command '/miniforge3/envs/sage/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1

[Saraaqzs]

Hello,

After installing sage successfully, I am trying to install surface_dynamics on macOS 12.6.7

But no matter which way I try, I get an error which to me seems to be related to CPP-related dependencies.
I manually checked some of them and to me it looked like all the required versions are installed correctly for instance cysignals, cypari2, cython, etc.

Also via gcc --version I confirm that a C compiler is installed on my machine:

Apple clang version 14.0.0 (clang-1400.0.29.202)
Target: x86_64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

I did not manage to pin down the problem. But this is the log for command sage -pip install surface-dynamics:

Collecting surface-dynamics
Using cached surface_dynamics-0.6.0.tar.gz (8.4 MB)
Preparing metadata (setup.py) ... done
Building wheels for collected packages: surface-dynamics
Building wheel for surface-dynamics (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [409 lines of output]
Adding extension surface_dynamics.flat_surfaces.origamis.origami_dense:
sources = ['origami_dense.pyx', 'normal_form.c', 'lyapunov_exponents.c']
headers = ['origami_dense.pxd', 'lyapunov_exponents.h', 'normal_form.h']
Adding extension surface_dynamics.interval_exchanges.lyapunov_exponents:
sources = ['lyapunov_exponents.pyx', 'generalized_permutation.c', 'lin_alg.c', 'quad_cover.c', 'random.c', 'permutation.c']
headers = ['lyapunov_exponents.h']
Adding extension surface_dynamics.interval_exchanges.integer_iet:
sources = ['integer_iet.pyx', 'int_iet.c', 'int_vector.c']
headers = ['integer_iet.pxd', 'int_iet.h']
Adding extension surface_dynamics.interval_exchanges.iet_family:
sources = ['iet_family.pyx']
headers = []
surface_dynamics/flat_surfaces/origamis/lyapunov_exponents.c:68:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
68 | while(bb = r)
| ~~~^~~
surface_dynamics/flat_surfaces/origamis/lyapunov_exponents.c:68:11: note: place parentheses around the assignment to silence this warning
68 | while(bb = r)
| ^
| ( )
surface_dynamics/flat_surfaces/origamis/lyapunov_exponents.c:68:11: note: use '==' to turn this assignment into an equality comparison
68 | while(bb = r)
| ^
| ==
surface_dynamics/flat_surfaces/origamis/lyapunov_exponents.c:90:8: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
90 | if(j < s[j])
| ~ ^ ~~~~
surface_dynamics/flat_surfaces/origamis/lyapunov_exponents.c:118:8: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
118 | if(j == s[j])
| ~ ^ ~~~~
surface_dynamics/flat_surfaces/origamis/lyapunov_exponents.c:121:8: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
121 | if(j < s[j])
| ~ ^ ~~~~
surface_dynamics/flat_surfaces/origamis/lyapunov_exponents.c:52:22: warning: unused function 'drandGauss' [-Wunused-function]
52 | static inline double drandGauss()
| ^~~~~~~~~~
5 warnings generated.
surface_dynamics/flat_surfaces/origamis/normal_form.c:15:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
15 | if(test = x1[i] - x2[i]) return test;
| ~~~~~^~~~~~~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/normal_form.c:15:11: note: place parentheses around the assignment to silence this warning
15 | if(test = x1[i] - x2[i]) return test;
| ^
| ( )
surface_dynamics/flat_surfaces/origamis/normal_form.c:15:11: note: use '==' to turn this assignment into an equality comparison
15 | if(test = x1[i] - x2[i]) return test;
| ^
| ==
surface_dynamics/flat_surfaces/origamis/normal_form.c:26:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
26 | if(test = g1[i] - g2[i]) return test;
| ~~~~~^~~~~~~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/normal_form.c:26:11: note: place parentheses around the assignment to silence this warning
26 | if(test = g1[i] - g2[i]) return test;
| ^
| ( )
surface_dynamics/flat_surfaces/origamis/normal_form.c:26:11: note: use '==' to turn this assignment into an equality comparison
26 | if(test = g1[i] - g2[i]) return test;
| ^
| ==
surface_dynamics/flat_surfaces/origamis/normal_form.c:129:15: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
129 | for(i=0; i<n; ++i)
| ^
surface_dynamics/flat_surfaces/origamis/normal_form.c:142:12: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
142 | for(i=0; i<n; ++i)
| ^
surface_dynamics/flat_surfaces/origamis/normal_form.c:161:15: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
161 | for(i=0; i<n; ++i)
| ^
surface_dynamics/flat_surfaces/origamis/normal_form.c:170:13: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
170 | for(i=0; i<n; SF_seen[i++] = 1);
| ^
surface_dynamics/flat_surfaces/origamis/normal_form.c:184:16: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
184 | for(mi=0; mi < n; ++mi)
| ~~ ^ ~
surface_dynamics/flat_surfaces/origamis/normal_form.c:202:13: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
202 | for(i=0; i<n; ++i)
| ^
surface_dynamics/flat_surfaces/origamis/normal_form.c:210:13: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
210 | for(i=0; i<n-1; ++i)
| ~^~~~
surface_dynamics/flat_surfaces/origamis/normal_form.c:221:8: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
221 | if(i == n-1) /* here SF_xx = SF_xxx */
| ~ ^ ~~~
surface_dynamics/flat_surfaces/origamis/normal_form.c:222:15: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
222 | for(i=0; i < n-1; ++i)
| ~ ^ ~~~
surface_dynamics/flat_surfaces/origamis/normal_form.c:238:13: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
238 | for(i=0; i < n; ++i)
| ~ ^ ~
12 warnings generated.
surface_dynamics/flat_surfaces/origamis/origami_dense.c:12640:33: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
12640 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/origami_dense.c:12740:33: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
12740 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/origami_dense.c:26757:33: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'long' [-Wsign-compare]
26757 | for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_10; __pyx_t_2+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/origami_dense.c:29499:33: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
29499 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/origami_dense.c:39561:35: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
39561 | for (__pyx_t_15 = 0; __pyx_t_15 < __pyx_t_16; __pyx_t_15+=1) {
| ~~~~~~~~~~ ^ ~~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/origami_dense.c:39573:37: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'long' [-Wsign-compare]
39573 | for (__pyx_t_19 = 0; __pyx_t_19 < __pyx_t_18; __pyx_t_19+=1) {
| ~~~~~~~~~~ ^ ~~~~~~~~~~
surface_dynamics/flat_surfaces/origamis/origami_dense.c:69688:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
69688 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:69699:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
69699 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:69821:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
69821 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:69832:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
