New patch to fix some undefined pointer (mainly on amd64). Trying to fix bug #195619 by forcing a fixed numpy version and rewrite of site configuration file. Removed some obsolete versions.

Package-Manager: portage-2.1.4

13 files changed, 15 insertions, 759 deletions

diff --git a/sci-libs/scipy/files/digest-scipy-0.5.2.1 b/sci-libs/scipy/files/digest-scipy-0.5.2.1
deleted file mode 100644
index f6b82a7707d9..000000000000
--- a/sci-libs/scipy/files/digest-scipy-0.5.2.1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 8d9083b94b0bbbc96a96099f68e62526 scipy-0.5.2.1.tar.gz 6000165
-RMD160 bfcd38d1ca9319fe173b23781ce01265c4695803 scipy-0.5.2.1.tar.gz 6000165
-SHA256 c347b55f8f3fcf4048b6f5f46fd006d52fb1d6d07a688199758066307382d0f8 scipy-0.5.2.1.tar.gz 6000165
diff --git a/sci-libs/scipy/files/digest-scipy-0.6.0-r1 b/sci-libs/scipy/files/digest-scipy-0.6.0-r1
deleted file mode 100644
index aa28d16fa675..000000000000
--- a/sci-libs/scipy/files/digest-scipy-0.6.0-r1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 417adf3bfe03f4c23c9fb265018e545c scipy-0.6.0.tar.gz 6572954
-RMD160 391f2067f7dcc133e7e8622df93a2a0cd5ebbe5b scipy-0.6.0.tar.gz 6572954
-SHA256 5f70390963fb4e3ae8cf5effa301c160ef68c791098e2ea95b99380e298eac4f scipy-0.6.0.tar.gz 6572954
diff --git a/sci-libs/scipy/files/digest-scipy-0.6.0 b/sci-libs/scipy/files/digest-scipy-0.6.0-r4
index aa28d16fa675..aa28d16fa675 100644
--- a/sci-libs/scipy/files/digest-scipy-0.6.0
+++ b/sci-libs/scipy/files/digest-scipy-0.6.0-r4
diff --git a/sci-libs/scipy/files/enabled_packages.txt b/sci-libs/scipy/files/enabled_packages.txt
deleted file mode 100644
index 9f1a335d9055..000000000000
--- a/sci-libs/scipy/files/enabled_packages.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-ann
-arpack
-arraysetops
-buildgrid
-constants
-cow
-delaunay
-exmplpackage
-fdfpack
-ga
-gplt
-image
-models
-montecarlo
-netcdf
-newoptimize
-numexpr
-plt
-pyem
-rkern
-spline
-stats
-svm
-umfpack
-xplt
diff --git a/sci-libs/scipy/files/scipy-0.5.2-bspline.patch b/sci-libs/scipy/files/scipy-0.5.2-bspline.patch
deleted file mode 100644
index 2169438c6997..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-bspline.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- Lib/sandbox/models/bspline_module.py~	2006-12-07 01:13:15.000000000 +0000
-+++ Lib/sandbox/models/bspline_module.py	2007-06-06 22:16:13.556342500 +0100
-@@ -128,7 +128,7 @@
- 
-     eval_ext_code = '''
- 
--    int dim[2] = {upper-lower, Nx[0]};
-+    npy_intp dim[2] = {upper-lower, Nx[0]};
-     PyArrayObject *basis;
-     double *data;
- 
-@@ -252,7 +252,7 @@
- 
-     gram_ext_code = '''
- 
--    int dim[2] = {Nknots[0]-m, m};
-+    npy_intp dim[2] = {Nknots[0]-m, m};
-     double *data;
-     PyArrayObject *gram;
- 
-@@ -315,7 +315,7 @@
- 
-     invband_ext_code = '''
- 
--    int dim[2] = {NL[0], NL[1]};
-+    npy_intp dim[2] = {NL[0], NL[1]};
-     int i, j;
-     double *data;
-     PyArrayObject *invband;
diff --git a/sci-libs/scipy/files/scipy-0.5.2-cdf.patch b/sci-libs/scipy/files/scipy-0.5.2-cdf.patch
deleted file mode 100644
index 99a334071c15..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-cdf.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- Lib/special/setup.py.orig	2007-09-11 18:11:04.457232054 +0100
-+++ Lib/special/setup.py	2007-09-11 18:09:23.103456231 +0100
-@@ -20,9 +20,9 @@
-     # Fortran libraries
-     config.add_library('mach',sources=[join('mach','*.f')],
-                        config_fc={'noopt':(__file__,1)})
--    config.add_library('toms',sources=[join('amos','*.f')])
