.venv-python3.9/include -I/usr/include/python3.9 -c lib/src/classifier_naccess.c -o build/temp.linux-x86_64-cpython-39/lib/src/classifier_naccess.o -DHAVE_CONFIG_H -std=gnu99
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/apps/haddock/3.0/2023-11-15/.venv-python3.9/include -I/usr/include/python3.9 -c lib/src/classifier_oons.c -o build/temp.linux-x86_64-cpython-39/lib/src/classifier_oons.o -DHAVE_CONFIG_H -std=gnu99
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/apps/haddock/3.0/2023-11-15/.venv-python3.9/include -I/usr/include/python3.9 -c lib/src/classifier_protor.c -o build/temp.linux-x86_64-cpython-39/lib/src/classifier_protor.o -DHAVE_CONFIG_H -std=gnu99
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/apps/haddock/3.0/2023-11-15/.venv-python3.9/include -I/usr/include/python3.9 -c lib/src/coord.c -o build/temp.linux-x86_64-cpython-39/lib/src/coord.o -DHAVE_CONFIG_H -std=gnu99
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/apps/haddock/3.0/2023-11-15/.venv-python3.9/include -I/usr/include/python3.9 -c lib/src/freesasa.c -o build/temp.linux-x86_64-cpython-39/lib/src/freesasa.o -DHAVE_CONFIG_H -std=gnu99
 lib/src/freesasa.c: In function ‘freesasa_alg_name’:
  lib/src/freesasa.c:266:1: error: control reaches end of non-void function [-Werror=return-type]
    266 | }
        | ^
  cc1: some warnings being treated as errors
  error: command '/usr/bin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for freesasa
Running setup.py clean for freesasa
Failed to build freesasa
ERROR: Could not build wheels for freesasa, which is required to install pyproject.toml-based projects

[vcojocaru]

I should add that the regular (non-python) freesasa (both 2.1.2 and freshly downloaded repo) can be built on the system without any error. The freesasa.c file shows some difference between the 2 cloned repositories (freesasa and freesasa-python). When playing a little more I noticed that adding a "return 0;" statement after the assert macro in the last function of freesasa.c (line 266) resolves the build. I am not sure though if this is acceptable for the code. It is still a mystery why this issues only comes with the python module of freesasa and not with the regular freesasa

[mittinatten]

Hmm, thanks for pointing out. Seems compilers are getting stricter. I had a look at the code, and in this particular case it's not an actual error. But I think it's an easy fix to make the compiler happy, so I'll see if I can get un update published.

[vcojocaru]

Great, thanks. If you can tell why the regular freesasa code builds without issues with the same compiler version and without this return statement, I'd be curious about it.

[mittinatten]

I'm not sure, but I assume Cython sets -Werror=return-type and that's not a standard flag. I have pushed what I hope is a fix to the master branch here. Can you verify that it works for you from there, before I publish it as 2.2.1?

[vcojocaru]

gcc -v on my system shows the -Werror=return-type flag but maybe its not actually used when building directly the C code.

Now the repo seems to build correctly (last lines of build below). I will have to test it in the context of Haddock3.

Thanks a lot.

--- last lines of build output ---

gcc -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/usr/include/python3.11 -c lib/src/util.c -o build/temp.linux-x86_64-cpython-311/lib/src/util.o -DHAVE_CONFIG_H -std=gnu99
gcc -Wsign-compare -DNDEBUG -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -DOPENSSL_LOAD_CONF -fwrapv -fno-semantic-interposition -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -g -IVendor/ -fPIC -Ilib/src -I. -I/usr/include/python3.11 -c src/freesasa.c -o build/temp.linux-x86_64-cpython-311/src/freesasa.o -DHAVE_CONFIG_H -std=gnu99
creating build/lib.linux-x86_64-cpython-311
gcc -shared build/temp.linux-x86_64-cpython-311/lib/src/classifier.o build/temp.linux-x86_64-cpython-311/lib/src/classifier_naccess.o build/temp.linux-x86_64-cpython-311/lib/src/classifier_oons.o build/temp.linux-x86_64-cpython-311/lib/src/classifier_protor.o build/temp.linux-x86_64-cpython-311/lib/src/coord.o build/temp.linux-x86_64-cpython-311/lib/src/freesasa.o build/temp.linux-x86_64-cpython-311/lib/src/lexer.o build/temp.linux-x86_64-cpython-311/lib/src/log.o build/temp.linux-x86_64-cpython-311/lib/src/nb.o build/temp.linux-x86_64-cpython-311/lib/src/node.o build/temp.linux-x86_64-cpython-311/lib/src/parser.o build/temp.linux-x86_64-cpython-311/lib/src/pdb.o build/temp.linux-x86_64-cpython-311/lib/src/rsa.o build/temp.linux-x86_64-cpython-311/lib/src/sasa_lr.o build/temp.linux-x86_64-cpython-311/lib/src/sasa_sr.o build/temp.linux-x86_64-cpython-311/lib/src/selection.o build/temp.linux-x86_64-cpython-311/lib/src/structure.o build/temp.linux-x86_64-cpython-311/lib/src/util.o build/temp.linux-x86_64-cpython-311/src/freesasa.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/freesasa.cpython-311-x86_64-linux-gnu.so

[mittinatten]

I experimented with compiler flags too, and couldn't trigger the error either. Strange 🤔

Anyway, great to hear that it works now, I will publish a patch later today.

[mittinatten]

Ok, I published version 2.2.1 with this fix. If you can verify that that also works for you I think we can close the issue. Thanks again for reporting!

[vcojocaru]

Great, thanks. Building the git repo works fine but if I download the archives (either .zip or .tar.gz the content of the lib directory is missing. On the other hand I managed to build another software (Haddock3) which requires freesasa using a requirements.txt file in which the freesasa version is set to 2.2.1 . This actually solved the problem I started with in the first place

[mittinatten]

Hmm, it could be possible that Github has changed what it packages in the release archives, but you should be able to get the C library by pulling the git submodules. Anyway, I was thinking of the PyPi-package primarily (that's where I assume you got it originally, judging from the logs in the original post).

[vcojocaru]

Yes, that works well. Thanks a lot for all the help