69832 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:71747:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
71747 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:71758:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
71758 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:72021:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
72021 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:72032:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
72032 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/flat_surfaces/origamis/origami_dense.c:588:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
588 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
14 warnings generated.
surface_dynamics/interval_exchanges/generalized_permutation.c:38:19: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
38 | for (i = 0; i < gp->k; ++i)
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/generalized_permutation.c:41:19: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
41 | for (i = 0; i < gp->k; ++i)
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/generalized_permutation.c:44:23: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
44 | for (i = gp->k; i < 2 * gp->n; ++i)
| ~ ^ ~~~~~~~~~
surface_dynamics/interval_exchanges/generalized_permutation.c:47:23: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
47 | for (i = gp->k; i < 2 * gp->n; ++i)
| ~ ^ ~~~~~~~~~
4 warnings generated.
surface_dynamics/interval_exchanges/lin_alg.c:42:17: warning: variable 'norm' set but not used [-Wunused-but-set-variable]
42 | double *vv, norm;
| ^
surface_dynamics/interval_exchanges/lin_alg.c:56:21: warning: variable 'norm' is uninitialized when used here [-Wuninitialized]
56 | norm += (qcc->labels)[i].v[j];
| ^~~~
surface_dynamics/interval_exchanges/lin_alg.c:42:21: note: initialize the variable 'norm' to silence this warning
42 | double *vv, norm;
| ^
| = 0.0
surface_dynamics/interval_exchanges/lin_alg.c:274:29: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
274 | for (i_char = 0; i_char < nb_char; ++i_char)
| ~~~~~~ ^ ~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:281:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
281 | for (j = 0; j < qcc->nb_labels; ++j)
| ~ ^ ~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:284:31: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
284 | for (k = 0; k < qcc->degree; ++k)
| ~ ^ ~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:295:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
295 | for (j = 0; j < qcc->nb_labels; ++j)
| ~ ^ ~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:298:31: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
298 | for (k = 0; k < qcc->degree; ++k)
| ~ ^ ~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:324:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
324 | for (j = 0; j < qcc->nb_labels; ++j)
| ~ ^ ~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:327:31: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
327 | for (k = 0; k < qcc->degree; ++k)
| ~ ^ ~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:341:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
341 | for (i = 1; i < dimensions[i_char] - 1; ++i)
| ~ ^ ~~~~~~~~~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:361:31: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
361 | for (j = 0; j < qcc->nb_labels; ++j)
| ~ ^ ~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:364:35: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
364 | for (k = 0; k < qcc->degree; ++k)
| ~ ^ ~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:407:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
407 | for (j = 0; j < qcc->nb_labels; ++j)
| ~ ^ ~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:410:31: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
410 | for (k = 0; k < qcc->degree; ++k)
| ~ ^ ~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:433:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
433 | for (j = 0; j < qcc->nb_labels; ++j)
| ~ ^ ~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lin_alg.c:436:31: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
436 | for (k = 0; k < qcc->degree; ++k)
| ~ ^ ~~~~~~~~~~~
16 warnings generated.
In file included from surface_dynamics/interval_exchanges/lyapunov_exponents.c:1256:
In file included from /Users/miniforge3/envs/sage/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/miniforge3/envs/sage/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/miniforge3/envs/sage/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
17 | #warning "Using deprecated NumPy API, disable it with "
| ^
surface_dynamics/interval_exchanges/lyapunov_exponents.c:5908:28: warning: comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
5908 | __pyx_t_7 = (__pyx_t_6 == __pyx_cur_scope->__pyx_outer_scope->__pyx_v_degree);
| ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/lyapunov_exponents.c:8058:35: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
8058 | for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_14; __pyx_v_i++) {
| ~~~~~~~~~ ^ ~~~~~~~~~~
surface_dynamics/interval_exchanges/lyapunov_exponents.c:13678:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
13678 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/interval_exchanges/lyapunov_exponents.c:573:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
573 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
surface_dynamics/interval_exchanges/lyapunov_exponents.c:13689:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
13689 | CYTHON_FALLTHROUGH;
| ^
surface_dynamics/interval_exchanges/lyapunov_exponents.c:573:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
573 | #define CYTHON_FALLTHROUGH attribute((fallthrough))
| ^
5 warnings generated.
surface_dynamics/interval_exchanges/permutation.c:33:15: warning: variable 'j' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
33 | ++j;
| ^
surface_dynamics/interval_exchanges/permutation.c:21:35: note: incremented here
21 | for (j = 0; j < degree; ++j)
| ^
1 warning generated.
surface_dynamics/interval_exchanges/quad_cover.c:167:19: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
167 | for (i = 0; i < gp->n; ++i)
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:170:19: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
170 | for (i = 0; i < gp->n; ++i)
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:195:19: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
195 | for (i = 0; i < 2 * gp->n; ++i)
| ~ ^ ~~~~~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:198:17: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
198 | ((i < gp->k) == ((gp->twin)[i] < gp->k));
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:200:28: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
200 | if ((i == 0) || (i == gp->k))
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:205:36: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
205 | if ((i == gp->k - 1) || (i == 2 * gp->n - 1))
| ~ ^ ~~~~~~~~~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:205:16: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
205 | if ((i == gp->k - 1) || (i == 2 * gp->n - 1))
