Backport upstream patch to fix xerbla linkage (bug #1172834)

Conflicts:
	numpy.spec

5392.patch

@@ -0,0 +1,127 @@
+From f0b2dd7d5151878f2b4b3ea20ff551b27243f27d Mon Sep 17 00:00:00 2001
+From: Charles Harris <charlesr.harris@gmail.com>
+Date: Wed, 24 Dec 2014 11:26:13 -0700
+Subject: [PATCH] BUG: Xerbla doesn't get linked in 1.9 on Fedora 21.
+
+Add our python_xerbla to the blasdot sources. That function is
+needed for all modules that link to the ATLAS 3.10 libraries, which
+in Fedora 21 are located in just two files: libsatlas and libtatlas.
+
+Also make the test for xerbla linkage work better. If xerbla is not
+linked the test will be skipped with a message.
+---
+ numpy/core/blasdot/python_xerbla.c | 51 ++++++++++++++++++++++++++++++++++++++
+ numpy/core/setup.py                |  3 ++-
+ numpy/linalg/tests/test_linalg.py  |  9 ++++---
+ 3 files changed, 59 insertions(+), 4 deletions(-)
+ create mode 100644 numpy/core/blasdot/python_xerbla.c
+
+diff --git a/numpy/core/blasdot/python_xerbla.c b/numpy/core/blasdot/python_xerbla.c
+new file mode 100644
+index 0000000..bdf0b90
+--- /dev/null
++++ b/numpy/core/blasdot/python_xerbla.c
+@@ -0,0 +1,51 @@
++#include "Python.h"
++
++/*
++ * From f2c.h, this should be safe unless fortran is set to use 64
++ * bit integers. We don't seem to have any good way to detect that.
++ */
++typedef int integer;
++
++/*
++  From the original manpage:
++  --------------------------
++  XERBLA is an error handler for the LAPACK routines.
++  It is called by an LAPACK routine if an input parameter has an invalid value.
++  A message is printed and execution stops.
++
++  Instead of printing a message and stopping the execution, a
++  ValueError is raised with the message.
++
++  Parameters:
++  -----------
++  srname: Subroutine name to use in error message, maximum six characters.
++          Spaces at the end are skipped.
++  info: Number of the invalid parameter.
++*/
++
++int xerbla_(char *srname, integer *info)
++{
++        static const char format[] = "On entry to %.*s" \
++                " parameter number %d had an illegal value";
++        char buf[sizeof(format) + 6 + 4];   /* 6 for name, 4 for param. num. */
++
++        int len = 0; /* length of subroutine name*/
++#ifdef WITH_THREAD
++        PyGILState_STATE save;
++#endif
++
++        while( len<6 && srname[len]!='\0' )
++                len++;
++        while( len && srname[len-1]==' ' )
++                len--;
++#ifdef WITH_THREAD
++        save = PyGILState_Ensure();
++#endif
++        PyOS_snprintf(buf, sizeof(buf), format, len, srname, *info);
++        PyErr_SetString(PyExc_ValueError, buf);
++#ifdef WITH_THREAD
++        PyGILState_Release(save);
++#endif
++
++        return 0;
++}
+diff --git a/numpy/core/setup.py b/numpy/core/setup.py
+index 1cd1ee1..baaee20 100644
+--- a/numpy/core/setup.py
++++ b/numpy/core/setup.py
+@@ -954,12 +954,13 @@ def get_dotblas_sources(ext, build_dir):
+         if blas_info:
+             if ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', []):
+                 return None # dotblas needs ATLAS, Fortran compiled blas will not be sufficient.
+-            return ext.depends[:2]
++            return ext.depends[:3]
+         return None # no extension module will be built
+ 
+     config.add_extension('_dotblas',
+                          sources = [get_dotblas_sources],
+                          depends = [join('blasdot', '_dotblas.c'),
++                                    join('blasdot', 'python_xerbla.c'),
+                                     join('blasdot', 'apple_sgemv_patch.c'),
+                                     join('blasdot', 'cblas.h'),
+                                   ],
+diff --git a/numpy/linalg/tests/test_linalg.py b/numpy/linalg/tests/test_linalg.py
+index 8edf36a..dec98db 100644
+--- a/numpy/linalg/tests/test_linalg.py
++++ b/numpy/linalg/tests/test_linalg.py
+@@ -1108,6 +1108,8 @@ def test_xerbla_override():
+     # and may, or may not, abort the process depending on the LAPACK package.
+     from nose import SkipTest
+ 
++    XERBLA_OK = 255
++
+     try:
+         pid = os.fork()
+     except (OSError, AttributeError):
+@@ -1137,15 +1139,16 @@ def test_xerbla_override():
+                 a, a, 0, 0)
+         except ValueError as e:
+             if "DORGQR parameter number 5" in str(e):
+-                # success
+-                os._exit(os.EX_OK)
++                # success, reuse error code to mark success as
++                # FORTRAN STOP returns as success.
++                os._exit(XERBLA_OK)
+ 
+         # Did not abort, but our xerbla was not linked in.
+         os._exit(os.EX_CONFIG)
+     else:
+         # parent
+         pid, status = os.wait()
+-        if os.WEXITSTATUS(status) != os.EX_OK or os.WIFSIGNALED(status):
++        if os.WEXITSTATUS(status) != XERBLA_OK:
+             raise SkipTest('Numpy xerbla not linked in.')
+ 
+ 

