sci-libs/scipy-1.4.1: fails with the following python3.6 setup.py build config_fc --noopt --noarch lapack_opt_info: system_info: NOT AVAILABLE flame_info: customize UnixCCompiler libraries flame not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/'] NOT AVAILABLE accelerate_info: NOT AVAILABLE lapack_info: customize UnixCCompiler FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib64'] language = f77 blas_opt_info: blas_info: customize UnixCCompiler customize UnixCCompiler C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -fPIC creating /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/var creating /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/var/tmp creating /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/var/tmp/portage creating /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/var/tmp/portage/sci-libs creating /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/var/tmp/portage/sci-libs/scipy-1.4.1 creating /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/var/tmp/portage/sci-libs/scipy-1.4.1/temp creating /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex compile options: '-I -c' x86_64-pc-linux-gnu-gcc: /var/tmp/portage/sci-libs/scipy-1.4.1/temp/tmpnqvoyuex/source.c /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-libs/scipy-1.4.1/temp/ccd4ApTM.o: in function `main': source.c:(.text.startup+0x8c): undefined reference to `cblas_ddot' collect2: error: ld returned 1 exit status FOUND: libraries = ['blas', 'cblas'] library_dirs = ['/usr/lib64'] include_dirs = [''] FOUND: define_macros = [('NO_ATLAS_INFO', 1)] libraries = ['blas', 'cblas'] library_dirs = ['/usr/lib64'] include_dirs = [''] FOUND: libraries = ['lapack', 'blas', 'cblas'] library_dirs = ['/usr/lib64'] language = f77 define_macros = [('NO_ATLAS_INFO', 1)] include_dirs = [''] Running from scipy source directory. /usr/lib64/python3.6/site-packages/numpy/distutils/system_info.py:669: UserWarning: Optimized (vendor) Blas libraries are not found. Falls back to netlib Blas library which has worse performance. A better performance should be easily gained by switching Blas library. self.calc_info() /usr/lib64/python3.6/site-packages/numpy/distutils/system_info.py:761: UserWarning: Specified path /usr/lib64/python3.6/site-packages/numpy/__init__.py/include/python3.6m is invalid. return self.get_paths(self.section, key) non-existing path in 'scipy/fft/_pocketfft': '/var/tmp/portage/sci-libs/scipy-1.4.1/homedir/.local/include/python3.6m' non-existing path in 'scipy/interpolate': 'src/multipack.h' Splitting linalg.interpolative Fortran source files non-existing path in 'scipy/signal/windows': 'tests' non-existing path in 'scipy/sparse': 'sparsetools/sparsetools_impl.h' non-existing path in 'scipy/sparse': 'sparsetools/bsr_impl.h' non-existing path in 'scipy/sparse': 'sparsetools/csc_impl.h' non-existing path in 'scipy/sparse': 'sparsetools/csr_impl.h' non-existing path in 'scipy/sparse': 'sparsetools/other_impl.h' Traceback (most recent call last): File "/usr/lib64/python3.6/site-packages/numpy/distutils/npy_pkg_config.py", line 371, in read_config return _CACHE[pkgname] KeyError: 'npymath' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "setup.py", line 540, in <module> setup_package() File "setup.py", line 536, in setup_package setup(**metadata) File "/usr/lib64/python3.6/site-packages/numpy/distutils/core.py", line 137, in setup config = configuration() File "setup.py", line 443, in configuration config.add_subpackage('scipy') File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 1035, in add_subpackage caller_level = 2) File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 1004, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 941, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 23, in configuration config.add_subpackage('spatial') File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 1035, in add_subpackage caller_level = 2) File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 1004, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 941, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/spatial/setup.py", line 76, in configuration extra_info=get_misc_info("npymath")) File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 2186, in get_info pkg_info = get_pkg_info(pkgname, dirs) File "/usr/lib64/python3.6/site-packages/numpy/distutils/misc_util.py", line 2138, in get_pkg_info return read_config(pkgname, dirs) File "/usr/lib64/python3.6/site-packages/numpy/distutils/npy_pkg_config.py", line 373, in read_config v = _read_config_imp(pkg_to_filename(pkgname), dirs) File "/usr/lib64/python3.6/site-packages/numpy/distutils/npy_pkg_config.py", line 309, in _read_config_imp meta, vars, sections, reqs = _read_config(filenames) File "/usr/lib64/python3.6/site-packages/numpy/distutils/npy_pkg_config.py", line 292, in _read_config meta, vars, sections, reqs = parse_config(f, dirs) File "/usr/lib64/python3.6/site-packages/numpy/distutils/npy_pkg_config.py", line 264, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/usr/lib64/python3.6/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini'] Reproducible: Always
Created attachment 633032 [details] output of emerge --info
Created attachment 633034 [details] output of emerge -pqv
Created attachment 633036 [details] buid log
Created attachment 633038 [details] environment
I have the same problem. I am using python3.7 and openblas. Happy to also upload the log files if necessary. A final remark: I also tried to emerge again openblas in case there was something broken... that didn't help.
