[sagemath] Update to sagemath 5.12
pcpa
pcpa at fedoraproject.org
Sat Oct 19 02:22:20 UTC 2013
commit d4a07df7d049bcc5c325955915d34d8e5bcbfb8a
Author: pcpa <paulo.cesar.pereira.de.andrade at gmail.com>
Date: Fri Oct 18 23:22:11 2013 -0300
Update to sagemath 5.12
.gitignore | 1 +
sagemath-4ti2.patch | 6 +-
sagemath-cbc.patch | 8 +-
sagemath-cremona.patch | 6 +-
sagemath-cryptominisat.patch | 8 +-
sagemath-ecl-unicode.patch | 12 ++--
sagemath-extensions.patch | 8 +-
sagemath-fes.patch | 8 +-
sagemath-flask.patch | 32 -------
sagemath-fplll.patch | 194 -----------------------------------------
sagemath-gap-hap.patch | 8 +-
sagemath-gmp.patch | 4 +-
sagemath-jmol.patch | 6 +-
sagemath-libgap.patch | 6 +-
sagemath-libmpc.patch | 65 --------------
sagemath-lrcalc.patch | 8 +-
sagemath-lrslib.patch | 8 +-
sagemath-m4rie.patch | 62 -------------
sagemath-maxima.patch | 12 ++--
sagemath-maxima.system.patch | 12 ---
sagemath-nauty.patch | 8 +-
sagemath-nolibgap.patch | 54 ------------
sagemath-nopari2.6.patch | 22 +++---
sagemath-ntl6.patch | 18 ++--
sagemath-pari.patch | 16 ++--
sagemath-png.patch | 12 ++--
sagemath-readonly.patch | 8 +-
sagemath-rh_bz_961372.patch | 14 ---
sagemath-rpmbuild.patch | 31 ++++---
sagemath-sagedoc.patch | 36 ++++----
sagemath-sagenb.patch | 63 +++++++-------
sagemath-scons.patch | 6 +-
sagemath-scripts.patch | 72 ++++++++-------
sagemath-sympy.patch | 6 +-
sagemath-unpatched_ntl.patch | 60 -------------
sagemath.spec | 198 +++++++++++++-----------------------------
sources | 2 +-
37 files changed, 269 insertions(+), 831 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index e4b18c8..b2b24fe 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
/sage-5.8.tar
/sage-5.9.tar
/sage-5.10.tar
+/sage-5.12.tar
diff --git a/sagemath-4ti2.patch b/sagemath-4ti2.patch
index 7d0a5dd..12e98dd 100644
--- a/sagemath-4ti2.patch
+++ b/sagemath-4ti2.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/sandpiles/sandpile.py.orig sage-5.10/spkg/build/sage-5.10/sage/sandpiles/sandpile.py
---- sage-5.10/spkg/build/sage-5.10/sage/sandpiles/sandpile.py.orig 2013-05-06 13:50:14.882749079 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/sandpiles/sandpile.py 2013-05-06 13:50:34.526749831 -0300
+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
@@ -24,8 +24,6 @@ packages. An alternative is to install
following variable to the correct path.
"""
diff --git a/sagemath-cbc.patch b/sagemath-cbc.patch
index af5dcef..90f227f 100644
--- a/sagemath-cbc.patch
+++ b/sagemath-cbc.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build/sage-5.10/module_list.py
---- sage-5.10/spkg/build/sage-5.10/module_list.py.orig 2013-07-29 20:05:39.844079175 -0300
-+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 20:05:59.925079944 -0300
-@@ -2007,7 +2007,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
+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"
libraries = ["csage", "stdc++", "cplex"])
)
diff --git a/sagemath-cremona.patch b/sagemath-cremona.patch
index 5e9220e..14bcd1b 100644
--- a/sagemath-cremona.patch
+++ b/sagemath-cremona.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/databases/cremona.py.orig sage-5.10/spkg/build/sage-5.10/sage/databases/cremona.py
---- sage-5.10/spkg/build/sage-5.10/sage/databases/cremona.py.orig 2013-02-22 17:33:50.579875129 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/databases/cremona.py 2013-02-22 17:34:05.051875683 -0300
+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
@@ -889,14 +889,9 @@ class MiniCremonaDatabase(SQLDatabase):
if N < self.largest_conductor():
message = "There is no elliptic curve with label " + label \
diff --git a/sagemath-cryptominisat.patch b/sagemath-cryptominisat.patch
index 829ee6f..59d148b 100644
--- a/sagemath-cryptominisat.patch
+++ b/sagemath-cryptominisat.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build/sage-5.10/module_list.py
---- sage-5.10/spkg/build/sage-5.10/module_list.py.orig 2013-07-29 20:09:16.498087472 -0300
-+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 20:09:30.624088013 -0300
-@@ -2017,7 +2017,7 @@ if 1:
+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 --git a/sagemath-ecl-unicode.patch b/sagemath-ecl-unicode.patch
index a7c8fc2..7763815 100644
--- a/sagemath-ecl-unicode.patch
+++ b/sagemath-ecl-unicode.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pxd.orig sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pxd
---- sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pxd.orig 2013-03-19 16:11:17.358705144 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pxd 2013-03-19 16:11:27.719705541 -0300
+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
@@ -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)
@@ -9,9 +9,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pxd.orig sage-5.10/spkg/bu
# S-expr evaluation and function calls
-diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pyx.orig sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pyx
---- sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pyx.orig 2013-03-19 16:11:07.489704766 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/libs/ecl.pyx 2013-03-19 16:11:27.719705541 -0300
+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
...