--    config.add_library('amos',sources=[join('toms','*.f')])
--    config.add_library('cdf',sources=[join('cdflib','*.f')])
-+    config.add_library('toms',sources=[join('toms','*.f')])
-+    config.add_library('amos',sources=[join('amos','*.f')])
-+    config.add_library('cdflib',sources=[join('cdflib','*.f')])
-     config.add_library('specfun',sources=[join('specfun','*.f')])
- 
-     # Extension _cephes
-@@ -30,7 +30,7 @@
-                'toms_wrappers.c','cdf_wrappers.c','ufunc_extras.c']
-     config.add_extension('_cephes', sources=sources,
-                          libraries=['amos','toms','c_misc','cephes','mach',
--                                    'cdf', 'specfun'],
-+                                    'cdflib', 'specfun'],
-                          define_macros = define_macros
-                          )
-     # Extension specfun
diff --git a/sci-libs/scipy/files/scipy-0.5.2-minpack.patch b/sci-libs/scipy/files/scipy-0.5.2-minpack.patch
deleted file mode 100644
index 496fd70e06f3..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-minpack.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- Lib/optimize/__minpack.h.orig	2007-06-06 17:34:35.232483750 +0100
-+++ Lib/optimize/__minpack.h	2007-06-06 17:34:37.788643500 +0100
-@@ -585,7 +585,6 @@
-   else {
-     Py_DECREF(ap_fvec);
-     Py_DECREF(ap_fjac);
--    Py_DECREF(ap_diag);
-     Py_DECREF(ap_ipvt);
-     Py_DECREF(ap_qtf);
-     return Py_BuildValue("Ni",PyArray_Return(ap_x),info);
diff --git a/sci-libs/scipy/files/scipy-0.5.2-montecarlo-test.patch b/sci-libs/scipy/files/scipy-0.5.2-montecarlo-test.patch
deleted file mode 100644
index 681b32057815..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-montecarlo-test.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Lib/sandbox/montecarlo/tests/test_dictsampler.py.orig	2007-06-06 14:25:47.000000000 +0100
-+++ Lib/sandbox/montecarlo/tests/test_dictsampler.py	2007-06-06 14:26:02.000000000 +0100
-@@ -37,7 +37,7 @@
-         #import pdb
-         #pdb.set_trace()
-         s = sampler.sample(n)
--        assert sum(s[i]=='b' for i in range(n),axis=0)*1./n > 0.75
-+        assert sum((s[i]=='b' for i in range(n)),axis=0)*1./n > 0.75
- 
-         #lam = 10.0
-         #n = 35
diff --git a/sci-libs/scipy/files/scipy-0.5.2-nonexisting.patch b/sci-libs/scipy/files/scipy-0.5.2-nonexisting.patch
deleted file mode 100644
index 182768dfeff2..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-nonexisting.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- Lib/maxentropy/setup.py.orig	2007-06-06 16:04:57.267196500 +0100
-+++ Lib/maxentropy/setup.py	2007-06-06 16:05:54.786791250 +0100
-@@ -10,7 +10,6 @@
- 
-     config.add_data_dir('tests')
-     config.add_data_dir('examples')
--    config.add_data_dir('doc')
- 
-     return config
- 
---- Lib/linsolve/setup.py.orig	2007-06-06 16:10:41.592715500 +0100
-+++ Lib/linsolve/setup.py	2007-06-06 16:11:01.929986500 +0100
-@@ -7,7 +7,6 @@
-     from numpy.distutils.system_info import get_info
- 
-     config = Configuration('linsolve',parent_package,top_path)
--    config.add_data_dir('tests')
- 
-     lapack_opt = get_info('lapack_opt',notfound_action=2)
-     if sys.platform=='win32':
---- Lib/sandbox/buildgrid/setup.py.orig	2007-06-06 16:49:49.411337500 +0100
-+++ Lib/sandbox/buildgrid/setup.py	2007-06-06 16:50:03.436214000 +0100
-@@ -10,7 +10,7 @@
-                           
-     config.add_extension('build_grid',
-                          sources = ['build_grid.c'])