| ~ ^ ~~~~~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:211:15: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
211 | if (i < gp->k)
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:213:31: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
213 | if ((gp->twin)[i] < i)
| ~~~~~~~~~~~~~ ^ ~
surface_dynamics/interval_exchanges/quad_cover.c:218:59: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
218 | if (((gp->twin)[i] < gp->k) || ((gp->twin)[i] > i))
| ~~~~~~~~~~~~~ ^ ~
surface_dynamics/interval_exchanges/quad_cover.c:223:40: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
223 | (qcc->intervals)[i].is_top = i < gp->k;
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:226:60: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
226 | || ((qcc->intervals)[i].orientation == -1 && i >= gp->k);
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:225:47: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
225 | && i < gp->k)
| ~ ^ ~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:457:18: warning: unused variable 'd' [-Wunused-variable]
457 | size_t j, n, d, k;
| ^
surface_dynamics/interval_exchanges/quad_cover.c:457:21: warning: unused variable 'k' [-Wunused-variable]
457 | size_t j, n, d, k;
| ^
surface_dynamics/interval_exchanges/quad_cover.c:458:9: warning: unused variable 'verbose' [-Wunused-variable]
458 | int verbose = 0;
| ^~~~~~~
surface_dynamics/interval_exchanges/quad_cover.c:798:15: warning: unused variable 'j' [-Wunused-variable]
798 | size_t i, j, nb_ren = 0;
| ^
surface_dynamics/interval_exchanges/quad_cover.c:799:12: warning: unused variable 'buffer' [-Wunused-variable]
799 | double buffer;
| ^~~~~~
18 warnings generated.
surface_dynamics/interval_exchanges/int_iet.c:282:66: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
282 | fprintf(stderr, "length top=%lu while length bot=%lu\n", ltop, lbot);
| ~~~ ^~~~
| %llu
surface_dynamics/interval_exchanges/int_iet.c:282:72: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
282 | fprintf(stderr, "length top=%lu while length bot=%lu\n", ltop, lbot);
| ~~~ ^~~~
| %llu
surface_dynamics/interval_exchanges/int_iet.c:310:33: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
310 | fprintf(stream, "%lu ", (t->labels[j]).length);
| ~~~ ^~~~~~~~~~~~~~~~~~~~~
| %llu
surface_dynamics/interval_exchanges/int_iet.c:315:33: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
315 | fprintf(stream, "%lu ", (t->labels[j]).height);
| ~~~ ^~~~~~~~~~~~~~~~~~~~~
| %llu
4 warnings generated.
surface_dynamics/interval_exchanges/int_vector.c:43:30: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
43 | printf("nfree = %lu\n", t->nfree);
| ~~~ ^~~~~~~~
| %llu
surface_dynamics/interval_exchanges/int_vector.c:44:30: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
44 | printf("nother = %lu\n", t->nother);
| ~~~ ^~~~~~~~~
| %llu
surface_dynamics/interval_exchanges/int_vector.c:47:25: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
47 | printf( " %lu", t->xfree[i]);
| ~~~ ^~~~~~~~~~~
| %llu
surface_dynamics/interval_exchanges/int_vector.c:51:24: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
51 | printf(" %lu", t->xtop[i]);
| ~~~ ^~~~~~~~~~
| %llu
surface_dynamics/interval_exchanges/int_vector.c:55:24: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
55 | printf(" %lu", t->xbot[i]);
| ~~~ ^~~~~~~~~~
| %llu
5 warnings generated.
In file included from surface_dynamics/interval_exchanges/integer_iet.c:1252:
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:117:5: error: use of undeclared identifier 'cysigs'
117 | cysigs.s = message;
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:132:9: error: use of undeclared identifier 'cysigs'
132 | if (cysigs.sig_on_count > 0)
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:134:9: error: use of undeclared identifier 'cysigs'
134 | cysigs.sig_on_count++;
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:149:9: error: call to undeclared function 'unlikely'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
149 | if (unlikely(jmpret > 0))
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:152:9: error: call to undeclared function '_sig_on_recover'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
152 | _sig_on_recover();
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:158:5: error: use of undeclared identifier 'cysigs'
158 | cysigs.sig_on_count = 1;
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:166:18: error: use of undeclared identifier 'cysigs'
166 | if (unlikely(cysigs.interrupt_received))
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:168:9: error: call to undeclared function '_sig_on_interrupt_received'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
168 | _sig_on_interrupt_received();
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:190:9: error: call to undeclared function 'unlikely'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
190 | if (unlikely(cysigs.sig_on_count <= 0))
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:190:18: error: use of undeclared identifier 'cysigs'
190 | if (unlikely(cysigs.sig_on_count <= 0))
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:192:9: error: call to undeclared function '_sig_off_warning'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
192 | _sig_off_warning(file, line);
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:196:11: error: use of undeclared identifier 'cysigs'
196 | --cysigs.sig_on_count;
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:218:9: error: call to undeclared function 'unlikely'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
218 | if (unlikely(cysigs.interrupt_received) && cysigs.sig_on_count == 0)
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:218:18: error: use of undeclared identifier 'cysigs'
218 | if (unlikely(cysigs.interrupt_received) && cysigs.sig_on_count == 0)
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:218:48: error: use of undeclared identifier 'cysigs'
218 | if (unlikely(cysigs.interrupt_received) && cysigs.sig_on_count == 0)
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:220:9: error: call to undeclared function '_sig_on_interrupt_received'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
220 | _sig_on_interrupt_received();
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:252:7: error: use of undeclared identifier 'cysigs'
252 | ++cysigs.block_sigint;
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:265:7: error: use of undeclared identifier 'cysigs'
265 | --cysigs.block_sigint;
| ^
/Users/miniforge3/envs/sage/lib/python3.12/site-packages/cysignals/macros.h:267:9: error: call to undeclared function 'unlikely'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
267 | if (unlikely(cysigs.interrupt_received))
| ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
error: command '/Users/miniforge3/envs/sage/bin/x86_64-apple-darwin13.4.0-clang' 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 surface-dynamics
Running setup.py clean for surface-dynamics
Failed to build surface-dynamics
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (surface-dynamics)