RuntimeError: ECL says: Console interrupt.
diff --git a/sagemath-extensions.patch b/sagemath-extensions.patch
index 6ff4114..bf701fd 100644
--- a/sagemath-extensions.patch
+++ b/sagemath-extensions.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build/sage-5.10/module_list.py
---- sage-5.10/spkg/build/sage-5.10/module_list.py.orig 2013-07-29 19:41:05.473022716 -0300
-+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 19:41:22.814023380 -0300
-@@ -1961,7 +1961,8 @@ ext_modules = [
+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 = [
# These extensions are to be compiled only if the
# corresponding packages have been installed
diff --git a/sagemath-fes.patch b/sagemath-fes.patch
index fc4f1a4..ca982d8 100644
--- a/sagemath-fes.patch
+++ b/sagemath-fes.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build/sage-5.10/module_list.py
---- sage-5.10/spkg/build/sage-5.10/module_list.py.orig 2013-07-29 20:07:59.033084505 -0300
-+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 20:08:09.815084918 -0300
-@@ -1966,7 +1966,7 @@ ext_modules = [
+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 = [
def is_package_installed(name):
return False
diff --git a/sagemath-gap-hap.patch b/sagemath-gap-hap.patch
index bd104ce..f45014f 100644
--- a/sagemath-gap-hap.patch
+++ b/sagemath-gap-hap.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/groups/perm_gps/permgroup.py.orig sage-5.10/spkg/build/sage-5.10/sage/groups/perm_gps/permgroup.py
---- sage-5.10/spkg/build/sage-5.10/sage/groups/perm_gps/permgroup.py.orig 2013-07-29 20:03:19.785073812 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/groups/perm_gps/permgroup.py 2013-07-29 20:03:29.426074181 -0300
+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
@@ -180,8 +180,7 @@ def hap_decorator(f):
"""
@wraps(f)
@@ -11,7 +11,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/groups/perm_gps/permgroup.py.orig s
load_hap()
from sage.rings.arith import is_prime
if not (p == 0 or is_prime(p)):
-@@ -3730,8 +3729,7 @@ class PermutationGroup_generic(group.Gro
+@@ -3865,8 +3864,7 @@ class PermutationGroup_generic(group.Gro
- David Joyner and Graham Ellis
"""
diff --git a/sagemath-gmp.patch b/sagemath-gmp.patch
index 8767f9c..8883cc0 100644
--- a/sagemath-gmp.patch
+++ b/sagemath-gmp.patch
@@ -1,5 +1,5 @@
---- sage-5.10/spkg/build/sage-5.10/c_lib/src/memory.c.orig 2012-07-10 11:46:54.516595967 -0400
-+++ sage-5.10/spkg/build/sage-5.10/c_lib/src/memory.c 2012-07-10 11:47:12.688596755 -0400
+--- 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 --git a/sagemath-jmol.patch b/sagemath-jmol.patch
index c993d1a..5e9c783 100644
--- a/sagemath-jmol.patch
+++ b/sagemath-jmol.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/jmoldata.py.orig sage-5.10/spkg/build/sage-5.10/sage/interfaces/jmoldata.py
---- sage-5.10/spkg/build/sage-5.10/sage/interfaces/jmoldata.py.orig 2012-11-10 12:03:07.742817945 -0200
-+++ sage-5.10/spkg/build/sage-5.10/sage/interfaces/jmoldata.py 2012-11-10 12:03:34.499818970 -0200
+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
@@ -86,7 +86,7 @@ class JmolData(SageObject):
sage_makedirs(jmolscratch)
scratchout = os.path.join(jmolscratch,"jmolout.txt")
diff --git a/sagemath-libgap.patch b/sagemath-libgap.patch
index 5a11e1a..3f5d8de 100644
--- a/sagemath-libgap.patch
+++ b/sagemath-libgap.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/gap/util.pyx.orig sage-5.10/spkg/build/sage-5.10/sage/libs/gap/util.pyx
---- sage-5.10/spkg/build/sage-5.10/sage/libs/gap/util.pyx.orig 2013-05-06 14:24:03.160826749 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/libs/gap/util.pyx 2013-05-06 14:25:25.806829913 -0300
+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
@@ -155,18 +155,9 @@ def gap_root():
sage: from sage.libs.gap.util import gap_root
diff --git a/sagemath-lrcalc.patch b/sagemath-lrcalc.patch
index 0de417c..1b325e7 100644
--- a/sagemath-lrcalc.patch
+++ b/sagemath-lrcalc.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build/sage-5.10/module_list.py
---- sage-5.10/spkg/build/sage-5.10/module_list.py.orig 2013-07-29 20:04:06.006075582 -0300
-+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 20:04:18.016076042 -0300
-@@ -2042,7 +2042,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
+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 --git a/sagemath-lrslib.patch b/sagemath-lrslib.patch
index 715fac4..037f6c3 100644
--- a/sagemath-lrslib.patch
+++ b/sagemath-lrslib.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/geometry/polyhedron/base.py.orig sage-5.10/spkg/build/sage-5.10/sage/geometry/polyhedron/base.py
---- sage-5.10/spkg/build/sage-5.10/sage/geometry/polyhedron/base.py.orig 2013-05-06 14:12:21.664799886 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/geometry/polyhedron/base.py 2013-05-06 14:12:28.625800152 -0300
-@@ -3281,11 +3281,6 @@ class Polyhedron_base(Element):
+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
+@@ -3291,11 +3291,6 @@ class Polyhedron_base(Element):
David Avis's lrs program.