--    config.add_data_files('README')
-+    config.add_data_files('README.txt')
-     return config
- 
- if __name__ == "__main__":
---- Lib/sandbox/montecarlo/setup.py.orig	2007-06-06 16:50:34.242139250 +0100
-+++ Lib/sandbox/montecarlo/setup.py	2007-06-06 16:52:00.442607500 +0100
-@@ -15,8 +15,6 @@
-                         ['_intsamplermodule.c', 'compact5table.c', 'randomkit.c']])
-     
-     config.add_data_dir('tests')
--    config.add_data_dir('examples')
--    config.add_data_dir('doc')
- 
-     return config
- 
diff --git a/sci-libs/scipy/files/scipy-0.5.2-randomkit.patch b/sci-libs/scipy/files/scipy-0.5.2-randomkit.patch
deleted file mode 100644
index 8ff523b1f866..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-randomkit.patch
+++ /dev/null
@@ -1,552 +0,0 @@
---- Lib/sandbox/montecarlo/src/randomkit.c.orig	1970-01-01 01:00:00.000000000 +0100
-+++ Lib/sandbox/montecarlo/src/randomkit.c	2007-06-06 17:15:22.505066000 +0100
-@@ -0,0 +1,357 @@
-+/* Random kit 1.3 */
-+
-+/*
-+ * Copyright (c) 2003-2005, Jean-Sebastien Roy (js@jeannot.org)
-+ *
-+ * The rk_random and rk_seed functions algorithms and the original design of 
-+ * the Mersenne Twister RNG:
-+ *
-+ *   Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
-+ *   All rights reserved.
-+ *
-+ *   Redistribution and use in source and binary forms, with or without
-+ *   modification, are permitted provided that the following conditions
-+ *   are met:
-+ * 
-+ *   1. Redistributions of source code must retain the above copyright
-+ *   notice, this list of conditions and the following disclaimer.
-+ *
-+ *   2. Redistributions in binary form must reproduce the above copyright
-+ *   notice, this list of conditions and the following disclaimer in the
-+ *   documentation and/or other materials provided with the distribution.
-+ *
-+ *   3. The names of its contributors may not be used to endorse or promote
-+ *   products derived from this software without specific prior written
-+ *   permission.
-+ *
-+ *   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-+ *   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-+ *   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-+ *   A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-+ *   CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-+ *   EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-+ *   PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-+ *   PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-+ *   LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-+ *   NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-+ *   SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-+ * 
-+ * Original algorithm for the implementation of rk_interval function from
-+ * Richard J. Wagner's implementation of the Mersenne Twister RNG, optimised by
-+ * Magnus Jonsson.
-+ *
-+ * Constants used in the rk_double implementation by Isaku Wada.
-+ * 
-+ * Permission is hereby granted, free of charge, to any person obtaining a
-+ * copy of this software and associated documentation files (the
-+ * "Software"), to deal in the Software without restriction, including
-+ * without limitation the rights to use, copy, modify, merge, publish,
-+ * distribute, sublicense, and/or sell copies of the Software, and to
-+ * permit persons to whom the Software is furnished to do so, subject to
-+ * the following conditions:
-+ * 
-+ * The above copyright notice and this permission notice shall be included
-+ * in all copies or substantial portions of the Software.
