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Update to sagemath 5.13

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This commit is contained in:
pcpa 2014-01-29 15:01:17 -02:00
parent b0cc81484c
commit d0a2caf3af
29 changed files with 206 additions and 206 deletions
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1
.gitignore vendored
View file

@ -2,3 +2,4 @@
/sage-5.9.tar
/sage-5.10.tar
/sage-5.12.tar
/sage-5.13.tar

8
sagemath-4ti2.patch
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@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/sandpiles/sandpile.py.orig sage-5.12/spkg/build/sage-5.12/sage/sandpiles/sandpile.py
--- sage-5.12/spkg/build/sage-5.12/sage/sandpiles/sandpile.py.orig 2013-05-06 13:50:14.882749079 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/sandpiles/sandpile.py 2013-05-06 13:50:34.526749831 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/sandpiles/sandpile.py.orig sage-5.13/spkg/build/sage-5.13/sage/sandpiles/sandpile.py
--- sage-5.13/spkg/build/sage-5.13/sage/sandpiles/sandpile.py.orig 2014-01-28 16:01:55.841188856 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/sandpiles/sandpile.py 2014-01-28 16:02:07.914189318 -0200
@@ -24,8 +24,6 @@ packages. An alternative is to install
following variable to the correct path.
"""
@ -10,7 +10,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/sandpiles/sandpile.py.orig sage-5.1
r"""
Sage Sandpiles
@@ -4098,7 +4096,7 @@ class SandpileDivisor(dict):
@@ -4097,7 +4095,7 @@ class SandpileDivisor(dict):
sign_file.close()
# compute
try:

8
sagemath-cbc.patch
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@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build/sage-5.12/module_list.py
--- sage-5.12/spkg/build/sage-5.12/module_list.py.orig 2013-10-16 12:11:43.002202675 -0300
+++ sage-5.12/spkg/build/sage-5.12/module_list.py 2013-10-16 12:11:47.063202831 -0300
@@ -2074,7 +2074,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
diff -up sage-5.13/spkg/build/sage-5.13/module_list.py.orig sage-5.13/spkg/build/sage-5.13/module_list.py
--- sage-5.13/spkg/build/sage-5.13/module_list.py.orig 2014-01-28 16:12:52.010213983 -0200
+++ sage-5.13/spkg/build/sage-5.13/module_list.py 2014-01-28 16:13:00.749214317 -0200
@@ -2097,7 +2097,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
libraries = ["csage", "stdc++", "cplex"])
)

6
sagemath-cremona.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/databases/cremona.py.orig sage-5.12/spkg/build/sage-5.12/sage/databases/cremona.py
--- sage-5.12/spkg/build/sage-5.12/sage/databases/cremona.py.orig 2013-02-22 17:33:50.579875129 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/databases/cremona.py 2013-02-22 17:34:05.051875683 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/databases/cremona.py.orig sage-5.13/spkg/build/sage-5.13/sage/databases/cremona.py
--- sage-5.13/spkg/build/sage-5.13/sage/databases/cremona.py.orig 2013-02-22 17:33:50.579875129 -0300
+++ sage-5.13/spkg/build/sage-5.13/sage/databases/cremona.py 2013-02-22 17:34:05.051875683 -0300
@@ -889,14 +889,9 @@ class MiniCremonaDatabase(SQLDatabase):
if N < self.largest_conductor():
message = "There is no elliptic curve with label " + label \

8
sagemath-cryptominisat.patch
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@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build/sage-5.12/module_list.py
--- sage-5.12/spkg/build/sage-5.12/module_list.py.orig 2013-10-16 12:39:05.925265588 -0300
+++ sage-5.12/spkg/build/sage-5.12/module_list.py 2013-10-16 12:39:14.072265900 -0300
@@ -2084,7 +2084,7 @@ if is_package_installed('cbc'):
diff -up sage-5.13/spkg/build/sage-5.13/module_list.py.orig sage-5.13/spkg/build/sage-5.13/module_list.py
--- sage-5.13/spkg/build/sage-5.13/module_list.py.orig 2014-01-28 16:20:58.178232600 -0200
+++ sage-5.13/spkg/build/sage-5.13/module_list.py 2014-01-28 16:21:11.779233120 -0200
@@ -2107,7 +2107,7 @@ if is_package_installed('cbc'):
)

24
sagemath-ecl-unicode.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pxd.orig sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pxd
--- sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pxd.orig 2013-03-19 16:11:17.358705144 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pxd 2013-03-19 16:11:27.719705541 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pxd.orig sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pxd
--- sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pxd.orig 2014-01-28 16:00:06.455184667 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pxd 2014-01-28 16:00:17.705185098 -0200
@@ -133,6 +133,7 @@ cdef extern from "ecl/ecl.h":
cl_object ecl_read_from_cstring_safe(char *s, cl_object err)
cl_object cl_write_to_string(cl_narg narg, cl_object o)
@ -9,10 +9,10 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pxd.orig sage-5.12/spkg/bu
# S-expr evaluation and function calls
diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx.orig sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx
--- sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx.orig 2013-03-19 16:11:07.489704766 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx 2013-03-19 16:11:27.719705541 -0300
@@ -238,17 +238,19 @@ cdef cl_object ecl_safe_eval(cl_object f
diff -up sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pyx.orig sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pyx
--- sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pyx.orig 2014-01-28 15:59:57.900184339 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/libs/ecl.pyx 2014-01-28 16:00:17.707185098 -0200
@@ -236,17 +236,19 @@ cdef cl_object ecl_safe_eval(cl_object f
...
RuntimeError: ECL says: Console interrupt.
"""
@ -34,7 +34,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx.orig sage-5.12/spkg/bu
l = cl_cons(func,cl_cons(arg,Cnil));
ecl_sig_on()
@@ -256,17 +258,20 @@ cdef cl_object ecl_safe_funcall(cl_objec
@@ -254,17 +256,20 @@ cdef cl_object ecl_safe_funcall(cl_objec
ecl_sig_off()
if ecl_nvalues > 1:
@ -57,7 +57,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx.orig sage-5.12/spkg/bu
else:
return ecl_values(0)
@@ -316,10 +321,11 @@ def print_objects():
@@ -314,10 +319,11 @@ def print_objects():
HELLO
"""
@ -71,7 +71,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx.orig sage-5.12/spkg/bu
c=cl_cadr(c)
if c == Cnil:
break
@@ -394,6 +400,7 @@ cdef cl_object python_to_ecl(pyobj) exce
@@ -392,6 +398,7 @@ cdef cl_object python_to_ecl(pyobj) exce
raise TypeError,"Unimplemented type for python_to_ecl"
cdef ecl_to_python(cl_object o):
@ -79,7 +79,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx.orig sage-5.12/spkg/bu
cdef Integer N
# conversions from an ecl object to a python object.
@@ -428,7 +435,8 @@ cdef ecl_to_python(cl_object o):
@@ -426,7 +433,8 @@ cdef ecl_to_python(cl_object o):
return tuple(L)
return L
else:
@ -89,7 +89,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ecl.pyx.orig sage-5.12/spkg/bu
#Maxima's BFLOAT multiprecision float type can be read with:
#def bfloat_to_python(e):
@@ -644,7 +652,7 @@ cdef class EclObject:
@@ -642,7 +650,7 @@ cdef class EclObject:
"""
cdef cl_object s