fix-library-ext.patch

@@ -0,0 +1,75 @@
+diff --git a/numpy/distutils/misc_util.py b/numpy/distutils/misc_util.py
+index 7a38bed..5bd3a90 100644
+--- a/numpy/distutils/misc_util.py
++++ b/numpy/distutils/misc_util.py
+@@ -605,11 +605,29 @@ def get_shared_lib_extension(is_python_ext=False):
+     Linux, but not on OS X.
+ 
+     """
+-    so_ext = distutils.sysconfig.get_config_var('SO') or ''
+-    # fix long extension for Python >=3.2, see PEP 3149.
+-    if (not is_python_ext) and 'SOABI' in distutils.sysconfig.get_config_vars():
+-        # Does nothing unless SOABI config var exists
+-        so_ext = so_ext.replace('.' + distutils.sysconfig.get_config_var('SOABI'), '', 1)
++    confvars = distutils.sysconfig.get_config_vars()
++    # SO is deprecated in 3.3.1, use EXT_SUFFIX instead
++    so_ext = confvars.get('EXT_SUFFIX', None)
++    if so_ext is None:
++        so_ext = confvars.get('SO', '')
++
++    if not is_python_ext:
++        # hardcode known values, config vars (including SHLIB_SUFFIX) are
++        # unreliable (see #3182)
++        # darwin, windows and debug linux are wrong in 3.3.1 and older
++        if (sys.platform.startswith('linux') or
++            sys.platform.startswith('gnukfreebsd')):
++            so_ext = '.so'
++        elif sys.platform.startswith('darwin'):
++            so_ext = '.dylib'
++        elif sys.platform.startswith('win'):
++            so_ext = '.dll'
++        else:
++            # fall back to config vars for unknown platforms
++            # fix long extension for Python >=3.2, see PEP 3149.
++            if 'SOABI' in confvars:
++                # Does nothing unless SOABI config var exists
++                so_ext = so_ext.replace('.' + confvars.get('SOABI'), '', 1)
+ 
+     return so_ext
+ 
+diff --git a/numpy/distutils/tests/test_misc_util.py b/numpy/distutils/tests/test_misc_util.py
+index 448800b..0f870d3 100644
+--- a/numpy/distutils/tests/test_misc_util.py
++++ b/numpy/distutils/tests/test_misc_util.py
+@@ -1,7 +1,8 @@
+ #!/usr/bin/env python
+ 
+ from numpy.testing import *
+-from numpy.distutils.misc_util import appendpath, minrelpath, gpaths, rel_path
++from numpy.distutils.misc_util import appendpath, minrelpath, \
++    gpaths, get_shared_lib_extension
+ from os.path import join, sep, dirname
+ 
+ ajoin = lambda *paths: join(*((sep,)+paths))
+@@ -53,6 +54,21 @@ class TestGpaths(TestCase):
+         f = gpaths('system_info.py', local_path)
+         assert_(join(local_path,'system_info.py')==f[0],`f`)
+ 
++class TestSharedExtension(TestCase):
++
++    def test_get_shared_lib_extension(self):
++        import sys
++        ext = get_shared_lib_extension(is_python_ext=False)
++        if sys.platform.startswith('linux'):
++            assert_equal(ext, '.so')
++        elif sys.platform.startswith('gnukfreebsd'):
++            assert_equal(ext, '.so')
++        elif sys.platform.startswith('darwin'):
++            assert_equal(ext, '.dylib')
++        elif sys.platform.startswith('win'):
++            assert_equal(ext, '.dll')
++        # just check for no crash
++        assert_(get_shared_lib_extension(is_python_ext=True))
+ 
+ if __name__ == "__main__":
+     run_module_suite()