I have also tried installation from the source via cloning from github repo and running python setup.py. But it was also the same; something was wrong with the CPP backends.

Any idea what is problematic here?

[videlec]

Indeed, there seems to be a problem with the recent version of cysignals, see pyodide/pyodide#5221

[Saraaqzs]

I see!
So do you think downgrading cysignals from 1.12.0 would help?

[videlec]

According to the messages, it should. I am curious to know if you try it.

[Saraaqzs]

I downgraded cysignals to 1.11.3 and as a result, I could install surface_dynamics successfully! :)

But now I am facing an import issue with surface_dynamics itself both on versions 0.6.0 and 0.5.0 (I could not install 0.4.7 due to conflicts):

from surface_dynamics import *

Traceback (most recent call last):
File <stdin>, line 1, in
File "/Users/sage_test/surface-dynamics/surface_dynamics/init.py", line 20, in
from surface_dynamics.flat_surfaces.all import *
File "/Users/sage_test/surface-dynamics/surface_dynamics/flat_surfaces/all.py", line 17, in
from .origamis.all import *
File "/Users/sage_test/surface-dynamics/surface_dynamics/flat_surfaces/origamis/all.py", line 12, in
from .origami import Origami
File "/Users/sage_test/surface-dynamics/surface_dynamics/flat_surfaces/origamis/origami.py", line 49, in
from surface_dynamics.flat_surfaces.origamis.origami_dense import Origami_dense_pyx
ModuleNotFoundError: No module named 'surface_dynamics.flat_surfaces.origamis.origami_dense'

I have a hunch that it is an internal bug.
Do you know a solution or how I can fix it manually myself?

[videlec]

That seems related to a compiled part of the module (with cython). Could you post the complete list of conda list in your environment? I could try to reproduce and fix it.

[Saraaqzs]

Yes, that would be amazing! There you go:

# packages in environment at /Users/miniforge3/envs/sage:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
alabaster                 0.7.16             pyhd8ed1ab_0    conda-forge
anyio                     4.7.0              pyhd8ed1ab_0    conda-forge
appnope                   0.1.4              pyhd8ed1ab_1    conda-forge
arb                       2.9.0                         0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_1    conda-forge
argon2-cffi-bindings      21.2.0          py312hb553811_5    conda-forge
arpack                    3.9.1           nompi_hf81eadf_101    conda-forge
arrow                     1.3.0              pyhd8ed1ab_1    conda-forge
asttokens                 3.0.0              pyhd8ed1ab_1    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_1    conda-forge
attrs                     24.2.0             pyh71513ae_1    conda-forge
babel                     2.16.0             pyhd8ed1ab_1    conda-forge
bdw-gc                    8.0.6                h940c156_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_1    conda-forge
beniget                   0.4.2.post1        pyhd8ed1ab_1    conda-forge
blas-devel                3.9.0           25_osx64_openblas    conda-forge
bleach                    6.2.0              pyhd8ed1ab_1    conda-forge
brial                     1.2.12             pyh694c41f_3    conda-forge
brotli                    1.1.0                h00291cd_2    conda-forge
brotli-bin                1.1.0                h00291cd_2    conda-forge
brotli-python             1.1.0           py312h5861a67_2    conda-forge
bwidget                   1.10.1               h694c41f_0    conda-forge
bzip2                     1.0.8                hfdf4475_7    conda-forge
c-ares                    1.34.4               hf13058a_0    conda-forge
ca-certificates           2024.12.14           h8857fd0_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.18.2               h950ec3b_1    conda-forge
cctools_osx-64            1010.6               hadbd6bd_2    conda-forge
cddlib                    1!0.94m              h0f52abe_0    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py312hf857d28_0    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_1    conda-forge
clang                     19.1.5          default_h576c50e_0    conda-forge
clang-19                  19.1.5          default_h3571c67_0    conda-forge
clang_impl_osx-64         19.1.5              h7c3691e_23    conda-forge
clang_osx-64              19.1.5              h7e5c614_23    conda-forge
clangxx                   19.1.5          default_heb2e8d1_0    conda-forge
clangxx_impl_osx-64       19.1.5              h1f7e832_23    conda-forge
clangxx_osx-64            19.1.5              h7e5c614_23    conda-forge
cliquer                   1.22                 h10d778d_1    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
comm                      0.2.2              pyhd8ed1ab_1    conda-forge
compiler-rt               19.1.5               h52031e2_0    conda-forge
compiler-rt_osx-64        19.1.5               hc6f8467_0    conda-forge
contourpy                 1.3.1           py312hc47a885_0    conda-forge
conway-polynomials        0.10               pyhd8ed1ab_0    conda-forge
cpython                   3.12.8          py312hd8ed1ab_1    conda-forge
curl                      8.11.1               h5dec5d8_0    conda-forge
cvxopt                    1.3.2           py312h4cdf924_3    conda-forge
cycler                    0.12.1             pyhd8ed1ab_1    conda-forge
cypari2                   2.1.5           py312h88009e3_0    conda-forge
cysignals                 1.11.3                   pypi_0    pypi
cython                    3.0.11          py312h6891801_3    conda-forge
debugpy                   1.8.11          py312haafddd8_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_1    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.21.2             pyhd8ed1ab_1    conda-forge
dsdp                      5.8               h6e329d1_1203    conda-forge
ecl                       24.5.10              h56bac16_0    conda-forge
eclib                     20231211             h02435c3_0    conda-forge
ecm                       7.0.5                h4f6b447_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_1    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
executing                 2.1.0              pyhd8ed1ab_1    conda-forge
fflas-ffpack              2.5.0                h5898d61_0    conda-forge
fftw                      3.3.10          nompi_h292e606_110    conda-forge
flintqs                   1.0               ha6586c5_1001    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.15.0               h37eeddb_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.55.3          py312h3520af0_0    conda-forge
fplll                     5.4.5                hb7981ad_0    conda-forge
fpylll                    0.6.1           py312ha9f3631_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_1    conda-forge
freetype                  2.12.1               h60636b9_2    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
future                    1.0.0              pyhd8ed1ab_1    conda-forge
gap-core                  4.12.2               hc16eb5f_3    conda-forge
gap-defaults              4.12.2               h694c41f_3    conda-forge
gast                      0.5.5              pyhd8ed1ab_0    conda-forge
gettext                   0.22.5               hdfe23c8_3    conda-forge
gettext-tools             0.22.5               hdfe23c8_3    conda-forge
gf2x                      1.3.0                h35ac7d9_3    conda-forge
gfan                      0.6.2             hd793b56_1003    conda-forge
gfortran_impl_osx-64      13.2.0               h2bc304d_3    conda-forge
gfortran_osx-64           13.2.0               h18f7dce_1    conda-forge
giac                      1.9.0.21             h92f3f65_1    conda-forge
givaro                    4.2.0                h1b3d6f7_0    conda-forge
glpk                      5.0                  h3cb5acd_0    conda-forge
gmp                       6.3.0                hf036a51_2    conda-forge
gmpy2                     2.1.5           py312h068713c_3    conda-forge
graphite2                 1.3.13            h73e2aa4_1003    conda-forge
gsl                       2.7                  h93259b0_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_1    conda-forge
h2                        4.1.0              pyhd8ed1ab_1    conda-forge
harfbuzz                  9.0.0                h098a298_1    conda-forge
hpack                     4.0.0              pyhd8ed1ab_1    conda-forge
httpcore                  1.0.7              pyh29332c3_1    conda-forge
httpx                     0.28.1             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_1    conda-forge
icu                       75.1                 h120a0e1_0    conda-forge
idna                      3.10               pyhd8ed1ab_1    conda-forge
igraph                    0.10.15              h5479cbe_1    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
iml                       1.0.5             h61918c1_1004    conda-forge
importlib-metadata        8.5.0              pyha770c72_1    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_1    conda-forge
ipykernel                 6.29.5             pyh57ce528_0    conda-forge
ipython                   8.30.0             pyh707e725_0    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_1    conda-forge
isl                       0.26            imath32_h2e86a7b_101    conda-forge
isoduration               20.11.0            pyhd8ed1ab_1    conda-forge
jedi                      0.19.2             pyhd8ed1ab_1    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_1    conda-forge
jmol                      14.32.9              h694c41f_0    conda-forge
json5                     0.10.0             pyhd8ed1ab_1    conda-forge
jsonpointer               3.0.0           py312hb401068_1    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2024.10.1          pyhd8ed1ab_1    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_1    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_1    conda-forge