8
sagemath-extensions.patch
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@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build/sage-5.12/module_list.py
--- sage-5.12/spkg/build/sage-5.12/module_list.py.orig 2013-10-16 11:54:03.841162116 -0300
+++ sage-5.12/spkg/build/sage-5.12/module_list.py 2013-10-16 11:54:14.330162518 -0300
@@ -2029,7 +2029,8 @@ ext_modules = [
diff -up sage-5.13/spkg/build/sage-5.13/module_list.py.orig sage-5.13/spkg/build/sage-5.13/module_list.py
--- sage-5.13/spkg/build/sage-5.13/module_list.py.orig 2014-01-28 15:56:04.699175409 -0200
+++ sage-5.13/spkg/build/sage-5.13/module_list.py 2014-01-28 15:56:14.210175773 -0200
@@ -2052,7 +2052,8 @@ ext_modules = [
# These extensions are to be compiled only if the
# corresponding packages have been installed

8
sagemath-fes.patch
View file

@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build/sage-5.12/module_list.py
--- sage-5.12/spkg/build/sage-5.12/module_list.py.orig 2013-10-16 12:13:30.643206797 -0300
+++ sage-5.12/spkg/build/sage-5.12/module_list.py 2013-10-16 12:13:41.295207205 -0300
@@ -2033,7 +2033,7 @@ ext_modules = [
diff -up sage-5.13/spkg/build/sage-5.13/module_list.py.orig sage-5.13/spkg/build/sage-5.13/module_list.py
--- sage-5.13/spkg/build/sage-5.13/module_list.py.orig 2014-01-28 16:14:01.061216627 -0200
+++ sage-5.13/spkg/build/sage-5.13/module_list.py 2014-01-28 16:14:03.961216738 -0200
@@ -2056,7 +2056,7 @@ ext_modules = [
def is_package_installed(name):
return False

6
sagemath-gap-hap.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/groups/perm_gps/permgroup.py.orig sage-5.12/spkg/build/sage-5.12/sage/groups/perm_gps/permgroup.py
--- sage-5.12/spkg/build/sage-5.12/sage/groups/perm_gps/permgroup.py.orig 2013-10-16 12:10:08.670199063 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/groups/perm_gps/permgroup.py 2013-10-16 12:10:21.342199548 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/groups/perm_gps/permgroup.py.orig sage-5.13/spkg/build/sage-5.13/sage/groups/perm_gps/permgroup.py
--- sage-5.13/spkg/build/sage-5.13/sage/groups/perm_gps/permgroup.py.orig 2013-10-16 12:10:08.670199063 -0300
+++ sage-5.13/spkg/build/sage-5.13/sage/groups/perm_gps/permgroup.py 2013-10-16 12:10:21.342199548 -0300
@@ -180,8 +180,7 @@ def hap_decorator(f):
"""
@wraps(f)

11
sagemath-gmp.patch
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@ -1,11 +1,12 @@
--- sage-5.12/spkg/build/sage-5.12/c_lib/src/memory.c.orig 2012-07-10 11:46:54.516595967 -0400
+++ sage-5.12/spkg/build/sage-5.12/c_lib/src/memory.c 2012-07-10 11:47:12.688596755 -0400
@@ -17,7 +17,7 @@ AUTHORS:
* http://www.gnu.org/licenses/
diff -up sage-5.13/spkg/build/sage-5.13/c_lib/src/memory.c.orig sage-5.13/spkg/build/sage-5.13/c_lib/src/memory.c
--- sage-5.13/spkg/build/sage-5.13/c_lib/src/memory.c.orig 2014-01-28 15:45:05.920150182 -0200
+++ sage-5.13/spkg/build/sage-5.13/c_lib/src/memory.c 2014-01-28 15:45:14.225150500 -0200
@@ -18,7 +18,7 @@ AUTHORS:
****************************************************************************/
#include <Python.h>
-#include <mpir.h>
+#include <gmp.h>
#include "interrupt.h"
#include "memory.h"
/* mpir memory functions */

6
sagemath-jmol.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/interfaces/jmoldata.py.orig sage-5.12/spkg/build/sage-5.12/sage/interfaces/jmoldata.py
--- sage-5.12/spkg/build/sage-5.12/sage/interfaces/jmoldata.py.orig 2012-11-10 12:03:07.742817945 -0200
+++ sage-5.12/spkg/build/sage-5.12/sage/interfaces/jmoldata.py 2012-11-10 12:03:34.499818970 -0200
diff -up sage-5.13/spkg/build/sage-5.13/sage/interfaces/jmoldata.py.orig sage-5.13/spkg/build/sage-5.13/sage/interfaces/jmoldata.py
--- sage-5.13/spkg/build/sage-5.13/sage/interfaces/jmoldata.py.orig 2012-11-10 12:03:07.742817945 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/interfaces/jmoldata.py 2012-11-10 12:03:34.499818970 -0200
@@ -86,7 +86,7 @@ class JmolData(SageObject):
sage_makedirs(jmolscratch)
scratchout = os.path.join(jmolscratch,"jmolout.txt")

6
sagemath-libgap.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/gap/util.pyx.orig sage-5.12/spkg/build/sage-5.12/sage/libs/gap/util.pyx
--- sage-5.12/spkg/build/sage-5.12/sage/libs/gap/util.pyx.orig 2013-05-06 14:24:03.160826749 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/libs/gap/util.pyx 2013-05-06 14:25:25.806829913 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/libs/gap/util.pyx.orig sage-5.13/spkg/build/sage-5.13/sage/libs/gap/util.pyx
--- sage-5.13/spkg/build/sage-5.13/sage/libs/gap/util.pyx.orig 2013-05-06 14:24:03.160826749 -0300
+++ sage-5.13/spkg/build/sage-5.13/sage/libs/gap/util.pyx 2013-05-06 14:25:25.806829913 -0300
@@ -155,18 +155,9 @@ def gap_root():
sage: from sage.libs.gap.util import gap_root

8
sagemath-lrcalc.patch
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@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build/sage-5.12/module_list.py
--- sage-5.12/spkg/build/sage-5.12/module_list.py.orig 2013-10-16 12:10:52.183200729 -0300
+++ sage-5.12/spkg/build/sage-5.12/module_list.py 2013-10-16 12:11:01.725201094 -0300
@@ -2109,7 +2109,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
diff -up sage-5.13/spkg/build/sage-5.13/module_list.py.orig sage-5.13/spkg/build/sage-5.13/module_list.py
--- sage-5.13/spkg/build/sage-5.13/module_list.py.orig 2014-01-28 16:12:03.635212130 -0200
+++ sage-5.13/spkg/build/sage-5.13/module_list.py 2014-01-28 16:12:12.674212476 -0200
@@ -2132,7 +2132,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
)

6
sagemath-lrslib.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/geometry/polyhedron/base.py.orig sage-5.12/spkg/build/sage-5.12/sage/geometry/polyhedron/base.py
--- sage-5.12/spkg/build/sage-5.12/sage/geometry/polyhedron/base.py.orig 2013-10-16 12:08:54.546196224 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/geometry/polyhedron/base.py 2013-10-16 12:09:04.060196589 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/geometry/polyhedron/base.py.orig sage-5.13/spkg/build/sage-5.13/sage/geometry/polyhedron/base.py
--- sage-5.13/spkg/build/sage-5.13/sage/geometry/polyhedron/base.py.orig 2013-10-16 12:08:54.546196224 -0300
+++ sage-5.13/spkg/build/sage-5.13/sage/geometry/polyhedron/base.py 2013-10-16 12:09:04.060196589 -0300
@@ -3291,11 +3291,6 @@ class Polyhedron_base(Element):
David Avis's lrs program.