-+ * 
-+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-+ * IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-+ * CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-+ * TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-+ * SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-+ */
-+
-+/* static char const rcsid[] =
-+  "@(#) $Jeannot: randomkit.c,v 1.28 2005/07/21 22:14:09 js Exp $"; */
-+
-+#include <stddef.h>
-+#include <stdio.h>
-+#include <stdlib.h>
-+#include <errno.h>
-+#include <time.h>
-+#include <limits.h>
-+#include <math.h>
-+
-+#ifdef _WIN32
-+/* Windows */
-+#include <sys/timeb.h>
-+#ifndef RK_NO_WINCRYPT
-+/* Windows crypto */
-+#ifndef _WIN32_WINNT
-+#define _WIN32_WINNT 0x0400
-+#endif
-+#include <windows.h>
-+#include <wincrypt.h>
-+#endif
-+#else
-+/* Unix */
-+#include <sys/time.h>
-+#include <unistd.h>
-+#endif
-+
-+#include "randomkit.h"
-+
-+#ifndef RK_DEV_URANDOM
-+#define RK_DEV_URANDOM "/dev/urandom"
-+#endif
-+
-+#ifndef RK_DEV_RANDOM
-+#define RK_DEV_RANDOM "/dev/random"
-+#endif
-+
-+char *rk_strerror[RK_ERR_MAX] =
-+{
-+	"no error",
-+	"random device unvavailable"
-+};
-+
-+/* static functions */
-+static unsigned long rk_hash(unsigned long key);
-+
-+void rk_seed(unsigned long seed, rk_state *state)
-+{
-+	int pos;
-+	seed &= 0xffffffffUL;
-+
-+	/* Knuth's PRNG as used in the Mersenne Twister reference implementation */
-+	for (pos=0; pos<RK_STATE_LEN; pos++)
-+	{
-+		state->key[pos] = seed;
-+		seed = (1812433253UL * (seed ^ (seed >> 30)) + pos + 1) & 0xffffffffUL;
-+	}
-+
-+	state->pos = RK_STATE_LEN;
-+	state->has_gauss = 0;
-+        state->has_binomial = 0;
-+}
-+
-+/* Thomas Wang 32 bits integer hash function */
-+unsigned long rk_hash(unsigned long key)
-+{
-+  key += ~(key << 15);
-+  key ^=  (key >> 10);
-+  key +=  (key << 3);
-+  key ^=  (key >> 6);
-+  key += ~(key << 11);
-+  key ^=  (key >> 16);
-+  return key;
-+}
-+
-+rk_error rk_randomseed(rk_state *state)
-+{
-+#ifndef _WIN32
-+	struct timeval tv;
-+#else
-+	struct _timeb	tv;
-+#endif
-+        int i;
-+
-+	if(rk_devfill(state->key, sizeof(state->key), 0) == RK_NOERR)
-+	{
-+		state->key[0] |= 0x80000000UL; /* ensures non-zero key */
-+		state->pos = RK_STATE_LEN;
-+		state->has_gauss = 0;
-+                state->has_binomial = 0;
-+
-+                for (i=0; i<624; i++)
-+                {
-+                    state->key[i] &= 0xffffffffUL;
-+                }
-+
-+		return RK_NOERR;
-+	}
-+
-+#ifndef _WIN32
-+	gettimeofday(&tv, NULL);
-+	rk_seed(rk_hash(getpid()) ^ rk_hash(tv.tv_sec) ^ rk_hash(tv.tv_usec)
-+		^ rk_hash(clock()), state);
-+#else
-+	_ftime(&tv);
-+	rk_seed(rk_hash(tv.time) ^ rk_hash(tv.millitm) ^ rk_hash(clock()), state);
-+#endif
-+
-+	return RK_ENODEV;
-+}
-+
-+/* Magic Mersenne Twister constants */
-+#define N 624
-+#define M 397
-+#define MATRIX_A 0x9908b0dfUL
-+#define UPPER_MASK 0x80000000UL
-+#define LOWER_MASK 0x7fffffffUL
-+