numpy-xerbla.patch

@@ -0,0 +1,85 @@
+diff -up numpy-1.8.2/numpy/core/blasdot/python_xerbla.c.xerbla numpy-1.8.2/numpy/core/blasdot/python_xerbla.c
+--- numpy-1.8.2/numpy/core/blasdot/python_xerbla.c.xerbla	2015-01-12 11:04:43.981867493 -0700
++++ numpy-1.8.2/numpy/core/blasdot/python_xerbla.c	2015-01-12 11:04:43.980867500 -0700
+@@ -0,0 +1,51 @@
++#include "Python.h"
++
++/*
++ * From f2c.h, this should be safe unless fortran is set to use 64
++ * bit integers. We don't seem to have any good way to detect that.
++ */
++typedef int integer;
++
++/*
++  From the original manpage:
++  --------------------------
++  XERBLA is an error handler for the LAPACK routines.
++  It is called by an LAPACK routine if an input parameter has an invalid value.
++  A message is printed and execution stops.
++
++  Instead of printing a message and stopping the execution, a
++  ValueError is raised with the message.
++
++  Parameters:
++  -----------
++  srname: Subroutine name to use in error message, maximum six characters.
++          Spaces at the end are skipped.
++  info: Number of the invalid parameter.
++*/
++
++int xerbla_(char *srname, integer *info)
++{
++        static const char format[] = "On entry to %.*s" \
++                " parameter number %d had an illegal value";
++        char buf[sizeof(format) + 6 + 4];   /* 6 for name, 4 for param. num. */
++
++        int len = 0; /* length of subroutine name*/
++#ifdef WITH_THREAD
++        PyGILState_STATE save;
++#endif
++
++        while( len<6 && srname[len]!='\0' )
++                len++;
++        while( len && srname[len-1]==' ' )
++                len--;
++#ifdef WITH_THREAD
++        save = PyGILState_Ensure();
++#endif
++        PyOS_snprintf(buf, sizeof(buf), format, len, srname, *info);
++        PyErr_SetString(PyExc_ValueError, buf);
++#ifdef WITH_THREAD
++        PyGILState_Release(save);
++#endif
++
++        return 0;
++}
+diff -up numpy-1.8.2/numpy/core/setup.py.xerbla numpy-1.8.2/numpy/core/setup.py
+--- numpy-1.8.2/numpy/core/setup.py.xerbla	2015-01-12 11:04:43.978867512 -0700
++++ numpy-1.8.2/numpy/core/setup.py	2015-01-12 15:35:42.593240782 -0700
+@@ -947,12 +947,13 @@ def configuration(parent_package='',top_
+         if blas_info:
+             if ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', []):
+                 return None # dotblas needs ATLAS, Fortran compiled blas will not be sufficient.
+-            return ext.depends[:1]
++            return ext.depends[:2]
+         return None # no extension module will be built
+ 
+     config.add_extension('_dotblas',
+                          sources = [get_dotblas_sources],
+                          depends = [join('blasdot', '_dotblas.c'),
++                                  join('blasdot', 'python_xerbla.c'),
+                                   join('blasdot', 'cblas.h'),
+                                   ],
+                          include_dirs = ['blasdot'],
+diff -up numpy-1.8.2/numpy/linalg/tests/test_linalg.py.xerbla numpy-1.8.2/numpy/linalg/tests/test_linalg.py
+--- numpy-1.8.2/numpy/linalg/tests/test_linalg.py.xerbla	2014-08-05 12:04:19.000000000 -0600
++++ numpy-1.8.2/numpy/linalg/tests/test_linalg.py	2015-01-12 11:04:43.981867493 -0700
+@@ -1108,6 +1108,8 @@ def test_xerbla_override():
+     # and may, or may not, abort the process depending on the LAPACK package.
+     from nose import SkipTest
+ 
++    XERBLA_OK = 255
++
+     try:
+         pid = os.fork()
+     except (OSError, AttributeError):