12
sagemath-maxima.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/interfaces/maxima.py.orig sage-5.12/spkg/build/sage-5.12/sage/interfaces/maxima.py
--- sage-5.12/spkg/build/sage-5.12/sage/interfaces/maxima.py.orig 2013-07-29 19:54:04.395052544 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/interfaces/maxima.py 2013-07-29 19:55:18.259055373 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/interfaces/maxima.py.orig sage-5.13/spkg/build/sage-5.13/sage/interfaces/maxima.py
--- sage-5.13/spkg/build/sage-5.13/sage/interfaces/maxima.py.orig 2013-07-29 19:54:04.395052544 -0300
+++ sage-5.13/spkg/build/sage-5.13/sage/interfaces/maxima.py 2013-07-29 19:55:18.259055373 -0300
@@ -544,7 +544,7 @@ class Maxima(MaximaAbstract, Expect):
Expect.__init__(self,
name = 'maxima',
@ -20,9 +20,9 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/interfaces/maxima.py.orig sage-5.12
self._eval_line('0;')
def __reduce__(self):
diff -up sage-5.12/spkg/build/sage_scripts-5.12/sage-maxima.lisp.orig sage-5.12/spkg/build/sage_scripts-5.12/sage-maxima.lisp
--- sage-5.12/spkg/build/sage_scripts-5.12/sage-maxima.lisp.orig 2013-07-29 19:54:04.402052544 -0300
+++ sage-5.12/spkg/build/sage_scripts-5.12/sage-maxima.lisp 2013-07-29 19:55:33.867055970 -0300
diff -up sage-5.13/spkg/build/sage_scripts-5.13/sage-maxima.lisp.orig sage-5.13/spkg/build/sage_scripts-5.13/sage-maxima.lisp
--- sage-5.13/spkg/build/sage_scripts-5.13/sage-maxima.lisp.orig 2013-07-29 19:54:04.402052544 -0300
+++ sage-5.13/spkg/build/sage_scripts-5.13/sage-maxima.lisp 2013-07-29 19:55:33.867055970 -0300
@@ -3,4 +3,8 @@
;(setf *general-display-prefix* "<sage-display>")

8
sagemath-nauty.patch
View file

@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/graphs/graph_generators.py.orig sage-5.12/spkg/build/sage-5.12/sage/graphs/graph_generators.py
--- sage-5.12/spkg/build/sage-5.12/sage/graphs/graph_generators.py.orig 2013-10-16 12:18:25.218218077 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/graphs/graph_generators.py 2013-10-16 12:18:46.709218900 -0300
@@ -793,7 +793,7 @@ class GraphGenerators():
diff -up sage-5.13/spkg/build/sage-5.13/sage/graphs/graph_generators.py.orig sage-5.13/spkg/build/sage-5.13/sage/graphs/graph_generators.py
--- sage-5.13/spkg/build/sage-5.13/sage/graphs/graph_generators.py.orig 2014-01-28 16:10:40.018208928 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/graphs/graph_generators.py 2014-01-28 16:10:49.569209294 -0200
@@ -810,7 +810,7 @@ class GraphGenerators():
"""
import subprocess
from sage.misc.package import is_package_installed

22
sagemath-nopari2.6.patch
View file

@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/pari/decl.pxi.orig sage-5.12/spkg/build/sage-5.12/sage/libs/pari/decl.pxi
--- sage-5.12/spkg/build/sage-5.12/sage/libs/pari/decl.pxi.orig 2013-10-16 12:36:08.386258790 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/libs/pari/decl.pxi 2013-10-16 12:36:42.853260110 -0300
@@ -856,7 +856,6 @@ cdef extern from 'pari/pari.h':
diff -up sage-5.13/spkg/build/sage-5.13/sage/libs/pari/decl.pxi.orig sage-5.13/spkg/build/sage-5.13/sage/libs/pari/decl.pxi
--- sage-5.13/spkg/build/sage-5.13/sage/libs/pari/decl.pxi.orig 2014-01-28 16:15:59.591221166 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/libs/pari/decl.pxi 2014-01-28 16:16:06.331221424 -0200
@@ -869,7 +869,6 @@ cdef extern from 'pari/pari.h':
GEN polredabs0(GEN x, long flag)
GEN polredabs2(GEN x)
GEN polredabsall(GEN x, long flun)
@ -9,17 +9,17 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/pari/decl.pxi.orig sage-5.12/s
GEN qflll0(GEN x, long flag)
GEN qflllgram0(GEN x, long flag)
GEN smallpolred(GEN x)
diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx.orig sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx
--- sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx.orig 2013-10-16 12:36:50.848260416 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx 2013-10-16 12:37:41.619262360 -0300
@@ -8081,10 +8081,6 @@ cdef class gen(sage.structure.element.Ri
diff -up sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx.orig sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx
--- sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx.orig 2014-01-28 16:16:21.446222003 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx 2014-01-28 16:16:33.024222446 -0200
@@ -8087,10 +8087,6 @@ cdef class gen(sage.structure.element.Ri
pari_catch_sig_on()
return self.new_gen(polredabs0(self.g, flag))
return P.new_gen(polredabs0(self.g, flag))
- def polredbest(self, flag=0):
- pari_catch_sig_on()
- return self.new_gen(polredbest(self.g, flag))
- return P.new_gen(polredbest(self.g, flag))
-
def polresultant(self, y, var=-1, flag=0):
t0GEN(y)
cdef gen t0 = objtogen(y)
pari_catch_sig_on()