jupyter_client            8.6.3              pyhd8ed1ab_1    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_1    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_1    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_1    conda-forge
jupyterlab                4.3.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_2    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_1    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_1    conda-forge
kiwisolver                1.4.7           py312hc5c4d5f_0    conda-forge
krb5                      1.21.3               h37d8d59_0    conda-forge
lcalc                     2.0.5                h547a6ed_2    conda-forge
lcms2                     2.16                 ha2f27b4_0    conda-forge
ld64_osx-64               951.9                h9d2de3d_2    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libamd                    3.3.3            ss783_hd70f86c    conda-forge
libasprintf               0.22.5               hdfe23c8_3    conda-forge
libasprintf-devel         0.22.5               hdfe23c8_3    conda-forge
libblas                   3.9.0           25_osx64_openblas    conda-forge
libbraiding               1.2                  hf0c8a7f_0    conda-forge
libbrial                  1.2.12               h81e9653_3    conda-forge
libbrotlicommon           1.1.0                h00291cd_2    conda-forge
libbrotlidec              1.1.0                h00291cd_2    conda-forge
libbrotlienc              1.1.0                h00291cd_2    conda-forge
libbtf                    2.3.2            ss783_ha7556f6    conda-forge
libcamd                   3.3.3            ss783_ha7556f6    conda-forge
libcblas                  3.9.0           25_osx64_openblas    conda-forge
libccolamd                3.3.4            ss783_ha7556f6    conda-forge
libcholmod                5.3.0            ss783_h7fe8f01    conda-forge
libclang-cpp19.1          19.1.5          default_h3571c67_0    conda-forge
libcolamd                 3.3.4            ss783_ha7556f6    conda-forge
libcurl                   8.11.1               h5dec5d8_0    conda-forge
libcxsparse               4.4.1            ss783_h6325aac    conda-forge
libcxx                    19.1.5               hf95d169_0    conda-forge
libcxx-devel              19.1.5               h7c275be_0    conda-forge
libdeflate                1.22                 h00291cd_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 h10d778d_2    conda-forge
libexpat                  2.6.4                h240833e_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libflint                  3.0.1           h240f438_ntl_101    conda-forge
libgd                     2.3.3               h2e77e4f_10    conda-forge
libgettextpo              0.22.5               hdfe23c8_3    conda-forge
libgettextpo-devel        0.22.5               hdfe23c8_3    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
libgfortran-devel_osx-64  13.2.0               h80d4556_3    conda-forge
libgfortran5              13.2.0               h2873a65_3    conda-forge
libglib                   2.82.2               hb6ef654_0    conda-forge
libhomfly                 1.02r6               h10d778d_1    conda-forge
libiconv                  1.17                 hd75f5a5_2    conda-forge
libintl                   0.22.5               hdfe23c8_3    conda-forge
libintl-devel             0.22.5               hdfe23c8_3    conda-forge
libjpeg-turbo             3.0.0                h0dc2134_1    conda-forge
libklu                    2.3.5            ss783_hdf6d925    conda-forge
liblapack                 3.9.0           25_osx64_openblas    conda-forge
liblapacke                3.9.0           25_osx64_openblas    conda-forge
libldl                    3.3.2            ss783_ha7556f6    conda-forge
libllvm19                 19.1.5               hc29ff6c_0    conda-forge
liblzma                   5.6.3                hd471939_1    conda-forge
liblzma-devel             5.6.3                hd471939_1    conda-forge
libnghttp2                1.64.0               hc7306c3_0    conda-forge
libopenblas               0.3.28          openmp_hbf64a52_1    conda-forge
libparu                   1.0.0            ss783_hd366fff    conda-forge
libpng                    1.6.44               h4b8f8c9_0    conda-forge
librbio                   4.3.4            ss783_ha7556f6    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libspex                   3.2.1            ss783_h2c43358    conda-forge
libspqr                   4.3.4            ss783_h0b03d82    conda-forge
libsqlite                 3.47.2               hdb6dae5_0    conda-forge
libssh2                   1.11.1               h3dc7d44_0    conda-forge
libsuitesparseconfig      7.8.3            ss783_he344b7b    conda-forge
libtiff                   4.7.0                hf4bdac2_2    conda-forge
libumfpack                6.3.5            ss783_h53c776b    conda-forge
libwebp-base              1.4.0                h10d778d_0    conda-forge
libxcb                    1.17.0               hf1f96e2_0    conda-forge
libxml2                   2.13.5               hebb159f_1    conda-forge
libzlib                   1.3.1                hd23fc13_2    conda-forge
linbox                    1.7.0                h7061c92_0    conda-forge
llvm-openmp               19.1.5               ha54dae1_0    conda-forge
llvm-tools                19.1.5               h3fe3016_0    conda-forge
llvm-tools-19             19.1.5               he90a8e3_0    conda-forge
lrcalc                    2.1                  hac325c4_7    conda-forge
m4ri                      20140914          hd82a5f3_1006    conda-forge
m4rie                     20150908          hc616cfc_1002    conda-forge
make                      4.4.1                h00291cd_2    conda-forge
markupsafe                3.0.2           py312h3520af0_1    conda-forge
matplotlib-base           3.9.4           py312h535dea3_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_1    conda-forge
maxima                    5.47.0               h3080a4d_3    conda-forge
memory-allocator          0.1.3           py312hb553811_1    conda-forge
metis                     5.1.0             h3023b02_1007    conda-forge
mistune                   3.0.2              pyhd8ed1ab_1    conda-forge
mpc                       1.3.1                h9d8efa1_1    conda-forge
mpfi                      1.5.4             h52b28e3_1001    conda-forge
mpfr                      4.2.1                haed47dc_3    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nauty                     2.8.8                h10d778d_1    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.16.4               hd8ed1ab_2    conda-forge
nbconvert-core            7.16.4             pyhff2d567_2    conda-forge
nbconvert-pandoc          7.16.4               hd8ed1ab_2    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_1    conda-forge
ncurses                   6.5                  hf036a51_1    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_1    conda-forge
networkx                  3.4.2              pyh267e887_2    conda-forge
notebook                  7.3.1              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_1    conda-forge
ntl                       11.4.3               h0ab3c2f_1    conda-forge
numpy                     1.26.4          py312he3a82b2_0    conda-forge
openblas                  0.3.28          openmp_h30af337_1    conda-forge
openjdk                   23.0.1               h18c9476_1    conda-forge
openjpeg                  2.5.3                h7fd6d84_0    conda-forge
openssl                   3.4.0                hd471939_0    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.2               pyhd8ed1ab_2    conda-forge
palp                      2.20                 hbcb3906_0    conda-forge
pandoc                    3.6                  h694c41f_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.54.0               hb83bde0_3    conda-forge
