pyodide: Unable to build on Ubuntu 18.04 | assertion fail in numpy
Executing make command in root gives off the following trace, ending up in an assertion error. I am unable to fix this myself. Google search results suggest to upgrade numpy and scipy, but that does not help. Here is the log:
building extension "scipy.interpolate._interpolate" sources
building extension "scipy.io.matlab.streams" sources
building extension "scipy.io.matlab.mio_utils" sources
building extension "scipy.io.matlab.mio5_utils" sources
building extension "scipy.linalg._fblas" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg' to include_dirs.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scipy/linalg/_fblas-f2pywrappers.f' to sources.
building extension "scipy.linalg._flapack" sources
f2py options: []
f2py: build/src.linux-x86_64-3.7/scipy/linalg/flapack.pyf
Reading fortran codes...
Reading file 'build/src.linux-x86_64-3.7/scipy/linalg/flapack.pyf' (format:free)
Traceback (most recent call last):
File "setup.py", line 265, in <module>
setup_package()
File "setup.py", line 262, in setup_package
setup(**metadata)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/distutils/command/install.py", line 60, in run
r = old_install.run(self)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/distutils/command/build_src.py", line 325, in build_extension_sources
sources = self.f2py_sources(sources, ext)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/distutils/command/build_src.py", line 542, in f2py_sources
+ ['--build-dir', target_dir, source])
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/f2py2e.py", line 425, in run_main
postlist = callcrackfortran(files, options)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/f2py2e.py", line 329, in callcrackfortran
postlist = crackfortran.crackfortran(files)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/crackfortran.py", line 3251, in crackfortran
readfortrancode(files, crackline)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/crackfortran.py", line 501, in readfortrancode
dowithline(finalline)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/crackfortran.py", line 796, in crackline
analyzeline(m, pat[1], line)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/crackfortran.py", line 1098, in analyzeline
last_name = updatevars(typespec, selector, attr, edecl)
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/crackfortran.py", line 1542, in updatevars
attrspec = [x.strip() for x in markoutercomma(attrspec).split('@,@')]
File "/home/anant/testpy/pyodide/cpython/build/3.7.0/host/lib/python3.7/site-packages/numpy/f2py/crackfortran.py", line 833, in markoutercomma
assert not f, repr((f, line, l))
AssertionError: (-1, 'intent(in))', 'intent(in))')
Traceback (most recent call last):
File "/home/anant/anaconda3/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/home/anant/anaconda3/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/anant/testpy/pyodide/pyodide_build/__main__.py", line 30, in <module>
main()
File "/home/anant/testpy/pyodide/pyodide_build/__main__.py", line 24, in main
args.func(args)
File "/home/anant/testpy/pyodide/pyodide_build/buildall.py", line 93, in main
build_packages(packagesdir, outputdir, args)
File "/home/anant/testpy/pyodide/pyodide_build/buildall.py", line 50, in build_packages
build_package(pkgname, dependencies, packagesdir, outputdir, args)
File "/home/anant/testpy/pyodide/pyodide_build/buildall.py", line 24, in build_package
buildpkg.build_package(packagesdir / pkgname / 'meta.yaml', args)
File "/home/anant/testpy/pyodide/pyodide_build/buildpkg.py", line 162, in build_package
compile(path, srcpath, pkg, args)
File "/home/anant/testpy/pyodide/pyodide_build/buildpkg.py", line 100, in compile
'--target', args.target], env=env, check=True)
File "/home/anant/anaconda3/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/home/anant/testpy/pyodide/cpython/build/3.7.0/host/bin/python3', '-m', 'pyodide_build', 'pywasmcross', '--cflags', ' -I../../../../CLAPACK/CLAPACK-WA/INCLUDE -Wno-implicit-function-declaration', '--ldflags', '-O3 -s BINARYEN_METHOD=native-wasm -Werror -s EMULATED_FUNCTION_POINTERS=1 -s EMULATE_FUNCTION_POINTER_CASTS=1 -s SIDE_MODULE=1 -s WASM=1 -s BINARYEN_TRAP_MODE=clamp --memory-init-file 0 -s LINKABLE=1 -s EXPORT_ALL=1 ', '--host', '/home/anant/testpy/pyodide/cpython/build/3.7.0/host', '--target', '/home/anant/testpy/pyodide/cpython/installs/python-3.7.0']' returned non-zero exit status 1.
Makefile:5: recipe for target 'all' failed
make[1]: *** [all] Error 1
make[1]: Leaving directory '/home/anant/testpy/pyodide/packages'
Makefile:225: recipe for target 'build/packages.json' failed
make: *** [build/packages.json] Error 2
About this issue
- Original URL
- State: closed
- Created 5 years ago
- Comments: 15 (9 by maintainers)
I think the actual output from
f2pyis getting swallowed here, so we can’t see the root cause of the error.Have you had success with the docker image, which should give a consistent dev environment and hopefully work around anything that’s different about your machine?