-+/* Slightly optimised reference implementation of the Mersenne Twister */
-+unsigned long rk_random(rk_state *state)
-+{
-+  unsigned long y;
-+
-+  if (state->pos == RK_STATE_LEN)
-+	{
-+    int i;
-+
-+    for (i=0;i<N-M;i++)
-+		{
-+      y = (state->key[i] & UPPER_MASK) | (state->key[i+1] & LOWER_MASK);
-+      state->key[i] = state->key[i+M] ^ (y>>1) ^ (-(y & 1) & MATRIX_A);
-+    }
-+    for (;i<N-1;i++)
-+		{
-+      y = (state->key[i] & UPPER_MASK) | (state->key[i+1] & LOWER_MASK);
-+      state->key[i] = state->key[i+(M-N)] ^ (y>>1) ^ (-(y & 1) & MATRIX_A);
-+    }
-+    y = (state->key[N-1] & UPPER_MASK) | (state->key[0] & LOWER_MASK);
-+    state->key[N-1] = state->key[M-1] ^ (y>>1) ^ (-(y & 1) & MATRIX_A);
-+
-+    state->pos = 0;
-+  }
-+  
-+  y = state->key[state->pos++];
-+
-+  /* Tempering */
-+  y ^= (y >> 11);
-+  y ^= (y << 7) & 0x9d2c5680UL;
-+  y ^= (y << 15) & 0xefc60000UL;
-+  y ^= (y >> 18);
-+
-+  return y;
-+}
-+
-+long rk_long(rk_state *state)
-+{
-+	return rk_ulong(state) >> 1;
-+}
-+
-+unsigned long rk_ulong(rk_state *state)
-+{
-+#if ULONG_MAX <= 0xffffffffUL
-+	return rk_random(state);
-+#else
-+	return (rk_random(state) << 32) | (rk_random(state));
-+#endif
-+}
-+
-+unsigned long rk_interval(unsigned long max, rk_state *state)
-+{
-+	unsigned long mask = max, value;
-+
-+	if (max == 0) return 0;
-+
-+	/* Smallest bit mask >= max */
-+	mask |= mask >> 1;
-+	mask |= mask >> 2;
-+	mask |= mask >> 4;
-+	mask |= mask >> 8;
-+	mask |= mask >> 16;
-+#if ULONG_MAX > 0xffffffffUL
-+	mask |= mask >> 32;
-+#endif
-+
-+	/* Search a random value in [0..mask] <= max */
-+	while ((value = (rk_ulong(state) & mask)) > max);
-+
-+	return value;
-+}
-+
-+double rk_double(rk_state *state)
-+{
-+	/* shifts : 67108864 = 0x4000000, 9007199254740992 = 0x20000000000000 */
-+	long a = rk_random(state) >> 5, b = rk_random(state) >> 6;
-+	return (a * 67108864.0 + b) / 9007199254740992.0;
-+}
-+
-+void rk_fill(void *buffer, size_t size, rk_state *state)
-+{
-+	unsigned long r;
-+	unsigned char *buf = buffer;
-+	
-+	for (; size >= 4; size -= 4)
-+	{
-+		r = rk_random(state);
-+		*(buf++) = r & 0xFF;
-+		*(buf++) = (r >> 8) & 0xFF;
-+		*(buf++) = (r >> 16) & 0xFF;
-+		*(buf++) = (r >> 24) & 0xFF;
-+	}
-+	
-+	if (!size) return;
-+
-+	r = rk_random(state);
-+
-+	for (; size; r >>= 8, size --)
-+		*(buf++) = (unsigned char)(r & 0xFF);
-+}
-+
-+rk_error rk_devfill(void *buffer, size_t size, int strong)
-+{
-+#ifndef _WIN32
-+	FILE *rfile;
-+	int done;
-+
-+	if (strong)
-+		rfile = fopen(RK_DEV_RANDOM, "rb");
-+	else
-+		rfile = fopen(RK_DEV_URANDOM, "rb");
-+	if (rfile == NULL)
-+		return RK_ENODEV;
-+	done = fread(buffer, size, 1, rfile);
-+	fclose(rfile);
-+	if (done)
-+		return RK_NOERR;
-+#else
-+
-+#ifndef RK_NO_WINCRYPT
-+	HCRYPTPROV hCryptProv;
-+	BOOL done;
-+
-+	if (!CryptAcquireContext(&hCryptProv, NULL, NULL, PROV_RSA_FULL,
-+		CRYPT_VERIFYCONTEXT) || !hCryptProv)
-+		return RK_ENODEV;