18
sagemath-ntl6.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/c_lib/include/ntl_wrap.h.orig sage-5.12/spkg/build/sage-5.12/c_lib/include/ntl_wrap.h
--- sage-5.12/spkg/build/sage-5.12/c_lib/include/ntl_wrap.h.orig 2013-07-29 19:40:07.189020485 -0300
+++ sage-5.12/spkg/build/sage-5.12/c_lib/include/ntl_wrap.h 2013-07-29 19:40:11.831020662 -0300
diff -up sage-5.13/spkg/build/sage-5.13/c_lib/include/ntl_wrap.h.orig sage-5.13/spkg/build/sage-5.13/c_lib/include/ntl_wrap.h
--- sage-5.13/spkg/build/sage-5.13/c_lib/include/ntl_wrap.h.orig 2013-07-29 19:40:07.189020485 -0300
+++ sage-5.13/spkg/build/sage-5.13/c_lib/include/ntl_wrap.h 2013-07-29 19:40:11.831020662 -0300
@@ -40,91 +40,92 @@ EXTERN void setup_NTL_error_callback(voi
//////// ZZ //////////
@ -451,9 +451,9 @@ diff -up sage-5.12/spkg/build/sage-5.12/c_lib/include/ntl_wrap.h.orig sage-5.12/
-EXTERN void mat_GF2_setitem(struct mat_GF2* x, int i, int j, const struct GF2* z);
+EXTERN void mat_GF2_setitem(mat_GF2* x, int i, int j, const GF2* z);
diff -up sage-5.12/spkg/build/sage-5.12/c_lib/src/ntl_wrap.cpp.orig sage-5.12/spkg/build/sage-5.12/c_lib/src/ntl_wrap.cpp
--- sage-5.12/spkg/build/sage-5.12/c_lib/src/ntl_wrap.cpp.orig 2013-07-29 19:40:07.197020485 -0300
+++ sage-5.12/spkg/build/sage-5.12/c_lib/src/ntl_wrap.cpp 2013-07-29 19:40:11.834020662 -0300
diff -up sage-5.13/spkg/build/sage-5.13/c_lib/src/ntl_wrap.cpp.orig sage-5.13/spkg/build/sage-5.13/c_lib/src/ntl_wrap.cpp
--- sage-5.13/spkg/build/sage-5.13/c_lib/src/ntl_wrap.cpp.orig 2013-07-29 19:40:07.197020485 -0300
+++ sage-5.13/spkg/build/sage-5.13/c_lib/src/ntl_wrap.cpp 2013-07-29 19:40:11.834020662 -0300
@@ -29,7 +29,7 @@ int ZZ_to_int(const ZZ* x)
/* Returns a *new* ZZ object.
@ -1350,9 +1350,9 @@ diff -up sage-5.12/spkg/build/sage-5.12/c_lib/src/ntl_wrap.cpp.orig sage-5.12/sp
{
//int j;
cpn.restore();
diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/ntl/decl.pxi.orig sage-5.12/spkg/build/sage-5.12/sage/libs/ntl/decl.pxi
--- sage-5.12/spkg/build/sage-5.12/sage/libs/ntl/decl.pxi.orig 2013-07-29 19:39:08.246018227 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/libs/ntl/decl.pxi 2013-07-29 19:40:11.836020662 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/libs/ntl/decl.pxi.orig sage-5.13/spkg/build/sage-5.13/sage/libs/ntl/decl.pxi
--- sage-5.13/spkg/build/sage-5.13/sage/libs/ntl/decl.pxi.orig 2013-07-29 19:39:08.246018227 -0300
+++ sage-5.13/spkg/build/sage-5.13/sage/libs/ntl/decl.pxi 2013-07-29 19:40:11.836020662 -0300
@@ -22,7 +22,7 @@ from sage.libs.ntl.ntl_ZZ_pEX_decl cimpo
cdef extern from "ntl_wrap.h":

30
sagemath-pari.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/interfaces/gp.py.orig sage-5.12/spkg/build/sage-5.12/sage/interfaces/gp.py
--- sage-5.12/spkg/build/sage-5.12/sage/interfaces/gp.py.orig 2013-10-16 12:06:10.261189933 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/interfaces/gp.py 2013-10-16 12:06:21.487190363 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/interfaces/gp.py.orig sage-5.13/spkg/build/sage-5.13/sage/interfaces/gp.py
--- sage-5.13/spkg/build/sage-5.13/sage/interfaces/gp.py.orig 2014-01-28 16:06:59.279200475 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/interfaces/gp.py 2014-01-28 16:07:36.218201890 -0200
@@ -977,11 +977,11 @@ def is_GpElement(x):
"""
return isinstance(x, GpElement)
@ -16,10 +16,10 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/interfaces/gp.py.orig sage-5.12/spk
# An instance
gp = Gp(logfile=os.path.join(DOT_SAGE,'gp-expect.log')) # useful for debugging!
diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx.orig sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx
--- sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx.orig 2013-10-16 12:06:00.720189568 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx 2013-10-16 12:06:21.498190364 -0300
@@ -183,6 +183,10 @@ include 'sage/ext/python.pxi'
diff -up sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx.orig sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx
--- sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx.orig 2014-01-28 16:07:00.806200534 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/libs/pari/gen.pyx 2014-01-28 16:08:42.169204415 -0200
@@ -194,6 +194,10 @@ cdef extern from "misc.h":
cdef extern from "mpz_pylong.h":
cdef int mpz_set_pylong(mpz_t dst, src) except -1
@ -27,19 +27,19 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/libs/pari/gen.pyx.orig sage-5.12/sp
+ cdef void mp_get_memory_functions(void**, void**, void**)
+ cdef void mp_set_memory_functions(void*, void*, void*)
+
# Make sure we don't use mpz_t_offset before initializing it by
# putting in a value that's likely to provoke a segmentation fault,
# rather than silently corrupting memory.
@@ -9292,7 +9296,12 @@ cdef class PariInstance(sage.structure.p
# Will be imported as needed
Integer = None
@@ -9319,7 +9323,12 @@ cdef class PariInstance(sage.structure.p
# The size here doesn't really matter, because we will allocate
# our own stack anyway. We ask PARI not to set up signal handlers.
# our own stack anyway. We ask PARI not to set up signal and
# error handlers.
+ cdef void *_gmp_malloc
+ cdef void *_gmp_realloc
+ cdef void *_gmp_free
+ mp_get_memory_functions(&_gmp_malloc, &_gmp_realloc, &_gmp_free)
pari_init_opts(10000, maxprime, INIT_JMPm | INIT_DFTm)
pari_init_opts(10000, maxprime, INIT_DFTm)
+ mp_set_memory_functions(_gmp_malloc, _gmp_realloc, _gmp_free)
num_primes = maxprime
# NOTE: pari_catch_sig_on() can only come AFTER pari_init_opts()!
_pari_init_error_handling()