"""
diff --git a/sagemath-maxima.patch b/sagemath-maxima.patch
index 3918aa9..a1a164c 100644
--- a/sagemath-maxima.patch
+++ b/sagemath-maxima.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima.py.orig sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima.py
---- sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima.py.orig 2013-07-29 19:54:04.395052544 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima.py 2013-07-29 19:55:18.259055373 -0300
+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
@@ -544,7 +544,7 @@ class Maxima(MaximaAbstract, Expect):
Expect.__init__(self,
name = 'maxima',
@@ -20,9 +20,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima.py.orig sage-5.10
self._eval_line('0;')
def __reduce__(self):
-diff -up sage-5.10/spkg/build/sage_scripts-5.10/sage-maxima.lisp.orig sage-5.10/spkg/build/sage_scripts-5.10/sage-maxima.lisp
---- sage-5.10/spkg/build/sage_scripts-5.10/sage-maxima.lisp.orig 2013-07-29 19:54:04.402052544 -0300
-+++ sage-5.10/spkg/build/sage_scripts-5.10/sage-maxima.lisp 2013-07-29 19:55:33.867055970 -0300
+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
@@ -3,4 +3,8 @@
;(setf *general-display-prefix* "<sage-display>")
diff --git a/sagemath-nauty.patch b/sagemath-nauty.patch
index f47d3e8..7076c24 100644
--- a/sagemath-nauty.patch
+++ b/sagemath-nauty.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/graphs/graph_generators.py.orig sage-5.10/spkg/build/sage-5.10/sage/graphs/graph_generators.py
---- sage-5.10/spkg/build/sage-5.10/sage/graphs/graph_generators.py.orig 2013-07-29 20:02:33.894072055 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/graphs/graph_generators.py 2013-07-29 20:02:42.421072381 -0300
-@@ -774,7 +774,7 @@ class GraphGenerators():
+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():
"""
import subprocess
from sage.misc.package import is_package_installed
diff --git a/sagemath-nopari2.6.patch b/sagemath-nopari2.6.patch
index 6b45cc8..31c434f 100644
--- a/sagemath-nopari2.6.patch
+++ b/sagemath-nopari2.6.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/pari/decl.pxi.orig sage-5.10/spkg/build/sage-5.10/sage/libs/pari/decl.pxi
---- sage-5.10/spkg/build/sage-5.10/sage/libs/pari/decl.pxi.orig 2013-07-29 20:08:46.678086330 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/libs/pari/decl.pxi 2013-07-29 20:08:56.965086724 -0300
-@@ -595,7 +595,6 @@ cdef extern from 'pari/pari.h':
+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':
GEN polredabs0(GEN x, long flag)
GEN polredabs2(GEN x)
GEN polredabsall(GEN x, long flun)
@@ -9,17 +9,17 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/pari/decl.pxi.orig sage-5.10/s
GEN qflll0(GEN x, long flag)
GEN qflllgram0(GEN x, long flag)
GEN smallpolred(GEN x)
-diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx.orig sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx
---- sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx.orig 2013-07-29 20:08:37.060085961 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx 2013-07-29 20:08:56.971086724 -0300
-@@ -8029,10 +8029,6 @@ cdef class gen(sage.structure.element.Ri
- sig_on()
+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
+ pari_catch_sig_on()
return self.new_gen(polredabs0(self.g, flag))
- def polredbest(self, flag=0):
-- sig_on()
+- pari_catch_sig_on()
- return self.new_gen(polredbest(self.g, flag))
-
def polresultant(self, y, var=-1, flag=0):
t0GEN(y)
- sig_on()
+ pari_catch_sig_on()
diff --git a/sagemath-ntl6.patch b/sagemath-ntl6.patch
index 130b71d..59c0c89 100644
--- a/sagemath-ntl6.patch
+++ b/sagemath-ntl6.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/c_lib/include/ntl_wrap.h.orig sage-5.10/spkg/build/sage-5.10/c_lib/include/ntl_wrap.h
---- sage-5.10/spkg/build/sage-5.10/c_lib/include/ntl_wrap.h.orig 2013-07-29 19:40:07.189020485 -0300
-+++ sage-5.10/spkg/build/sage-5.10/c_lib/include/ntl_wrap.h 2013-07-29 19:40:11.831020662 -0300
+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
@@ -40,91 +40,92 @@ EXTERN void setup_NTL_error_callback(voi
//////// ZZ //////////
@@ -451,9 +451,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/c_lib/include/ntl_wrap.h.orig sage-5.10/
-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-5.10/spkg/build/sage-5.10/c_lib/src/ntl_wrap.cpp.orig sage-5.10/spkg/build/sage-5.10/c_lib/src/ntl_wrap.cpp
---- sage-5.10/spkg/build/sage-5.10/c_lib/src/ntl_wrap.cpp.orig 2013-07-29 19:40:07.197020485 -0300
-+++ sage-5.10/spkg/build/sage-5.10/c_lib/src/ntl_wrap.cpp 2013-07-29 19:40:11.834020662 -0300
+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
@@ -29,7 +29,7 @@ int ZZ_to_int(const ZZ* x)
/* Returns a *new* ZZ object.
@@ -1350,9 +1350,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/c_lib/src/ntl_wrap.cpp.orig sage-5.10/sp
{
//int j;
cpn.restore();
-diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/ntl/decl.pxi.orig sage-5.10/spkg/build/sage-5.10/sage/libs/ntl/decl.pxi
---- sage-5.10/spkg/build/sage-5.10/sage/libs/ntl/decl.pxi.orig 2013-07-29 19:39:08.246018227 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/libs/ntl/decl.pxi 2013-07-29 19:40:11.836020662 -0300
+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
@@ -22,7 +22,7 @@ from sage.libs.ntl.ntl_ZZ_pEX_decl cimpo
cdef extern from "ntl_wrap.h":
diff --git a/sagemath-pari.patch b/sagemath-pari.patch
index bb38b96..cc13c2e 100644
--- a/sagemath-pari.patch
+++ b/sagemath-pari.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/gp.py.orig sage-5.10/spkg/build/sage-5.10/sage/interfaces/gp.py
---- sage-5.10/spkg/build/sage-5.10/sage/interfaces/gp.py.orig 2013-07-29 19:56:27.093058008 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/interfaces/gp.py 2013-07-29 19:56:38.015058427 -0300
+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
@@ -977,11 +977,11 @@ def is_GpElement(x):
"""
return isinstance(x, GpElement)
@@ -16,9 +16,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/gp.py.orig sage-5.10/spk
# An instance
gp = Gp(logfile=os.path.join(DOT_SAGE,'gp-expect.log')) # useful for debugging!
-diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx.orig sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx
---- sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx.orig 2013-07-29 19:56:11.479057411 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx 2013-07-29 19:56:38.025058427 -0300
+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'
cdef extern from "mpz_pylong.h":
cdef int mpz_set_pylong(mpz_t dst, src) except -1
@@ -30,7 +30,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx.orig sage-5.10/sp
# 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.
-@@ -9240,7 +9244,12 @@ cdef class PariInstance(sage.structure.p
+@@ -9292,7 +9296,12 @@ 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.
@@ -42,4 +42,4 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/pari/gen.pyx.orig sage-5.10/sp
+ mp_set_memory_functions(_gmp_malloc, _gmp_realloc, _gmp_free)
num_primes = maxprime
- # NOTE: sig_on() can only come AFTER pari_init_opts()!