pari                      2.15.5          h7ba67ff_2_pthread    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
parso                     0.8.4              pyhd8ed1ab_1    conda-forge
pcre2                     10.44                h7634a1b_2    conda-forge
perl                      5.32.1          7_h10d778d_perl5    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_1    conda-forge
pickleshare               0.7.5           pyhd8ed1ab_1004    conda-forge
pillow                    10.4.0          py312h683ea77_1    conda-forge
pip                       24.3.1             pyh8b19718_0    conda-forge
pixman                    0.44.2               h1fd1274_0    conda-forge
pkg-config                0.29.2            hf7e621a_1009    conda-forge
pkgconfig                 1.5.5              pyhd8ed1ab_5    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_2    conda-forge
planarity                 3.0.2.0              h10d778d_0    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_1    conda-forge
ply                       3.11               pyhd8ed1ab_3    conda-forge
ppl                       1.2               ha60d53e_1006    conda-forge
pplpy                     0.8.9           py312hb4417ad_1    conda-forge
primecount                7.6                  ha894c9a_0    conda-forge
primecountpy              0.1.0           py312h49ebfd2_4    conda-forge
primesieve                11.0                 hf0c8a7f_0    conda-forge
prometheus_client         0.21.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.48             pyha770c72_1    conda-forge
psutil                    6.1.0           py312h3d0f464_0    conda-forge
pthread-stubs             0.4               h00291cd_1002    conda-forge
ptyprocess                0.7.0              pyhd8ed1ab_1    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_1    conda-forge
pycparser                 2.22               pyh29332c3_1    conda-forge
pygments                  2.18.0             pyhd8ed1ab_1    conda-forge
pyobjc-core               10.3.2          py312h2365019_0    conda-forge
pyobjc-framework-cocoa    10.3.2          py312h2365019_0    conda-forge
pyparsing                 3.2.0              pyhd8ed1ab_2    conda-forge
pysocks                   1.7.1              pyha55dd90_7    conda-forge
python                    3.12.8          h9ccd52b_1_cpython    conda-forge
python-dateutil           2.9.0.post0        pyhff2d567_1    conda-forge
python-fastjsonschema     2.21.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-lrcalc             2.1             py312h5861a67_7    conda-forge
python_abi                3.12                    5_cp312    conda-forge
pythran                   0.14.0          py312hb54c7b1_1    conda-forge
pytz                      2024.2             pyhd8ed1ab_1    conda-forge
pyyaml                    6.0.2           py312hb553811_1    conda-forge
pyzmq                     25.1.2          py312hc789acb_0    conda-forge
qd                        2.3.22            h2beb688_1004    conda-forge
qhull                     2020.2               h3c5361c_5    conda-forge
r-base                    4.3.3               hc011bdf_15    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_1    conda-forge
requests                  2.32.3             pyhd8ed1ab_1    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_1    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.22.3          py312h0d0de52_0    conda-forge
rpy2                      3.5.11          py312r43h5d6a8aa_3    conda-forge
rubiks                    20070912          h370ebc4_1001    conda-forge
rw                        0.9                  h10d778d_2    conda-forge
sage                      10.4                 hd8ed1ab_0    conda-forge
sagelib                   10.4            py312h1f73b89_0    conda-forge
sagemath-db-combinatorial-designs 20140630                      1    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20210214             hd8ed1ab_0    conda-forge
sagemath-db-polytopes     20170220                      1    conda-forge
sagetex                   3.6.1              pyhd8ed1ab_0    conda-forge
scipy                     1.14.1          py312h3b0f538_2    conda-forge
send2trash                1.8.3              pyh31c8845_1    conda-forge
setuptools                75.6.0             pyhff2d567_1    conda-forge
sigtool                   0.1.3                h88f4db0_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singular                  4.3.2.p8             h0d51a9f_1    conda-forge
six                       1.17.0             pyhd8ed1ab_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_1    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    7.4.7              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   2.0.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-devhelp     2.0.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-htmlhelp    2.1.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_1    conda-forge
sphinxcontrib-qthelp      2.0.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-serializinghtml 1.1.10             pyhd8ed1ab_1    conda-forge
sqlite                    3.47.2               h2e4c9dc_0    conda-forge
stack_data                0.6.3              pyhd8ed1ab_1    conda-forge
suitesparse               7.8.3            ss783_h8b3df4c    conda-forge
surface-dynamics          0.5.0                    pypi_0    pypi
symmetrica                3.0.1                hf0c8a7f_0    conda-forge
sympow                    2.023.6              h115ba6a_3    conda-forge
sympy                     1.13.3           pyh2585a3b_104    conda-forge
tachyon                   0.99b6            h3a1d103_1002    conda-forge
tapi                      1300.6.5             h390ca13_0    conda-forge
terminado                 0.18.1             pyh31c8845_0    conda-forge
three.js                  122                  hd8ed1ab_2    conda-forge
threejs-sage              122                  hd8ed1ab_2    conda-forge
tinycss2                  1.4.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
tktable                   2.10                 hba9d6f1_6    conda-forge
tomli                     2.2.1              pyhd8ed1ab_1    conda-forge
tornado                   6.4.2           py312h01d7ebd_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_1    conda-forge
types-python-dateutil     2.9.0.20241206     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_1    conda-forge
typing_extensions         4.12.2             pyha770c72_1    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_1    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
tzlocal                   5.2             py312hb401068_1    conda-forge
unicodedata2              15.1.0          py312h3d0f464_1    conda-forge
uri-template              1.3.0              pyhd8ed1ab_1    conda-forge
urllib3                   2.2.3              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_1    conda-forge
webcolors                 24.11.1            pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_3    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.13             pyhd8ed1ab_1    conda-forge
xorg-libxau               1.0.11               h00291cd_1    conda-forge
xorg-libxdmcp             1.1.5                h00291cd_0    conda-forge
xz                        5.6.3                h357f2ed_1    conda-forge
xz-gpl-tools              5.6.3                h357f2ed_1    conda-forge
xz-tools                  5.6.3                hd471939_1    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.5                hde137ed_4    conda-forge
zipp                      3.21.0             pyhd8ed1ab_1    conda-forge
zlib                      1.3.1                hd23fc13_2    conda-forge
zn_poly                   0.9.2                h0f52abe_0    conda-forge
zstandard                 0.23.0          py312h7122b0e_1    conda-forge
zstd                      1.5.6                h915ae27_0    conda-forge