12
sagemath-png.patch
View file

@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build/sage-5.12/module_list.py
--- sage-5.12/spkg/build/sage-5.12/module_list.py.orig 2013-10-16 12:04:58.107187170 -0300
+++ sage-5.12/spkg/build/sage-5.12/module_list.py 2013-10-16 12:05:13.747187769 -0300
@@ -1028,7 +1028,7 @@ ext_modules = [
diff -up sage-5.13/spkg/build/sage-5.13/module_list.py.orig sage-5.13/spkg/build/sage-5.13/module_list.py
--- sage-5.13/spkg/build/sage-5.13/module_list.py.orig 2014-01-28 16:00:48.914186293 -0200
+++ sage-5.13/spkg/build/sage-5.13/module_list.py 2014-01-28 16:00:58.259186651 -0200
@@ -1035,7 +1035,7 @@ ext_modules = [
Extension('sage.matrix.matrix_mod2_dense',
sources = ['sage/matrix/matrix_mod2_dense.pyx'],
@ -10,7 +10,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
@@ -1323,7 +1323,7 @@ ext_modules = [
@@ -1333,7 +1333,7 @@ ext_modules = [
Extension('sage.modules.vector_mod2_dense',
sources = ['sage/modules/vector_mod2_dense.pyx'],
@ -19,7 +19,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
@@ -1801,7 +1801,7 @@ ext_modules = [
@@ -1824,7 +1824,7 @@ ext_modules = [
Extension('sage.rings.polynomial.pbori',
sources = ['sage/rings/polynomial/pbori.pyx'],
libraries=['polybori-' + polybori_major_version,

8
sagemath-readonly.patch
View file

@ -1,7 +1,7 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/all.py.orig sage-5.12/spkg/build/sage-5.12/sage/all.py
--- sage-5.12/spkg/build/sage-5.12/sage/all.py.orig 2013-10-16 12:04:06.447185192 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/all.py 2013-10-16 12:04:16.661185583 -0300
@@ -311,11 +311,11 @@ def _write_started_file():
diff -up sage-5.13/spkg/build/sage-5.13/sage/all.py.orig sage-5.13/spkg/build/sage-5.13/sage/all.py
--- sage-5.13/spkg/build/sage-5.13/sage/all.py.orig 2014-01-28 15:59:04.029182276 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/all.py 2014-01-28 15:59:15.560182718 -0200
@@ -304,11 +304,11 @@ def _write_started_file():
Check that the file exists when Sage is running::

20
sagemath-rpmbuild.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig sage-5.12/spkg/build/conway_polynomials-0.4.p0/spkg-install
--- sage-5.12/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig 2013-10-16 11:55:08.703164600 -0300
+++ sage-5.12/spkg/build/conway_polynomials-0.4.p0/spkg-install 2013-10-16 11:55:11.351164701 -0300
diff -up sage-5.13/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig sage-5.13/spkg/build/conway_polynomials-0.4.p0/spkg-install
--- sage-5.13/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig 2014-01-28 15:57:09.773177901 -0200
+++ sage-5.13/spkg/build/conway_polynomials-0.4.p0/spkg-install 2014-01-28 15:57:15.720178129 -0200
@@ -2,9 +2,10 @@
import os
@ -14,9 +14,9 @@ diff -up sage-5.12/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig sage-5
def create_db():
db = {}
diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build/sage-5.12/module_list.py
--- sage-5.12/spkg/build/sage-5.12/module_list.py.orig 2013-10-16 11:54:46.324163743 -0300
+++ sage-5.12/spkg/build/sage-5.12/module_list.py 2013-10-16 11:55:11.353164701 -0300
diff -up sage-5.13/spkg/build/sage-5.13/module_list.py.orig sage-5.13/spkg/build/sage-5.13/module_list.py
--- sage-5.13/spkg/build/sage-5.13/module_list.py.orig 2014-01-28 15:56:51.221177191 -0200
+++ sage-5.13/spkg/build/sage-5.13/module_list.py 2014-01-28 15:57:15.722178129 -0200
@@ -5,7 +5,7 @@ from distutils.core import setup
from distutils.extension import Extension
from sage.env import *
@ -49,7 +49,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build
polybori_major_version = '0.8'
@@ -672,7 +673,7 @@ ext_modules = [
@@ -675,7 +676,7 @@ ext_modules = [
sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx',
'Lfunction', 'stdc++'],
@ -58,9 +58,9 @@ diff -up sage-5.12/spkg/build/sage-5.12/module_list.py.orig sage-5.12/spkg/build
extra_compile_args=["-O3", "-ffast-math"],
language = 'c++'),
diff -up sage-5.12/spkg/build/sage-5.12/setup.py.orig sage-5.12/spkg/build/sage-5.12/setup.py
--- sage-5.12/spkg/build/sage-5.12/setup.py.orig 2013-10-18 11:46:06.182555124 -0300
+++ sage-5.12/spkg/build/sage-5.12/setup.py 2013-10-18 11:46:29.092556002 -0300
diff -up sage-5.13/spkg/build/sage-5.13/setup.py.orig sage-5.13/spkg/build/sage-5.13/setup.py
--- sage-5.13/spkg/build/sage-5.13/setup.py.orig 2014-01-28 15:57:09.788177902 -0200
+++ sage-5.13/spkg/build/sage-5.13/setup.py 2014-01-28 15:57:15.723178129 -0200
@@ -36,23 +36,13 @@ except KeyError:
compile_result_dir = None
keep_going = False