The same affects to sci-libs/scipy-python2-1.1.0 too
It is also caused by dev-python/numpy-1.17.4-r2 and dev-python/numpy-python2 not installing their /usr/lib64/python*/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini files with --skip-build is used https://gitweb.gentoo.org/repo/gentoo.git/commit/eclass/distutils-r1.eclass?id=180fa85d7d00aea463c399f70348beaad9166eb7
I read this in Fedora .spec file: https://src.fedoraproject.org/rpms/numpy/blob/master/f/numpy.spec#_137 But I think they didn't report to upstream (or I couldn't find a report there)
The complete list of missing files: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h /usr/lib/python3.8/site-packages/numpy/core/include/numpy/multiarray_api.txt /usr/lib/python3.8/site-packages/numpy/core/include/numpy/_numpyconfig.h /usr/lib/python3.8/site-packages/numpy/core/include/numpy/__ufunc_api.h /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ufunc_api.txt /usr/lib/python3.8/site-packages/numpy/core/lib/npy-pkg-config/mlib.ini /usr/lib/python3.8/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini
*** Bug 717594 has been marked as a duplicate of this bug. ***
*** Bug 717820 has been marked as a duplicate of this bug. ***
Mgorny currently has a fix ready and is testing it.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e79ba40b728834f97b0eea4b596601477ca3210f commit e79ba40b728834f97b0eea4b596601477ca3210f Author: Michał Górny <mgorny@gentoo.org> AuthorDate: 2020-04-17 11:51:04 +0000 Commit: Michał Górny <mgorny@gentoo.org> CommitDate: 2020-04-17 14:10:03 +0000 dev-python/numpy-python2: Fix installing generated files Closes: https://bugs.gentoo.org/717502 Signed-off-by: Michał Górny <mgorny@gentoo.org> .../{numpy-python2-1.16.5.ebuild => numpy-python2-1.16.5-r1.ebuild} | 2 ++ 1 file changed, 2 insertions(+) https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1b53d722d793c11f16e81bc2c468cbb74d0c8a32 commit 1b53d722d793c11f16e81bc2c468cbb74d0c8a32 Author: Michał Górny <mgorny@gentoo.org> AuthorDate: 2020-04-17 11:50:35 +0000 Commit: Michał Górny <mgorny@gentoo.org> CommitDate: 2020-04-17 14:10:01 +0000 dev-python/numpy: Fix installing generated files Closes: https://bugs.gentoo.org/717502 Signed-off-by: Michał Górny <mgorny@gentoo.org> dev-python/numpy/{numpy-1.16.5.ebuild => numpy-1.16.5-r1.ebuild} | 2 ++ dev-python/numpy/{numpy-1.17.4-r2.ebuild => numpy-1.17.4-r3.ebuild} | 2 ++ 2 files changed, 4 insertions(+)
*** Bug 717804 has been marked as a duplicate of this bug. ***
*** Bug 717828 has been marked as a duplicate of this bug. ***
*** Bug 717906 has been marked as a duplicate of this bug. ***
*** Bug 717986 has been marked as a duplicate of this bug. ***
dev-python/numpy-1.17.4-r3 does fix the opencv (https://bugs.gentoo.org/show_bug.cgi?id=717804) and vigra variations of the problem (missing _numpyconfig.h)
*** Bug 718354 has been marked as a duplicate of this bug. ***