[videlec]

Sadly I can not reproduce (the built packages might differ depending on platforms?):

error    libmamba Could not solve for environment specs
    The following packages are incompatible
    ├─ cpython 3.12.8  is installable and it requires
    │  └─ python 3.12.8.* , which requires
    │     └─ python_abi 3.12.* *_cp312, which can be installed;
    ├─ cysignals 1.11.3  does not exist (perhaps a typo or a missing channel);
    ├─ ecl 24.5.10  is requested and can be installed;
    ├─ libgfortran 5.0.0  does not exist (perhaps a typo or a missing channel);
    ├─ libgfortran5 13.2.0  is requested and can be installed;
    ├─ libintl-devel 0.22.5  does not exist (perhaps a typo or a missing channel);
    ├─ libintl 0.22.5  does not exist (perhaps a typo or a missing channel);
    ├─ libsuitesparseconfig 7.8.3  is not installable because it requires
    │  └─ libgfortran5 >=13.3.0 , which conflicts with any installable versions previously reported;
    ├─ primecount 7.6  is requested and can be installed;
    ├─ primecountpy 0.1.0  is not installable because there are no viable options
    │  ├─ primecountpy 0.1.0 would require
    │  │  └─ primecount >=7.2,<7.3.0a0  but there are no viable options
    │  │     ├─ primecount 7.2 would require
    │  │     │  └─ primesieve >=7.6,<7.7.0a0 , which can be installed;
    │  │     └─ primecount 7.2 would require
    │  │        └─ primesieve >=7.8,<7.9.0a0 , which can be installed;
    │  ├─ primecountpy 0.1.0 would require
    │  │  └─ primecount >=7.4,<7.5.0a0 , which requires
    │  │     └─ primesieve >=8.0,<8.1.0a0 , which can be installed;
    │  ├─ primecountpy 0.1.0 would require
    │  │  └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
    │  ├─ primecountpy 0.1.0 would require
    │  │  └─ primecount >=7.9,<7.10.0a0 , which requires
    │  │     └─ primesieve >=11.1,<11.2.0a0 , which can be installed;
    │  ├─ primecountpy 0.1.0 would require
    │  │  └─ python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
    │  ├─ primecountpy 0.1.0 would require
    │  │  └─ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
    │  └─ primecountpy 0.1.0 would require
    │     └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported;
    ├─ primesieve 11.0  is not installable because it conflicts with any installable versions previously reported;
    ├─ pyobjc-core 10.3.2  does not exist (perhaps a typo or a missing channel);
    ├─ pyobjc-framework-cocoa 10.3.2  does not exist (perhaps a typo or a missing channel);
    ├─ python 3.12.8 , which can be installed (as previously explained);
    ├─ sage 10.4  is not installable because it requires
    │  └─ primecountpy >=0.1.0,<0.2.0 , which cannot be installed (as previously explained);
    └─ surface-dynamics 0.5.0  is not installable because there are no viable options
       ├─ surface-dynamics 0.5.0 would require
       │  └─ sagelib [10.0.* |10.1.* |...|9.8.* ], which requires
       │     └─ ecl >=21.2.1,<21.3.0a0 , which conflicts with any installable versions previously reported;
       ├─ surface-dynamics 0.5.0 would require
       │  └─ sagelib 10.3.* , which requires
       │     └─ ecl >=23.9.9,<23.10.0a0 , which conflicts with any installable versions previously reported;
       └─ surface-dynamics 0.5.0 would require
          └─ sagelib 9.2.* , which requires
             └─ ecl >=20.4.24,<20.5.0a0 , which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

[videlec]

@Saraaqzs you can "fix" it manually by disabling the import of the culprit module. Namely, edit /Users/sage_test/surface-dynamics/surface_dynamics/flat_surfaces/all.py and remove line 17 from .origamis.all import *.

[Saraaqzs]

Amazing! It works fine after commenting that line out. Many thanks for your help. 🥇
So I will close this issue.
Only one more (and probably the final) question:
What does this error exactly mean?

------------------------------------------------------------------------
(no backtrace available)
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------
Segmentation fault: 11

Is it the equivalent of a "dead kernel" in Jupyter?

[videlec]

A segmentation fault occurs when a program tries to access memory that it has no right to access to. It frequently happen with (poorly written) C programs manipulating pointers.

[videlec]

I am reopening the issue as it is a major problem that the compiled cython modules are not installable. I am glad that the workaround was sufficient for you purpose.

[Saraaqzs]

Got it! Thanks a lot! 👍