+ # NOTE: pari_catch_sig_on() can only come AFTER pari_init_opts()!
diff --git a/sagemath-png.patch b/sagemath-png.patch
index 0d24608..ef21340 100644
--- a/sagemath-png.patch
+++ b/sagemath-png.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build/sage-5.10/module_list.py
---- sage-5.10/spkg/build/sage-5.10/module_list.py.orig 2013-07-29 19:52:06.543048031 -0300
-+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 19:52:26.005048776 -0300
-@@ -1014,7 +1014,7 @@ ext_modules = [
+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 = [
Extension('sage.matrix.matrix_mod2_dense',
sources = ['sage/matrix/matrix_mod2_dense.pyx'],
@@ -10,7 +10,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
-@@ -1273,7 +1273,7 @@ ext_modules = [
+@@ -1323,7 +1323,7 @@ ext_modules = [
Extension('sage.modules.vector_mod2_dense',
sources = ['sage/modules/vector_mod2_dense.pyx'],
@@ -19,7 +19,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
-@@ -1748,7 +1748,7 @@ ext_modules = [
+@@ -1801,7 +1801,7 @@ ext_modules = [
Extension('sage.rings.polynomial.pbori',
sources = ['sage/rings/polynomial/pbori.pyx'],
libraries=['polybori-' + polybori_major_version,
diff --git a/sagemath-readonly.patch b/sagemath-readonly.patch
index 29a3477..1b310b0 100644
--- a/sagemath-readonly.patch
+++ b/sagemath-readonly.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/all.py.orig sage-5.10/spkg/build/sage-5.10/sage/all.py
---- sage-5.10/spkg/build/sage-5.10/sage/all.py.orig 2013-05-06 13:45:07.053737291 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/all.py 2013-05-06 13:45:35.317738373 -0300
-@@ -307,11 +307,11 @@ def _write_started_file():
+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():
Check that the file exists when Sage is running::
diff --git a/sagemath-rpmbuild.patch b/sagemath-rpmbuild.patch
index ed803fd..3e57217 100644
--- a/sagemath-rpmbuild.patch
+++ b/sagemath-rpmbuild.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig sage-5.10/spkg/build/conway_polynomials-0.4.p0/spkg-install
---- sage-5.10/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig 2013-07-29 19:43:09.049027449 -0300
-+++ sage-5.10/spkg/build/conway_polynomials-0.4.p0/spkg-install 2013-07-29 19:43:39.434028612 -0300
+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
@@ -2,9 +2,10 @@
import os
@@ -14,9 +14,9 @@ diff -up sage-5.10/spkg/build/conway_polynomials-0.4.p0/spkg-install.orig sage-5
def create_db():
db = {}
-diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build/sage-5.10/module_list.py
---- sage-5.10/spkg/build/sage-5.10/module_list.py.orig 2013-07-29 19:43:09.023027448 -0300
-+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 19:44:52.051031393 -0300
+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
@@ -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-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build
polybori_major_version = '0.8'
-@@ -653,7 +654,7 @@ ext_modules = [
+@@ -672,7 +673,7 @@ ext_modules = [
sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx',
'Lfunction', 'stdc++'],
@@ -58,12 +58,15 @@ diff -up sage-5.10/spkg/build/sage-5.10/module_list.py.orig sage-5.10/spkg/build
extra_compile_args=["-O3", "-ffast-math"],
language = 'c++'),
-diff -up sage-5.10/spkg/build/sage-5.10/setup.py.orig sage-5.10/spkg/build/sage-5.10/setup.py
---- sage-5.10/spkg/build/sage-5.10/setup.py.orig 2013-07-29 19:43:09.041027448 -0300
-+++ sage-5.10/spkg/build/sage-5.10/setup.py 2013-07-29 19:48:14.195039134 -0300
-@@ -38,21 +38,11 @@ except KeyError:
-
- SAGE_INC = os.path.join(SAGE_LOCAL,'include')
+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
+@@ -36,23 +36,13 @@ except KeyError:
+ compile_result_dir = None
+ keep_going = False
+
+-SAGE_INC = os.path.join(SAGE_LOCAL,'include')
++SAGE_INC = '/usr/include'
-SITE_PACKAGES = '%s/lib/python%s/site-packages/'%(SAGE_LOCAL,platform.python_version().rsplit('.', 1)[0])
-if not os.path.exists(SITE_PACKAGES):
@@ -104,7 +107,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/setup.py.orig sage-5.10/spkg/build/sage-
m.extra_compile_args += extra_compile_args
m.extra_link_args += extra_link_args
- m.library_dirs += ['%s/lib' % SAGE_LOCAL]
-+ m.library_dirs += ['@@libdir@@/atlas', 'c_lib', '%s/lib' % SAGE_LOCAL]
++ m.library_dirs += ['c_lib', '%s/lib' % SAGE_LOCAL]
diff --git a/sagemath-sagedoc.patch b/sagemath-sagedoc.patch
index 88a27d4..0adf030 100644
--- a/sagemath-sagedoc.patch
+++ b/sagemath-sagedoc.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/doc/common/builder.py.orig sage-5.10/spkg/build/sage-5.10/doc/common/builder.py
---- sage-5.10/spkg/build/sage-5.10/doc/common/builder.py.orig 2013-07-29 19:49:41.413042474 -0300
-+++ sage-5.10/spkg/build/sage-5.10/doc/common/builder.py 2013-07-29 19:49:53.076042920 -0300
+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
@@ -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-5.10/spkg/build/sage-5.10/doc/common/builder.py.orig sage-5.10/spk
##########################################
-diff -up sage-5.10/spkg/build/sage-5.10/doc/common/conf.py.orig sage-5.10/spkg/build/sage-5.10/doc/common/conf.py
---- sage-5.10/spkg/build/sage-5.10/doc/common/conf.py.orig 2013-07-29 19:49:41.420042474 -0300
-+++ sage-5.10/spkg/build/sage-5.10/doc/common/conf.py 2013-07-29 19:49:53.077042920 -0300
+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
@@ -1,5 +1,5 @@
import sys, os, sphinx
-from sage.env import SAGE_DOC
@@ -30,9 +30,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/doc/common/conf.py.orig sage-5.10/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-5.10/spkg/build/sage-5.10/sage/doctest/control.py.orig sage-5.10/spkg/build/sage-5.10/sage/doctest/control.py
---- sage-5.10/spkg/build/sage-5.10/sage/doctest/control.py.orig 2013-07-29 19:48:53.706040647 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/doctest/control.py 2013-07-29 19:49:53.079042920 -0300
+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):
self.valgrind = False
self.massif = False
@@ -41,7 +41,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/doctest/control.py.orig sage-5.10/s
self.failed = False
self.new = False
self.show_skipped = False
-@@ -213,7 +212,7 @@ class DocTestController(SageObject):
+@@ -210,7 +209,7 @@ class DocTestController(SageObject):
if options.gdb or options.debug:
# Interactive debuggers: "infinite" timeout
options.timeout = 0
@@ -50,7 +50,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/doctest/control.py.orig sage-5.10/s
# Non-interactive debuggers: 48 hours
options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
elif options.long:
-@@ -809,13 +808,8 @@ class DocTestController(SageObject):
+@@ -806,13 +805,8 @@ class DocTestController(SageObject):
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@@ -64,7 +64,7 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/doctest/control.py.orig sage-5.10/s
if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd
-@@ -875,10 +869,10 @@ class DocTestController(SageObject):
+@@ -872,10 +866,10 @@ class DocTestController(SageObject):
0
"""
opt = self.options
@@ -77,9 +77,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/doctest/control.py.orig sage-5.10/s
return 2
return self.run_val_gdb()
else:
-diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/singular.py.orig sage-5.10/spkg/build/sage-5.10/sage/interfaces/singular.py
---- sage-5.10/spkg/build/sage-5.10/sage/interfaces/singular.py.orig 2013-07-29 19:49:41.443042475 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/interfaces/singular.py 2013-07-29 19:49:53.081042920 -0300
+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
@@ -2149,7 +2149,7 @@ def generate_docstring_dictionary():
nodes.clear()
node_names.clear()
@@ -89,9 +89,9 @@ diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/singular.py.orig sage-5.
new_node = re.compile("File: singular\.hlp, Node: ([^,]*),.*")
new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
-diff -up sage-5.10/spkg/build/sage-5.10/sage/misc/latex_macros.py.orig sage-5.10/spkg/build/sage-5.10/sage/misc/latex_macros.py
---- sage-5.10/spkg/build/sage-5.10/sage/misc/latex_macros.py.orig 2013-07-29 19:49:41.450042475 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/misc/latex_macros.py 2013-07-29 19:49:53.082042920 -0300
+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
@@ -142,7 +142,7 @@ def convert_latex_macro_to_mathjax(macro
return name + ': ["' + defn + '",' + str(num_args) + ']'
diff --git a/sagemath-sagenb.patch b/sagemath-sagenb.patch
index 3763273..3be21a0 100644
--- a/sagemath-sagenb.patch
+++ b/sagemath-sagenb.patch
@@ -1,7 +1,7 @@
-diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.orig sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py
---- sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.orig 2012-10-20 11:29:36.315150735 -0300
-+++ sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py 2012-10-20 11:29:56.569151510 -0300
-@@ -27,7 +27,7 @@ class SageNBFlask(Flask):
+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
+@@ -33,7 +33,7 @@ class SageNBFlask(Flask):
self.add_static_path('/javascript', DATA)
self.add_static_path('/static', DATA)
self.add_static_path('/java', DATA)
@@ -10,10 +10,10 @@ diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py.ori
import mimetypes
mimetypes.add_type('text/plain','.jmol')
-diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html
---- sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html.orig 2012-10-20 11:31:17.315154602 -0300
-+++ sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/notebook/base.html 2012-10-20 11:31:41.764155539 -0300
-@@ -69,7 +69,7 @@ INPUT:
+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
+@@ -46,7 +46,7 @@ INPUT:
<!-- Jmol - embedded 3D graphics -->
<script type="text/javascript" src="/java/jmol/appletweb/Jmol.js"></script>
<!-- This must stay in head -->
@@ -22,10 +22,23 @@ diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/html/not
{% if JEDITABLE_TINYMCE and not worksheet.docbrowser() and not worksheet.is_published() %}
<!-- TinyMCE and jEditable - in-place editing of text cells -->
-diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.orig sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py
---- sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.orig 2012-10-20 11:33:00.483158553 -0300
-+++ sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py 2012-10-20 11:33:17.700159212 -0300
-@@ -2367,7 +2367,7 @@ class Cell(Cell_generic):
+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
+@@ -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
+ panelHTML +='<button onClick="sleepJmol('+n+',jmolStatus)"> Get Static Image to Save (Sleep) </button> Right-click or Cmd-click on image to get download options.<hr/>';
+- //save file to local disk
+- panelHTML += '<button title="Download View" onClick="javascript:void(jmolFileDownload('+n+'))">Download this view</button> will require loading signed applet if not already done.';
+- panelHTML +='<hr/>';
+ //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
+@@ -2369,7 +2369,7 @@ class Cell(Cell_generic):
jmol_script = jmol_file.read()
jmol_file.close()
@@ -34,16 +47,14 @@ diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/cell.py.o
jmol_file = open(jmol_name, 'w')
jmol_file.write(jmol_script)
-diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py.orig sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py
---- sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py.orig 2012-10-20 11:31:55.106156049 -0300
-+++ sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_notebook.py 2012-10-20 11:32:51.460158207 -0300
-@@ -46,15 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
+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
+@@ -46,12 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
# Flask #
#########
import os, sys, random
--flask_dir = os.path.join(os.environ['SAGE_ROOT'], 'devel', 'sagenb', 'flask_version')
--sys.path.append(flask_dir)
--import base as flask_base
+-import sagenb.flask_version.base as flask_base
+sagenb_dir = os.path.join(os.environ['SAGE_ROOT'], 'src', 'sagenb')
+sys.path.append(sagenb_dir)
+import flask_version.base as flask_base
@@ -52,21 +63,7 @@ diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/notebook/run_noteb
if %(automatic_login)s:
opts['startup_token'] = startup_token
-flask_app = flask_base.create_app(%(notebook_opts)s, **opts)
--sys.path.remove(flask_dir)
+flask_app = flask_base.create_app(%(notebook_opts)s, startup_token=startup_token)
def save_notebook(notebook):
print "Quitting all running worksheets..."
-diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js
---- sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js.orig 2012-11-14 22:46:56.488853512 -0200
-+++ sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_lib.js 2012-11-14 22:49:02.772858348 -0200
-@@ -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
- panelHTML +='<button onClick="sleepJmol('+n+',jmolStatus)"> Get Static Image to Save (Sleep) </button> Right-click or Cmd-click on image to get download options.<hr/>';
-- //save file to local disk
-- panelHTML += '<button title="Download View" onClick="javascript:void(jmolFileDownload('+n+'))">Download this view</button> will require loading signed applet if not already done.';
-- panelHTML +='<hr/>';
- //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 --git a/sagemath-scons.patch b/sagemath-scons.patch
index 07eb3f2..6a31b13 100644
--- a/sagemath-scons.patch
+++ b/sagemath-scons.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/c_lib/SConstruct.orig sage-5.10/spkg/build/sage-5.10/c_lib/SConstruct
---- sage-5.10/spkg/build/sage-5.10/c_lib/SConstruct.orig 2013-02-23 12:55:48.382841120 -0300
-+++ sage-5.10/spkg/build/sage-5.10/c_lib/SConstruct 2013-02-23 12:56:25.037842523 -0300
+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
@@ -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
diff --git a/sagemath-scripts.patch b/sagemath-scripts.patch
index f2241ec..b9f92c9 100644
--- a/sagemath-scripts.patch
+++ b/sagemath-scripts.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
---- sage-5.10/spkg/bin/sage.orig 2013-07-29 19:28:12.913993132 -0300
-+++ sage-5.10/spkg/bin/sage 2013-07-29 19:37:54.835015416 -0300
+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
@@ -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-5.10/spkg/bin/sage.orig sage-5.10/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"
-@@ -109,74 +96,6 @@ usage_advanced() {
+@@ -109,79 +96,10 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@@ -139,7 +139,12 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
echo "Documentation:"
echo " -coverage <files> -- give info about doctest coverage of files"
echo " -coverageall -- give summary info about doctest coverage of all"
-@@ -199,19 +118,6 @@ usage_advanced() {
+ echo " files in the Sage library"
+- echo " -docbuild [lang/]<document> <html|pdf|...> -- Build the Sage documentation"
+ 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() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@@ -159,7 +164,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/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"
-@@ -225,9 +131,6 @@ usage_advanced() {
+@@ -227,9 +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"
@@ -169,7 +174,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/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'."
-@@ -247,15 +150,6 @@ if [ "$1" = '--nodotsage' ]; then
+@@ -249,15 +151,6 @@ if [ "$1" = '--nodotsage' ]; then
exit $status
fi
@@ -185,8 +190,11 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
if [ $# -gt 0 ]; then
if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
usage
-@@ -268,25 +162,11 @@ fi
+@@ -267,28 +160,13 @@ if [ $# -gt 0 ]; then
+ fi
+ fi
+-
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
- # Check that we're not in a source tarball which hasn't been built yet (#13561).
@@ -211,10 +219,11 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
-@@ -297,20 +177,6 @@ sage_setup() {
+@@ -298,21 +176,6 @@ sage_setup() {
+ sage-cleaner &>/dev/null &
}
-
+-
-# 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
@@ -232,7 +241,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
-@@ -349,12 +215,6 @@ if [ "$1" = '-root' -o "$1" = '--root'
+@@ -353,12 +216,6 @@ if [ "$1" = '-root' -o "$1" = '--root'
exit 0
fi
@@ -245,7 +254,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
#####################################################################
# Run Sage's versions of the standard Algebra/Geometry etc. software
#####################################################################
-@@ -364,74 +224,59 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom'
+@@ -368,29 +225,24 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom'
exec axiom "$@"
fi
@@ -278,6 +287,9 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
+ exec sqlite3 "$@"
fi
+ if [ "$1" = '-sws2rst' -o "$1" = '--sws2rst' ]; then
+@@ -400,47 +252,37 @@ fi
+
if [ "$1" = '-twistd' -o "$1" = '--twistd' ]; then
shift
- exec "$SAGE_LOCAL/bin/twistd" "$@"
@@ -331,7 +343,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
fi
if [ "$1" = '-python' -o "$1" = '--python' ]; then
-@@ -441,12 +286,12 @@ fi
+@@ -450,12 +292,12 @@ fi
if [ "$1" = '-R' -o "$1" = '--R' ]; then
shift
@@ -346,7 +358,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
fi
if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
-@@ -567,28 +412,6 @@ EOF
+@@ -576,28 +418,6 @@ EOF
exit $status
fi
@@ -375,7 +387,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
#####################################################################