38
sagemath-sagedoc.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/doc/common/builder.py.orig sage-5.12/spkg/build/sage-5.12/doc/common/builder.py
--- sage-5.12/spkg/build/sage-5.12/doc/common/builder.py.orig 2013-10-16 11:56:12.984167061 -0300
+++ sage-5.12/spkg/build/sage-5.12/doc/common/builder.py 2013-10-16 11:56:20.433167347 -0300
diff -up sage-5.13/spkg/build/sage-5.13/doc/common/builder.py.orig sage-5.13/spkg/build/sage-5.13/doc/common/builder.py
--- sage-5.13/spkg/build/sage-5.13/doc/common/builder.py.orig 2014-01-28 15:58:17.552180497 -0200
+++ sage-5.13/spkg/build/sage-5.13/doc/common/builder.py 2014-01-28 15:58:19.905180587 -0200
@@ -32,7 +32,7 @@ from sage.env import SAGE_DOC, SAGE_SRC
# SAGE_DOC, LANGUAGES, SPHINXOPTS, PAPER, OMIT,
# PAPEROPTS, ALLSPHINXOPTS, NUM_THREADS, WEBSITESPHINXOPTS
@ -10,9 +10,9 @@ diff -up sage-5.12/spkg/build/sage-5.12/doc/common/builder.py.orig sage-5.12/spk
##########################################
diff -up sage-5.12/spkg/build/sage-5.12/doc/common/conf.py.orig sage-5.12/spkg/build/sage-5.12/doc/common/conf.py
--- sage-5.12/spkg/build/sage-5.12/doc/common/conf.py.orig 2013-10-16 11:56:12.999167062 -0300
+++ sage-5.12/spkg/build/sage-5.12/doc/common/conf.py 2013-10-16 11:56:20.436167347 -0300
diff -up sage-5.13/spkg/build/sage-5.13/doc/common/conf.py.orig sage-5.13/spkg/build/sage-5.13/doc/common/conf.py
--- sage-5.13/spkg/build/sage-5.13/doc/common/conf.py.orig 2014-01-28 15:58:17.562180497 -0200
+++ sage-5.13/spkg/build/sage-5.13/doc/common/conf.py 2014-01-28 15:58:19.908180587 -0200
@@ -1,5 +1,5 @@
import sys, os, sphinx
-from sage.env import SAGE_DOC
@ -30,10 +30,10 @@ diff -up sage-5.12/spkg/build/sage-5.12/doc/common/conf.py.orig sage-5.12/spkg/b
mathjax_relative = os.path.join('sagenb','data','mathjax')
# It would be really nice if sphinx would copy the entire mathjax directory,
diff -up sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py.orig sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py
--- sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py.orig 2013-10-16 11:55:44.534165972 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py 2013-10-16 11:56:20.440167347 -0300
@@ -88,7 +88,6 @@ class DocTestDefaults(SageObject):
diff -up sage-5.13/spkg/build/sage-5.13/sage/doctest/control.py.orig sage-5.13/spkg/build/sage-5.13/sage/doctest/control.py
--- sage-5.13/spkg/build/sage-5.13/sage/doctest/control.py.orig 2014-01-28 15:57:50.711179469 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/doctest/control.py 2014-01-28 15:58:19.909180587 -0200
@@ -89,7 +89,6 @@ class DocTestDefaults(SageObject):
self.valgrind = False
self.massif = False
self.cachegrind = False
@ -41,7 +41,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py.orig sage-5.12/s
self.failed = False
self.new = False
self.show_skipped = False
@@ -210,7 +209,7 @@ class DocTestController(SageObject):
@@ -211,7 +210,7 @@ class DocTestController(SageObject):
if options.gdb or options.debug:
# Interactive debuggers: "infinite" timeout
options.timeout = 0
@ -50,7 +50,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py.orig sage-5.12/s
# Non-interactive debuggers: 48 hours
options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
elif options.long:
@@ -806,13 +805,8 @@ class DocTestController(SageObject):
@@ -822,13 +821,8 @@ class DocTestController(SageObject):
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@ -64,7 +64,7 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py.orig sage-5.12/s
if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd
@@ -872,10 +866,10 @@ class DocTestController(SageObject):
@@ -888,10 +882,10 @@ class DocTestController(SageObject):
0
"""
opt = self.options
@ -77,9 +77,9 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/doctest/control.py.orig sage-5.12/s
return 2
return self.run_val_gdb()
else:
diff -up sage-5.12/spkg/build/sage-5.12/sage/interfaces/singular.py.orig sage-5.12/spkg/build/sage-5.12/sage/interfaces/singular.py
--- sage-5.12/spkg/build/sage-5.12/sage/interfaces/singular.py.orig 2013-10-16 11:56:13.020167063 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/interfaces/singular.py 2013-10-16 11:56:20.442167347 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/interfaces/singular.py.orig sage-5.13/spkg/build/sage-5.13/sage/interfaces/singular.py
--- sage-5.13/spkg/build/sage-5.13/sage/interfaces/singular.py.orig 2014-01-28 15:58:17.580180498 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/interfaces/singular.py 2014-01-28 15:58:19.911180587 -0200
@@ -2149,7 +2149,7 @@ def generate_docstring_dictionary():
nodes.clear()
node_names.clear()
@ -89,9 +89,9 @@ diff -up sage-5.12/spkg/build/sage-5.12/sage/interfaces/singular.py.orig sage-5.
new_node = re.compile("File: singular\.hlp, Node: ([^,]*),.*")
new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
diff -up sage-5.12/spkg/build/sage-5.12/sage/misc/latex_macros.py.orig sage-5.12/spkg/build/sage-5.12/sage/misc/latex_macros.py
--- sage-5.12/spkg/build/sage-5.12/sage/misc/latex_macros.py.orig 2013-10-16 11:56:13.029167063 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/misc/latex_macros.py 2013-10-16 11:56:20.443167347 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/misc/latex_macros.py.orig sage-5.13/spkg/build/sage-5.13/sage/misc/latex_macros.py
--- sage-5.13/spkg/build/sage-5.13/sage/misc/latex_macros.py.orig 2014-01-28 15:58:17.585180498 -0200
+++ sage-5.13/spkg/build/sage-5.13/sage/misc/latex_macros.py 2014-01-28 15:58:19.912180587 -0200
@@ -142,7 +142,7 @@ def convert_latex_macro_to_mathjax(macro
return name + ': ["' + defn + '",' + str(num_args) + ']'

30
sagemath-sagenb.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py.orig sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py
--- sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py.orig 2013-10-16 11:57:47.963170699 -0300
+++ sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py 2013-10-16 11:58:10.515171562 -0300
diff -up sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py.orig sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py
--- sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py.orig 2013-10-16 11:57:47.963170699 -0300
+++ sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py 2013-10-16 11:58:10.515171562 -0300
@@ -33,7 +33,7 @@ class SageNBFlask(Flask):
self.add_static_path('/javascript', DATA)
self.add_static_path('/static', DATA)
@ -10,9 +10,9 @@ diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/flask_version/base.py.o
import mimetypes
mimetypes.add_type('text/plain','.jmol')
diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html
--- sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig 2013-10-16 11:58:21.871171997 -0300
+++ sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html 2013-10-16 11:59:05.075173651 -0300
diff -up sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html
--- sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig 2013-10-16 11:58:21.871171997 -0300
+++ sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/notebook/base.html 2013-10-16 11:59:05.075173651 -0300
@@ -46,7 +46,7 @@ INPUT:
<!-- Jmol - embedded 3D graphics -->
<script type="text/javascript" src="/java/jmol/appletweb/Jmol.js"></script>
@ -22,9 +22,9 @@ diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/html/n
{% if JEDITABLE_TINYMCE and not worksheet.docbrowser() and not worksheet.is_published() %}
<!-- TinyMCE and jEditable - in-place editing of text cells -->
diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js
--- sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig 2013-10-16 12:02:59.809182640 -0300
+++ sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js 2013-10-16 12:03:26.748183672 -0300
diff -up sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js
--- sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig 2013-10-16 12:02:59.809182640 -0300
+++ sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmol_lib.js 2013-10-16 12:03:26.748183672 -0300
@@ -256,9 +256,6 @@ function makeCntrlPanels(url, n, functio
panelHTML +='<button title="Move to own window" onClick="javascript:void(jmol_popup(\''+n+'\'))">Move to own window</button> arbitrarily resizable.<hr/>';
//static image to save
@ -35,9 +35,9 @@ diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/data/sage/js/jmo
//spin on
panelHTML +='<input class="worksheet" type="checkbox" value="spin on" onchange="jmol_spin(this.checked,'+n+');" title="Enable/disable spin"/>Spin on';
//antialaisdisplay (smoothing of objects)
diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py.orig sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py
--- sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py.orig 2013-10-16 11:59:18.079174149 -0300
+++ sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py 2013-10-16 11:59:41.357175041 -0300
diff -up sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py.orig sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py
--- sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py.orig 2013-10-16 11:59:18.079174149 -0300
+++ sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py 2013-10-16 11:59:41.357175041 -0300
@@ -2369,7 +2369,7 @@ class Cell(Cell_generic):
jmol_script = jmol_file.read()
jmol_file.close()
@ -47,9 +47,9 @@ diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/cell.py
jmol_file = open(jmol_name, 'w')
jmol_file.write(jmol_script)
diff -up sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py.orig sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py
--- sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py.orig 2013-10-16 11:59:58.863175711 -0300
+++ sage-5.12/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py 2013-10-16 12:02:45.172182080 -0300
diff -up sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py.orig sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py
--- sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py.orig 2013-10-16 11:59:58.863175711 -0300
+++ sage-5.13/spkg/build/sagenb-0.10.7.2/src/sagenb/sagenb/notebook/run_notebook.py 2013-10-16 12:02:45.172182080 -0300
@@ -46,12 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
# Flask #
#########