-+	done = CryptGenRandom(hCryptProv, size, (unsigned char *)buffer);
-+	CryptReleaseContext(hCryptProv, 0);
-+	if (done)
-+		return RK_NOERR;
-+#endif
-+
-+#endif
-+
-+	return RK_ENODEV;
-+}
-+
-+rk_error rk_altfill(void *buffer, size_t size, int strong, rk_state *state)
-+{
-+	rk_error err;
-+
-+	err = rk_devfill(buffer, size, strong);
-+	if (err)
-+		rk_fill(buffer, size, state);
-+
-+	return err;
-+}
-+
-+double rk_gauss(rk_state *state)
-+{
-+	if (state->has_gauss)
-+	{
-+		state->has_gauss = 0;
-+		return state->gauss;
-+	}
-+	else
-+	{
-+		double f, x1, x2, r2;
-+		do
-+		{
-+			x1 = 2.0*rk_double(state) - 1.0;
-+			x2 = 2.0*rk_double(state) - 1.0;
-+			r2 = x1*x1 + x2*x2;
-+		}
-+		while (r2 >= 1.0 || r2 == 0.0);
-+		
-+		f = sqrt(-2.0*log(r2)/r2); /* Box-Muller transform */
-+		state->has_gauss = 1;
-+		state->gauss = f*x1; /* Keep for next call */
-+		return f*x2;
-+	}
-+}
-+
-+
---- Lib/sandbox/montecarlo/src/randomkit.h.orig	1970-01-01 01:00:00.000000000 +0100
-+++ Lib/sandbox/montecarlo/src/randomkit.h	2007-06-06 17:15:22.505066000 +0100
-@@ -0,0 +1,189 @@
-+/* Random kit 1.3 */
-+
-+/*
-+ * Copyright (c) 2003-2005, Jean-Sebastien Roy (js@jeannot.org)
-+ * 
-+ * Permission is hereby granted, free of charge, to any person obtaining a
-+ * copy of this software and associated documentation files (the
-+ * "Software"), to deal in the Software without restriction, including
-+ * without limitation the rights to use, copy, modify, merge, publish,
-+ * distribute, sublicense, and/or sell copies of the Software, and to
-+ * permit persons to whom the Software is furnished to do so, subject to
-+ * the following conditions:
-+ * 
-+ * The above copyright notice and this permission notice shall be included
-+ * in all copies or substantial portions of the Software.
-+ * 
-+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-+ * IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-+ * CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-+ * TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-+ * SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-+ */
-+
-+/* @(#) $Jeannot: randomkit.h,v 1.24 2005/07/21 22:14:09 js Exp $ */
-+
-+/*
-+ * Typical use:
-+ *
-+ * {
-+ * 	rk_state state;
-+ * 	unsigned long seed = 1, random_value;
-+ * 	
-+ * 	rk_seed(seed, &state); // Initialize the RNG
-+ * 	...
-+ * 	random_value = rk_random(&state); // Generate random values in [0..RK_MAX]
-+ * }
-+ * 
-+ * Instead of rk_seed, you can use rk_randomseed which will get a random seed
-+ * from /dev/urandom (or the clock, if /dev/urandom is unavailable):
-+ *
-+ * {
-+ * 	rk_state state;
-+ * 	unsigned long random_value;
-+ * 	
-+ * 	rk_randomseed(&state); // Initialize the RNG with a random seed
-+ * 	...
-+ * 	random_value = rk_random(&state); // Generate random values in [0..RK_MAX]
-+ * }
-+ */
-+ 
-+/*
-+ * Useful macro:
-+ * 	RK_DEV_RANDOM: the device used for random seeding.