# File conversion
#####################################################################
-@@ -604,36 +427,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
+@@ -613,36 +433,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
fi
#####################################################################
@@ -412,7 +424,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
-@@ -652,86 +454,14 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -661,79 +460,7 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0
fi
@@ -493,15 +505,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
if [ ! -f "$DOT_SAGE"/init.sage ]; then
echo >&2 "init.sage does not exist ... creating"
touch "$DOT_SAGE"/init.sage
- fi
- SAGE_BANNER="no"
- sage_setup
-- if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
-+ if [ "$1" = '-tp' ]; then
- shift
- exec sage-runtests -p "$@"
- else
-@@ -740,10 +470,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -749,10 +476,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@@ -513,7 +517,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
shift
SAGE_BANNER="no"
sage_setup
-@@ -757,12 +484,6 @@ if [ "$1" = '-testall' -o "$1" = "--test
+@@ -766,12 +490,6 @@ if [ "$1" = '-testall' -o "$1" = "--test
exec sage-runtests -a "$@"
fi
@@ -526,7 +530,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
if [ "$1" = '-c' ]; then
shift
SAGE_BANNER="no"
-@@ -771,166 +492,6 @@ if [ "$1" = '-c' ]; then
+@@ -780,166 +498,6 @@ if [ "$1" = '-c' ]; then
exec sage-eval "$@"
fi
@@ -693,7 +697,7 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
shift
sage_setup
-@@ -979,12 +540,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -988,12 +546,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi
@@ -706,9 +710,9 @@ diff -up sage-5.10/spkg/bin/sage.orig sage-5.10/spkg/bin/sage
if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
exec sage-startuptime.py "$@"
fi
-diff -up sage-5.10/spkg/build/sage_scripts-5.10/sage-runtests.orig sage-5.10/spkg/build/sage_scripts-5.10/sage-runtests
---- sage-5.10/spkg/build/sage_scripts-5.10/sage-runtests.orig 2013-07-29 19:28:12.926993133 -0300
-+++ sage-5.10/spkg/build/sage_scripts-5.10/sage-runtests 2013-07-29 19:29:16.809995579 -0300
+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
@@ -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 " +
@@ -720,9 +724,9 @@ diff -up sage-5.10/spkg/build/sage_scripts-5.10/sage-runtests.orig sage-5.10/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-5.10/spkg/build/sage_scripts-5.10/sage-valgrind.orig sage-5.10/spkg/build/sage_scripts-5.10/sage-valgrind
---- sage-5.10/spkg/build/sage_scripts-5.10/sage-valgrind.orig 2013-07-29 19:28:12.939993133 -0300
-+++ sage-5.10/spkg/build/sage_scripts-5.10/sage-valgrind 2013-07-29 19:28:42.761994275 -0300
+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
@@ -11,7 +11,7 @@ fi
LOG="$DOT_SAGE"/valgrind/sage-memcheck.%p
echo "Log file is $LOG"
diff --git a/sagemath-sympy.patch b/sagemath-sympy.patch
index 2725041..6da8397 100644
--- a/sagemath-sympy.patch
+++ b/sagemath-sympy.patch
@@ -1,6 +1,6 @@
-diff -up sage-5.10/spkg/build/sage-5.10/sage/env.py.orig sage-5.10/spkg/build/sage-5.10/sage/env.py
---- sage-5.10/spkg/build/sage-5.10/sage/env.py.orig 2013-08-12 15:14:58.586048479 -0300
-+++ sage-5.10/spkg/build/sage-5.10/sage/env.py 2013-08-12 15:15:55.102050643 -0300
+diff -up sage-5.12/spkg/build/sage-5.12/sage/env.py.orig sage-5.12/spkg/build/sage-5.12/sage/env.py
+--- sage-5.12/spkg/build/sage-5.12/sage/env.py.orig 2013-08-12 15:14:58.586048479 -0300
++++ sage-5.12/spkg/build/sage-5.12/sage/env.py 2013-08-12 15:15:55.102050643 -0300
@@ -85,7 +85,7 @@ _add_variable_or_fallback('HOSTNAME',
_add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
diff --git a/sagemath.spec b/sagemath.spec
index 7ad4aab..703faf4 100644
--- a/sagemath.spec
+++ b/sagemath.spec
@@ -34,10 +34,6 @@
# but are required to have the "basic" set of coin-or packages
%global have_coin_or_Cbc %{packager_debug}
-# https://bugzilla.redhat.com/show_bug.cgi?id=919703
-# https://bitbucket.org/vbraun/libgap/issue/1/please-make-tarball-downloads-available
-%global have_libgap 0
-
# https://bugzilla.redhat.com/show_bug.cgi?id=914936
%ifarch %{ix86} x86_64
%global have_fes %{packager_debug}
@@ -57,11 +53,9 @@
%global pexpect_pkg pexpect-2.0.p5
%global polytopes_db_pkg polytopes_db-20120220
%global rubiks_pkg rubiks-20070912.p18
-%global sagenb_pkg sagenb-0.10.4
+%global sagenb_pkg sagenb-0.10.7.2
%global sagetex_pkg sagetex-2.3.4
-%global sagemath_share %{_datadir}/%{name}
-
%global SAGE_ROOT %{_libdir}/sagemath
%global SAGE_LOCAL %{SAGE_ROOT}/local
%global SAGE_SRC %{SAGE_ROOT}/src
@@ -73,8 +67,8 @@
Name: sagemath
Group: Applications/Engineering
Summary: A free open-source mathematics software system
-Version: 5.10
-Release: 5%{?dist}
+Version: 5.12
+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
@@ -108,18 +102,13 @@ Patch1: %{name}-gmp.patch
# Set of patches to work with system wide packages
Patch2: %{name}-scripts.patch
-# Do not mandate a patched ntl. It was requested to ntl upstream to
-# provide an api to match what sagemath expects.