6
sagemath-scons.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/c_lib/SConstruct.orig sage-5.12/spkg/build/sage-5.12/c_lib/SConstruct
--- sage-5.12/spkg/build/sage-5.12/c_lib/SConstruct.orig 2013-02-23 12:55:48.382841120 -0300
+++ sage-5.12/spkg/build/sage-5.12/c_lib/SConstruct 2013-02-23 12:56:25.037842523 -0300
diff -up sage-5.13/spkg/build/sage-5.13/c_lib/SConstruct.orig sage-5.13/spkg/build/sage-5.13/c_lib/SConstruct
--- sage-5.13/spkg/build/sage-5.13/c_lib/SConstruct.orig 2013-02-23 12:55:48.382841120 -0300
+++ sage-5.13/spkg/build/sage-5.13/c_lib/SConstruct 2013-02-23 12:56:25.037842523 -0300
@@ -126,18 +126,31 @@ env['PYV']=platform.python_version().rsp
# The SCons convenience function Split is the only strange thing
# to python programmers. It just makes a list by splitting on

72
sagemath-scripts.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
--- sage-5.12/spkg/bin/sage.orig 2013-10-16 11:43:15.464137288 -0300
+++ sage-5.12/spkg/bin/sage 2013-10-16 11:51:01.675155140 -0300
diff -up sage-5.13/spkg/bin/sage.orig sage-5.13/spkg/bin/sage
--- sage-5.13/spkg/bin/sage.orig 2014-01-28 15:47:54.216156627 -0200
+++ sage-5.13/spkg/bin/sage 2014-01-28 15:55:18.058173623 -0200
@@ -11,17 +11,14 @@ usage() {
echo " file.<sage|py|spyx> -- run given .sage, .py or .spyx files"
echo " -advanced -- list all command line options"
@ -64,7 +64,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
echo " -maxima [...] -- run Sage's Maxima with given arguments"
echo " -mwrank [...] -- run Sage's mwrank with given arguments"
echo " -python [...] -- run the Python interpreter"
@@ -109,79 +96,10 @@ usage_advanced() {
@@ -109,83 +96,10 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -110,11 +110,15 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
- echo " -btnew [...] -- build and test modified files, options like -tnew"
- echo " -clone [new branch] -- clone a new branch of the Sage library from the"
- echo " current branch"
- echo " -fixdoctests <file.py> -- create <file.py>.out that would pass the doctests"
- echo " and output a patch"
- echo " -startuptime [module] -- display how long each component of Sage takes to"
- echo " start up; optionally specify a module to get more"
- echo " details about that particular module"
- echo " -fixdoctests <file.py> [output_file] [--long]"
- echo " -- writes a new version of file.py to output_file"
- echo " (defaults: to file.py.out) that will pass the doctests."
- echo " With the optional --long argument the long time tests"
- echo " are also checked."
- echo " A patch for the new file is printed to stdout."
- echo " -startuptime [module] -- display how long each component of Sage takes to"
- echo " start up; optionally specify a module to get more"
- echo " details about that particular module"
- echo " -t [options] <--all|files|dir>"
- echo " -- test examples in .py, .pyx, .sage, .tex or .rst files"
- echo " selected options:"
@ -144,7 +148,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
echo " -search_src <string> -- search through all the Sage library code for string"
echo " -search_doc <string> -- search through the Sage documentation for string"
echo " -grep <string> -- same as -search_src"
@@ -201,19 +119,6 @@ usage_advanced() {
@@ -205,19 +119,6 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -164,7 +168,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
echo "Valgrind memory debugging:"
echo " -cachegrind -- run Sage using Valgrind's cachegrind tool. The log"
echo " files are named sage-cachegrind.PID can be found in"
@@ -227,9 +132,6 @@ usage_advanced() {
@@ -231,9 +132,6 @@ usage_advanced() {
echo " -memcheck -- run Sage using Valgrind's memcheck tool. The log"
echo " files are named sage-memcheck.PID can be found in"
echo " $DOT_SAGE"
@ -174,7 +178,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
echo " -valgrind -- this is an alias for -memcheck"
echo
echo "You can also use -- before a long option, e.g., 'sage --optional'."
@@ -249,15 +151,6 @@ if [ "$1" = '--nodotsage' ]; then
@@ -253,15 +151,6 @@ if [ "$1" = '--nodotsage' ]; then
exit $status
fi
@ -190,11 +194,8 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
if [ $# -gt 0 ]; then
if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
usage
@@ -267,28 +160,13 @@ if [ $# -gt 0 ]; then
fi
fi
@@ -274,25 +163,11 @@ fi
-
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
- # Check that we're not in a source tarball which hasn't been built yet (#13561).
@ -219,11 +220,10 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
@@ -298,21 +176,6 @@ sage_setup() {
sage-cleaner &>/dev/null &
@@ -303,20 +178,6 @@ sage_setup() {
}
-
-# Check to see if the whole Sage install tree has moved. If so,
-# change various hardcoded paths. Skip this if we don't have write
-# access to $SAGE_LOCAL (e.g. when running as a different user) or
@ -241,7 +241,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
@@ -353,12 +216,6 @@ if [ "$1" = '-root' -o "$1" = '--root'
@@ -357,12 +218,6 @@ if [ "$1" = '-root' -o "$1" = '--root'
exit 0
fi
@ -254,7 +254,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
#####################################################################
# Run Sage's versions of the standard Algebra/Geometry etc. software
#####################################################################
@@ -368,29 +225,24 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom'
@@ -372,29 +227,24 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom'
exec axiom "$@"
fi
@ -288,7 +288,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
fi
if [ "$1" = '-sws2rst' -o "$1" = '--sws2rst' ]; then
@@ -400,47 +252,37 @@ fi
@@ -404,47 +254,37 @@ fi
if [ "$1" = '-twistd' -o "$1" = '--twistd' ]; then
shift
@ -343,7 +343,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
fi
if [ "$1" = '-python' -o "$1" = '--python' ]; then
@@ -450,12 +292,12 @@ fi
@@ -454,12 +294,12 @@ fi
if [ "$1" = '-R' -o "$1" = '--R' ]; then
shift
@ -358,7 +358,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
fi
if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
@@ -576,28 +418,6 @@ EOF
@@ -580,28 +420,6 @@ EOF
exit $status
fi
@ -387,7 +387,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
#####################################################################
# File conversion
#####################################################################
@@ -613,36 +433,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
@@ -617,36 +435,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
fi
#####################################################################
@ -424,7 +424,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
@@ -661,79 +460,7 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
@@ -665,79 +462,7 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0
fi
@ -505,7 +505,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
if [ ! -f "$DOT_SAGE"/init.sage ]; then
echo >&2 "init.sage does not exist ... creating"
touch "$DOT_SAGE"/init.sage
@@ -749,10 +476,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
@@ -753,10 +478,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@ -517,7 +517,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
shift
SAGE_BANNER="no"
sage_setup
@@ -766,12 +490,6 @@ if [ "$1" = '-testall' -o "$1" = "--test
@@ -770,12 +492,6 @@ if [ "$1" = '-testall' -o "$1" = "--test
exec sage-runtests -a "$@"
fi
@ -530,7 +530,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
if [ "$1" = '-c' ]; then
shift
SAGE_BANNER="no"
@@ -780,166 +498,6 @@ if [ "$1" = '-c' ]; then
@@ -784,166 +500,6 @@ if [ "$1" = '-c' ]; then
exec sage-eval "$@"
fi
@ -697,7 +697,7 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
shift
sage_setup
@@ -988,12 +546,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
@@ -992,12 +548,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi
@ -710,9 +710,9 @@ diff -up sage-5.12/spkg/bin/sage.orig sage-5.12/spkg/bin/sage
if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
exec sage-startuptime.py "$@"
fi
diff -up sage-5.12/spkg/build/sage_scripts-5.12/sage-runtests.orig sage-5.12/spkg/build/sage_scripts-5.12/sage-runtests
--- sage-5.12/spkg/build/sage_scripts-5.12/sage-runtests.orig 2013-10-16 11:51:22.487155937 -0300
+++ sage-5.12/spkg/build/sage_scripts-5.12/sage-runtests 2013-10-16 11:51:41.514156666 -0300
diff -up sage-5.13/spkg/build/sage_scripts-5.13/sage-runtests.orig sage-5.13/spkg/build/sage_scripts-5.13/sage-runtests
--- sage-5.13/spkg/build/sage_scripts-5.13/sage-runtests.orig 2014-01-28 15:46:59.796154543 -0200
+++ sage-5.13/spkg/build/sage_scripts-5.13/sage-runtests 2014-01-28 15:47:42.457156177 -0200
@@ -54,10 +54,6 @@ if __name__ == "__main__":
help="run doctests using Valgrind's cachegrind tool. The log "
"files are named sage-cachegrind.PID and can be found in " +
@ -724,9 +724,9 @@ diff -up sage-5.12/spkg/build/sage_scripts-5.12/sage-runtests.orig sage-5.12/spk
parser.add_option("-f", "--failed", action="store_true", default=False,
help="doctest only those files that failed in the previous run")
diff -up sage-5.12/spkg/build/sage_scripts-5.12/sage-valgrind.orig sage-5.12/spkg/build/sage_scripts-5.12/sage-valgrind
--- sage-5.12/spkg/build/sage_scripts-5.12/sage-valgrind.orig 2013-10-16 11:51:49.837156985 -0300
+++ sage-5.12/spkg/build/sage_scripts-5.12/sage-valgrind 2013-10-16 11:52:03.594157511 -0300
diff -up sage-5.13/spkg/build/sage_scripts-5.13/sage-valgrind.orig sage-5.13/spkg/build/sage_scripts-5.13/sage-valgrind
--- sage-5.13/spkg/build/sage_scripts-5.13/sage-valgrind.orig 2014-01-28 15:46:59.800154543 -0200
+++ sage-5.13/spkg/build/sage_scripts-5.13/sage-valgrind 2014-01-28 15:47:20.081155320 -0200
@@ -11,7 +11,7 @@ fi
LOG="$DOT_SAGE"/valgrind/sage-memcheck.%p
echo "Log file is $LOG"