-+ *                 defaults to "/dev/urandom"
-+ */
-+
-+#include <stddef.h>
-+
-+#ifndef _RANDOMKIT_
-+#define _RANDOMKIT_
-+
-+#define	RK_STATE_LEN 624
-+
-+typedef struct rk_state_
-+{
-+	unsigned long key[RK_STATE_LEN];
-+	int pos;
-+	int has_gauss; /* !=0: gauss contains a gaussian deviate */
-+	double gauss;
-+
-+    /* The rk_state structure has been extended to store the following
-+     * information for the binomial generator. If the input values of n or p
-+     * are different than nsave and psave, then the other parameters will be
-+     * recomputed. RTK 2005-09-02 */
-+
-+    int has_binomial; /* !=0: following parameters initialized for 
-+                              binomial */
-+    double psave;
-+    long nsave;
-+    double r;
-+    double q;
-+    double fm;
-+    long m;
-+    double p1;
-+    double xm;
-+    double xl;
-+    double xr;
-+    double c;
-+    double laml;
-+    double lamr;
-+    double p2;
-+    double p3;
-+    double p4;
-+
-+}
-+rk_state;
-+
-+typedef enum {
-+	RK_NOERR = 0, /* no error */
-+	RK_ENODEV = 1, /* no RK_DEV_RANDOM device */
-+	RK_ERR_MAX = 2
-+} rk_error;
-+
-+/* error strings */
-+extern char *rk_strerror[RK_ERR_MAX];
-+
-+/* Maximum generated random value */
-+#define RK_MAX 0xFFFFFFFFUL
-+
-+#ifdef __cplusplus
-+extern "C" {
-+#endif
-+
-+/*
-+ * Initialize the RNG state using the given seed.
-+ */
-+extern void rk_seed(unsigned long seed, rk_state *state);
-+
-+/*
-+ * Initialize the RNG state using a random seed.
-+ * Uses /dev/random or, when unavailable, the clock (see randomkit.c).
-+ * Returns RK_NOERR when no errors occurs.
-+ * Returns RK_ENODEV when the use of RK_DEV_RANDOM failed (for example because
-+ * there is no such device). In this case, the RNG was initialized using the
-+ * clock.
-+ */
-+extern rk_error rk_randomseed(rk_state *state);
-+
-+/*
-+ * Returns a random unsigned long between 0 and RK_MAX inclusive
-+ */
-+extern unsigned long rk_random(rk_state *state);
-+
-+/*
-+ * Returns a random long between 0 and LONG_MAX inclusive
-+ */
-+extern long rk_long(rk_state *state);
-+
-+/*
-+ * Returns a random unsigned long between 0 and ULONG_MAX inclusive
-+ */
-+extern unsigned long rk_ulong(rk_state *state);
-+
-+/*
-+ * Returns a random unsigned long between 0 and max inclusive.
-+ */
-+extern unsigned long rk_interval(unsigned long max, rk_state *state);
-+
-+/*
-+ * Returns a random double between 0.0 and 1.0, 1.0 excluded.
-+ */
-+extern double rk_double(rk_state *state);
-+
-+/*
-+ * fill the buffer with size random bytes
-+ */
-+extern void rk_fill(void *buffer, size_t size, rk_state *state);
-+
-+/*
-+ * fill the buffer with randombytes from the random device
-+ * Returns RK_ENODEV if the device is unavailable, or RK_NOERR if it is
-+ * On Unix, if strong is defined, RK_DEV_RANDOM is used. If not, RK_DEV_URANDOM
-+ * is used instead. This parameter has no effect on Windows.
-+ * Warning: on most unixes RK_DEV_RANDOM will wait for enough entropy to answer
-+ * which can take a very long time on quiet systems.
-+ */
-+extern rk_error rk_devfill(void *buffer, size_t size, int strong);
-+
-+/*
-+ * fill the buffer using rk_devfill if the random device is available and using
-+ * rk_fill if is is not
-+ * parameters have the same meaning as rk_fill and rk_devfill
-+ * Returns RK_ENODEV if the device is unavailable, or RK_NOERR if it is
-+ */
-+extern rk_error rk_altfill(void *buffer, size_t size, int strong,
-+	rk_state *state);
-+
-+/*
-+ * return a random gaussian deviate with variance unity and zero mean.
