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Bug 717502 - dev-python/numpy{,-python2}: missing files with --skip-build
Summary: dev-python/numpy{,-python2}: missing files with --skip-build
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard: Was: sci-libs/scipy-1.4.1 and sci-lib...
Keywords:
: 717594 717804 717820 717828 717906 717986 718354 (view as bug list)
Depends on:
Blocks: 714384
  Show dependency tree
 
Reported: 2020-04-15 11:19 UTC by Mathieu Chouinard
Modified: 2020-04-19 16:06 UTC (History)
12 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
output of emerge --info (emerge-info,7.86 KB, text/plain)
2020-04-15 11:26 UTC, Mathieu Chouinard
Details
output of emerge -pqv (emerge-pqv,112 bytes, text/plain)
2020-04-15 11:26 UTC, Mathieu Chouinard
Details
buid log (build.log,11.56 KB, text/x-log)
2020-04-15 11:26 UTC, Mathieu Chouinard
Details
environment (environment,163.11 KB, text/plain)
2020-04-15 11:27 UTC, Mathieu Chouinard
Details

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Description Mathieu Chouinard 2020-04-15 11:19:56 UTC
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
Comment 1 Mathieu Chouinard 2020-04-15 11:26:03 UTC
Created attachment 633032 [details]
output of emerge --info
Comment 2 Mathieu Chouinard 2020-04-15 11:26:23 UTC
Created attachment 633034 [details]
output of emerge -pqv
Comment 3 Mathieu Chouinard 2020-04-15 11:26:46 UTC
Created attachment 633036 [details]
buid log
Comment 4 Mathieu Chouinard 2020-04-15 11:27:07 UTC
Created attachment 633038 [details]
environment
Comment 5 Hugo Ribeiro 2020-04-16 08:50:13 UTC
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.
Comment 6 Pacho Ramos gentoo-dev 2020-04-16 18:52:37 UTC
The same affects to sci-libs/scipy-python2-1.1.0 too
Comment 7 Pacho Ramos gentoo-dev 2020-04-16 18:56:51 UTC
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
Comment 8 Pacho Ramos gentoo-dev 2020-04-16 19:04:32 UTC
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)
Comment 9 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-17 11:14:52 UTC
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
Comment 10 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-17 11:15:46 UTC
*** Bug 717594 has been marked as a duplicate of this bug. ***
Comment 11 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-17 11:15:55 UTC
*** Bug 717820 has been marked as a duplicate of this bug. ***
Comment 12 David Seifert gentoo-dev 2020-04-17 12:08:02 UTC
Mgorny currently has a fix ready and is testing it.
Comment 13 Larry the Git Cow gentoo-dev 2020-04-17 14:10:08 UTC
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(+)
Comment 14 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-18 05:29:32 UTC
*** Bug 717804 has been marked as a duplicate of this bug. ***
Comment 15 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-18 05:29:38 UTC
*** Bug 717828 has been marked as a duplicate of this bug. ***
Comment 16 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-18 05:29:45 UTC
*** Bug 717906 has been marked as a duplicate of this bug. ***
Comment 17 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-18 05:30:22 UTC
*** Bug 717828 has been marked as a duplicate of this bug. ***
Comment 18 Pacho Ramos gentoo-dev 2020-04-18 11:49:41 UTC
*** Bug 717986 has been marked as a duplicate of this bug. ***
Comment 19 John Bowler 2020-04-18 17:22:54 UTC
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)
Comment 20 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-19 16:06:59 UTC
*** Bug 718354 has been marked as a duplicate of this bug. ***