6
sagemath-sympy.patch
View file

@ -1,6 +1,6 @@
diff -up sage-5.12/spkg/build/sage-5.12/sage/env.py.orig sage-5.12/spkg/build/sage-5.12/sage/env.py
--- sage-5.12/spkg/build/sage-5.12/sage/env.py.orig 2013-08-12 15:14:58.586048479 -0300
+++ sage-5.12/spkg/build/sage-5.12/sage/env.py 2013-08-12 15:15:55.102050643 -0300
diff -up sage-5.13/spkg/build/sage-5.13/sage/env.py.orig sage-5.13/spkg/build/sage-5.13/sage/env.py
--- sage-5.13/spkg/build/sage-5.13/sage/env.py.orig 2013-08-12 15:14:58.586048479 -0300
+++ sage-5.13/spkg/build/sage-5.13/sage/env.py 2013-08-12 15:15:55.102050643 -0300
@@ -85,7 +85,7 @@ _add_variable_or_fallback('HOSTNAME',
_add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())

14
sagemath.spec
View file

@ -17,7 +17,7 @@
%global with_sage_pexpect 1
# https://bugzilla.redhat.com/show_bug.cgi?id=909510
%global have_lrcalc %{packager_debug}
%global have_lrcalc 1
# Cbc dependency under review is as follow:
# first need coin-or-CoinUtils
@ -67,8 +67,8 @@
Name: sagemath
Group: Applications/Engineering
Summary: A free open-source mathematics software system
Version: 5.12
Release: 3%{?dist}
Version: 5.13
Release: 1%{?dist}
# The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
# Additionally, every $files section has a comment with the license name
# before files with that license
@ -670,7 +670,6 @@ rm spkg/build/%{sagenb_pkg}/src/sagenb/sagenb/data/sage3d/lib/sage3d.jar
# remove binary egg
rm -r spkg/build/%{sagenb_pkg}/src/sagenb/sagenb.egg-info
###
########################################################################
%build
@ -766,10 +765,6 @@ pushd spkg/build/sage-%{version}
python setup.py install --root=%{buildroot}
cp -fa c_lib/libcsage.so.0 %{buildroot}%{_libdir}
ln -sf libcsage.so.0 %{buildroot}%{_libdir}/libcsage.so
pushd sage
# install sage notebook templates
cp -fa server/notebook/templates %{buildroot}%{python_sitearch}/sage/server/notebook
popd
# install documentation sources
rm -fr $SAGE_DOC/{common,en,fr}
cp -far doc/{common,de,en,fr,pt,ru,tr} $SAGE_DOC
@ -1371,6 +1366,9 @@ exit 0
########################################################################
%changelog
* Tue Jan 28 2014 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 5.13-1
- Update to sagemath 5.13
* Fri Jan 17 2014 Jerry James <loganjerry@gmail.com> - 5.12-3
- Also adapt Requires to the new gap subpackage structure

2
sources
View file

@ -1 +1 @@
21d62a8a61e351c3c124167b3eead46f sage-5.12.tar
b549c5ac6b292a2837d92ccf3740c451 sage-5.13.tar