-+ */
-+extern double rk_gauss(rk_state *state);
-+
-+#ifdef __cplusplus
-+}
-+#endif
-+
-+#endif /* _RANDOMKIT_ */ 
diff --git a/sci-libs/scipy/files/scipy-0.5.2-signals.patch b/sci-libs/scipy/files/scipy-0.5.2-signals.patch
deleted file mode 100644
index bbd6b3dcb812..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-signals.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- Lib/signal/filter_design.py.orig	2007-06-06 14:27:50.000000000 +0100
-+++ Lib/signal/filter_design.py	2007-06-06 14:43:14.000000000 +0100
-@@ -4,11 +4,11 @@
- """
- 
- import numpy
--from numpy.core.umath import *
--from numpy import atleast_1d, poly, polyval, roots, imag, real, asarray,\
--     allclose, resize, pi, concatenate, absolute, logspace
--from numpy import mintypecode, select
--from scipy import special, optimize, linalg
-+from numpy import atleast_1d, poly, polyval, roots, real, asarray, allclose, \
-+     resize, pi, absolute, logspace, r_, sqrt, tan, log10, arctan, arcsinh, \
-+     cos, exp, cosh, arccosh, ceil, conjugate, zeros, sinh
-+from numpy import mintypecode
-+from scipy import special, optimize
- from scipy.misc import comb
- import string, types
- 
diff --git a/sci-libs/scipy/files/scipy-0.5.2-viewer.patch b/sci-libs/scipy/files/scipy-0.5.2-viewer.patch
deleted file mode 100644
index 8c4bd2a6b9f9..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-viewer.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- Lib/misc/pilutil.py.orig	2007-06-06 14:28:07.000000000 +0100
-+++ Lib/misc/pilutil.py	2007-06-06 14:44:10.000000000 +0100
-@@ -2,6 +2,7 @@
- 
- import types
- import numpy
-+import tempfile
- 
- from numpy import amin, amax, ravel, asarray, cast, arange, \
-      ones, newaxis, transpose, mgrid, iscomplexobj, sum, zeros, uint8
-@@ -226,17 +227,20 @@
-     """Simple showing of an image through an external viewer.
-     """
-     im = toimage(arr)
--    if (len(arr.shape) == 3) and (arr.shape[2] == 4):
--        try:
--            import os
--            im.save('/tmp/scipy_imshow.png')
--            if os.system("(xv /tmp/scipy_imshow.png; rm -f /tmp/scipy_imshow.png)&"):
--                raise RuntimeError
--            return
--        except:
--            print "Warning: Alpha channel may not be handled correctly."
-+    fnum,fname = tempfile.mkstemp('.png')
-+    try:
-+        im.save(fname)
-+    except:
-+        raise RuntimeError("Error saving temporary image data.")
-+
-+    import os
-+    os.close(fnum)
-+    cmd = os.environ.get('SCIPY_PIL_IMAGE_VIEWER','see')
-+    status = os.system("%s %s" % (cmd,fname))
-+    os.unlink(fname)
-+    if status != 0:
-+        raise RuntimeError('Could not execute image viewer.')
- 
--    im.show()
-     return
- 
- def imresize(arr,size):
diff --git a/sci-libs/scipy/files/scipy-0.6.0-ndimage.patch b/sci-libs/scipy/files/scipy-0.6.0-ndimage.patch
new file mode 100644
index 000000000000..c5ee5b0fa442
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.6.0-ndimage.patch
@@ -0,0 +1,15 @@
+--- scipy/ndimage/src/nd_image.h.orig	2008-01-21 01:20:06.010806667 +0000
++++ scipy/ndimage/src/nd_image.h	2008-01-21 01:21:52.565386609 +0000
+@@ -273,12 +273,6 @@
+                                        NA_ByteOrder(), 1, 1);
+ }
+ 
+-#define  NA_OutputArray (*(PyArrayObject* (*) (PyObject*,NumarrayType,int) ) (void *) NA_OutputArray)
+-#define  NA_IoArray (*(PyArrayObject* (*) (PyObject*,NumarrayType,int) ) (void *) NA_IoArray)
+-#define  NA_NewArray (*(PyArrayObject* (*) (void* buffer, NumarrayType, int, ...) ) (void *) NA_NewArray )
+-#define  NA_elements (*(unsigned long (*) (PyArrayObject*) ) (void *) NA_elements)
+-#define  NA_InputArray (*(PyArrayObject* (*) (PyObject*,NumarrayType,int) ) (void *) NA_InputArray)
+-
+ #endif /* ND_IMPORT_ARRAY */
+ 
+ #endif /* ND_IMAGE_H */