Cython on Ubuntu 24.04

asked 2024-11-09 19:52:32 +0100

robertSage gravatar image

updated 2024-11-09 21:35:35 +0100

FrédéricC gravatar image

I'm running SageMath 10.4, which was installed using mamba. When trying the example of load("power2.spyx") in Coding in Cython documentation on the SageMath website, I get the following error. I tried to avoid the error by installing libgd3 and libgd-dev via apt, but the error remains.

$ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 10.4, Release Date: 2024-07-19                    │
│ Using Python 3.10.15. Type "help()" for help.                      │
└────────────────────────────────────────────────────────────────────┘
sage: load("power2.spyx")
Compiling power2.spyx...
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/misc/cachefunc.pyx:1010, in sage.misc.cachefunc.CachedFunction.__call__ (build/cythonized/sage/misc/cachefunc.c:8371)()
   1009 try:
-> 1010     return self.cache[k]
   1011 except TypeError:  # k is not hashable

KeyError: ((), ())

During handling of the above exception, another exception occurred:

PackageNotFoundError                      Traceback (most recent call last)
Cell In[1], line 1
----> 1 load("power2.spyx")

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/misc/persist.pyx:176, in sage.misc.persist.load (build/cythonized/sage/misc/persist.c:4564)()
    174 
    175     if sage.repl.load.is_loadable_filename(filename):
--> 176         sage.repl.load.load(filename, globals())
    177         return
    178 

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/repl/load.py:282, in load(filename, globals, attach)
    280     if attach:
    281         add_attached_file(fpath)
--> 282     exec(load_cython(fpath), globals)
    283 elif ext in ['.f', '.f90']:
    284     from sage.misc.inline_fortran import fortran

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/repl/load.py:73, in load_cython(name)
     60 """
     61 Helper function to load a Cython file.
     62 
   (...)
     70   module.
     71 """
     72 from sage.misc.cython import cython
---> 73 mod, dir = cython(str(name), compile_message=True, use_cache=True)
     74 import sys
     75 sys.path.append(dir)

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/misc/cython.py:317, in cython(filename, verbose, compile_message, use_cache, create_local_c_file, annotate, sage_namespace, create_local_so_file)
    313 shutil.copy(filename, pyxfile)
    315 # Add current working directory to includes. This is needed because
    316 # we cythonize from a different directory. See Issue #24764.
--> 317 standard_libs, standard_libdirs, standard_includes, aliases = _standard_libs_libdirs_incdirs_aliases()
    318 includes = [os.getcwd()] + standard_includes
    320 # Now do the actual build, directly calling Cython and distutils

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/misc/cachefunc.pyx:1015, in sage.misc.cachefunc.CachedFunction.__call__ (build/cythonized/sage/misc/cachefunc.c:8499)()
   1013         return self.cache[k]
   1014 except KeyError:
-> 1015     w = self.f(*args, **kwds)
   1016     self.cache[k] = w
   1017     return w

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/misc/cython.py:51, in _standard_libs_libdirs_incdirs_aliases()
     37 @cached_function
     38 def _standard_libs_libdirs_incdirs_aliases():
     39     r"""
     40     Return the list of libraries and library directories.
     41 
   (...)
     49          {...})
     50     """
---> 51     aliases = cython_aliases()
     52     standard_libs = [
     53         'mpfr', 'gmp', 'gmpxx', 'pari', 'm',
     54         'ec', 'gsl',
     55     ] + aliases["CBLAS_LIBRARIES"] + [
     56         'ntl']
     57     standard_libdirs = []

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/sage/env.py:442, in cython_aliases(required_modules, optional_modules)
    440 else:
    441     try:
--> 442         aliases[var + "CFLAGS"] = pkgconfig.cflags(lib).split()
    443         pc = pkgconfig.parse(lib)
    444         libs = pkgconfig.libs(lib)

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/pkgconfig/pkgconfig.py:144, in cflags(package)
    138 def cflags(package):
    139     """
    140     Return the CFLAGS string returned by pkg-config.
    141 
    142     If ``pkg-config`` is not on path, raises ``EnvironmentError``.
    143     """
--> 144     _raise_if_not_exists(package)
    145     return _query(package, '--cflags')

File ~/mambaforge/envs/sage104/lib/python3.10/site-packages/pkgconfig/pkgconfig.py:103, in _raise_if_not_exists(package)
    101 def _raise_if_not_exists(package):
    102     if not exists(package):
--> 103         raise PackageNotFoundError(package)

PackageNotFoundError: gdlib not found
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Comments

FWIW, the command

sage: load("power2.spyx")

works in SageMath 10.4 built from source (*) in Ubuntu 24.04

(*) according to these instructions

eric_g gravatar imageeric_g ( 2024-11-11 15:20:44 +0100 )edit