numpy.spec

@@ -9,7 +9,7 @@
 
 Name:           numpy
 Version:        1.8.2
-Release:        1%{?dist}
+Release:        2%{?dist}
 Epoch:          1
 Summary:        A fast multidimensional array facility for Python
 
@@ -18,8 +18,10 @@ Group:          Development/Languages
 License:        BSD and Python
 URL:            http://www.numpy.org/
 Source0:        http://downloads.sourceforge.net/numpy/%{name}-%{version}%{?relc}.tar.gz
-
 Patch0:         numpy-1.8.1.ppc64le.patch
+# Upstream patch to fix xerbla linkage
+# https://bugzilla.redhat.com/show_bug.cgi?id=1172834
+Patch1:         numpy-xerbla.patch
 
 BuildRequires:  python2-devel lapack-devel python-setuptools gcc-gfortran atlas-devel python-nose
 Requires:       python-nose
@@ -85,8 +87,8 @@ This package includes a version of f2py that works properly with NumPy.
 
 %prep
 %setup -q -n %{name}-%{version}%{?relc}
-
 %patch0 -p1
+%patch1 -p1 -b .xerbla
 
 # workaround for rhbz#849713
 # http://mail.scipy.org/pipermail/numpy-discussion/2012-July/063530.html
@@ -237,6 +239,9 @@ popd &> /dev/null
 
 
 %changelog
+* Mon Jan 12 2015 Orion Poplawski <orion@nwra.com> - 1:1.8.2-2
+- Backport upstream patch to fix xerbla linkage (bug #1172834)
+
 * Sun Aug 10 2014 Orion Poplawski <orion@nwra.com> - 1:1.8.2-1
 - Update to 1.8.2
 
@@ -267,29 +272,8 @@ popd &> /dev/null
 * Wed Oct 30 2013 Orion Poplawski <orion@nwra.com> - 1:1.8.0-1
 - Update to 1.8.0 final
 
-* Mon Oct 14 2013 Orion Poplawski <orion@nwra.com> - 1:1.8.0-0.7.rc2
-- Update to 1.8.0rc2
-- Create clean site.cfg
-- Use serial atlas
-
-* Mon Sep 23 2013 Orion Poplawski <orion@nwra.com> - 1:1.8.0-0.6.b2
-- Add [atlas] to site.cfg for new atlas library names
-
-* Sun Sep 22 2013 Orion Poplawski <orion@nwra.com> - 1:1.8.0-0.5.b2
-- Update site.cfg for new atlas library names
-
-* Sat Sep 21 2013 David Tardon <dtardon@redhat.com> - 1:1.8.0-0.4.b2
-- rebuild for atlas 3.10
-
-* Tue Sep 10 2013 Jon Ciesla <limburgher@gmail.com> - 1:1.8.0-0.3.b2
-- Fix libdir path in site.cfg, BZ 1006242.
-
-* Sun Sep 8 2013 Orion Poplawski <orion@nwra.com> - 1:1.8.0-0.2.b2
-- Update to 1.8.0b2
-
-* Wed Sep 4 2013 Orion Poplawski <orion@nwra.com> - 1:1.8.0-0.1.b1
-- Update to 1.8.0b1
-- Drop f2py patch applied upstream
+* Mon Oct 14 2013 Tomas Tomecek <ttomecek@redhat.com> - 1:1.7.1-6
+- fix name of shared library extensions (rhbz#1018783)
 
 * Tue Aug 27 2013 Jon Ciesla <limburgher@gmail.com> - 1:1.7.1-5
 - URL Fix, BZ 1001337