-# http://shoup.net/pipermail/ntl_shoup.net/2012-April/000033.html
-Patch3: %{name}-unpatched_ntl.patch
-
# Adapt to ntl 6.0.0.
-Patch4: %{name}-ntl6.patch
+Patch3: %{name}-ntl6.patch
# remove call to not implemented sagemath "is_package_installed" interfaces
# need to package coin-or solver in fedora
# remove check for non free solvers
-Patch5: %{name}-extensions.patch
+Patch4: %{name}-extensions.patch
# helper to:
# o respect a DESTDIR environment variable
@@ -127,101 +116,82 @@ Patch5: %{name}-extensions.patch
# o minor change to help in incremental builds by avoiding rebuilding
# files
# o do not assume there is an installed sagemath
-Patch6: %{name}-rpmbuild.patch
+Patch5: %{name}-rpmbuild.patch
# build documentation in buildroot environment
-Patch7: %{name}-sagedoc.patch
+Patch6: %{name}-sagedoc.patch
# sage notebook rpm and system environment adjustments
-Patch8: %{name}-sagenb.patch
+Patch7: %{name}-sagenb.patch
# do not attempt to create state files in system directories
-Patch9: %{name}-readonly.patch
+Patch8: %{name}-readonly.patch
# force coercion of ecl t_string to ecl t_base_string
# this is hackish and only required if ecl is built with unicode support
-Patch10: %{name}-ecl-unicode.patch
+Patch9: %{name}-ecl-unicode.patch
# do not link explicitly to png12
-Patch11: %{name}-png.patch
+Patch10: %{name}-png.patch
# work with all maxima-runtime lisp backend packages
-Patch12: %{name}-maxima.patch
+Patch11: %{name}-maxima.patch
# execute 4ti2 programs in $PATH not in $SAGE_ROOT/local/bin
-Patch13: %{name}-4ti2.patch
+Patch12: %{name}-4ti2.patch
# http://trac.sagemath.org/sage_trac/ticket/12992
# http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1317
-Patch14: %{name}-pari.patch
-
-# in fedora 18 it was updated to latest fplll
-Patch15: %{name}-fplll.patch
+Patch13: %{name}-pari.patch
# Portuguese translations: http://trac.sagemath.org/sage_trac/ticket/12822
-Patch16: trac_12502_pt_translation_of_a_tour_of_sage_rebase1.patch
-Patch17: trac_12822_pt_translation_of_tutorial.patch
-Patch18: trac_12822_pt_translation_of_tutorial_rev1.patch
-
-# wrappers for distros with libmpc 0.9
-Patch19: %{name}-libmpc.patch
+Patch14: trac_12502_pt_translation_of_a_tour_of_sage_rebase1.patch
+Patch15: trac_12822_pt_translation_of_tutorial.patch
+Patch16: trac_12822_pt_translation_of_tutorial_rev1.patch
# use jmol itself to export preview images
# FIXME besides not using X and told so, fails if DISPLAY is not set
-Patch20: %{name}-jmol.patch
-
-# adapt for maxima 5.29.1 package
-Patch21: %{name}-maxima.system.patch
+Patch17: %{name}-jmol.patch
# only cremona mini database built and installed
# FIXME add a package with the full cremona database
# FIXME actually it should be already available in pari-elldata
-Patch22: %{name}-cremona.patch
+Patch18: %{name}-cremona.patch
# lrslib is a requires
-Patch23: %{name}-lrslib.patch
+Patch19: %{name}-lrslib.patch
# nauty cannot be packaged due to license restrictions
# http://cs.anu.edu.au/~bdm/nauty/
# http://pallini.di.uniroma1.it/
-Patch24: %{name}-nauty.patch
+Patch20: %{name}-nauty.patch
# gap hap package not (yet) available
# http://www-gap.mcs.st-and.ac.uk/Packages/hap.html
-Patch25: %{name}-gap-hap.patch
+Patch21: %{name}-gap-hap.patch
# Patch to enable lrcalc once review request is done in Fedora
-Patch26: %{name}-lrcalc.patch
+Patch22: %{name}-lrcalc.patch
# Patch to enable cbc once review requests are done in Fedora
-Patch27: %{name}-cbc.patch
+Patch23: %{name}-cbc.patch
-# Patch to enable libgap once review request is done in Fedora
-Patch28: %{name}-libgap.patch
-
-# Patch to disable libgap because it is not optional by default
-Patch29: %{name}-nolibgap.patch
+# Use system gap directories
+Patch24: %{name}-libgap.patch
# Patch to enable fes once review requests are done in Fedora
-Patch30: %{name}-fes.patch
+Patch25: %{name}-fes.patch
# Get package to build with known problem if not yet updated to pari 2.6.
-Patch31: %{name}-nopari2.6.patch
+Patch26: %{name}-nopari2.6.patch
-# sagemath 5.8 (optionally) requires cryptominisat 2.9.6 (in rawhide)
+# sagemath 5.8 (optionally) requires cryptominisat 2.9.6 (in >= f19)
# and does not work with cryptominisat 2.9.5 (in f18)
-Patch32: %{name}-cryptominisat.patch
-
-# Adapt to m4rie 20130416
-Patch33: %{name}-m4rie.patch
+Patch27: %{name}-cryptominisat.patch
-# Until cython is fixed for f18 and f19; just override wrong cython definition
-# https://bugzilla.redhat.com/show_bug.cgi?id=961372
-Patch34: %{name}-rh_bz_961372.patch
-
-# Required if running python-flask-0.10.1
-# sagemath expects python-flask-0.9
-Patch35: %{name}-flask.patch
+# Side effect of using distro packages
+# https://bugzilla.redhat.com/show_bug.cgi?id=974769
+Patch28: %{name}-sympy.patch
BuildRequires: 4ti2
BuildRequires: atlas-devel
@@ -261,9 +231,7 @@ BuildRequires: iml-devel
BuildRequires: L-function-devel
BuildRequires: libfac-devel
BuildRequires: libfplll-devel
-%if %{have_libgap}
BuildRequires: libgap-devel
-%endif
BuildRequires: libmpc-devel
BuildRequires: linbox-devel
%if %{have_lrcalc}
@@ -345,7 +313,6 @@ Requires: python-ipython
Requires: python-matplotlib
Requires: python-networkx
Requires: python-polybori
-Requires: python-sphinx
Requires: python-twisted-web
Requires: python-twisted-web2
Requires: python-ZODB3
@@ -369,6 +336,7 @@ Requires: tachyon
Requires: texlive
Requires: vecmath
+# Missing build requires on armv7hl
ExclusiveArch: %{ix86} x86_64
%description
@@ -643,11 +611,8 @@ popd
%patch0 -p1
%patch1 -p1
%patch2 -p1
-%if 0%{?fedora} < 19
%patch3 -p1
-%else
%patch4 -p1
-%endif
%patch5 -p1
%patch6 -p1
%patch7 -p1
@@ -657,73 +622,44 @@ popd
%patch11 -p1
%patch12 -p1
%patch13 -p1
-%patch14 -p1
-
-%if 0%{?fedora} >= 18
-%patch15 -p1
-%endif
pushd spkg/build/sage-%{version}
mkdir -p doc/pt/a_tour_of_sage/
cp -fa doc/en/a_tour_of_sage/*.png doc/pt/a_tour_of_sage/
+%patch14 -p1
+%patch15 -p1
%patch16 -p1
-%patch17 -p1
-%patch18 -p1
popd
-%if 0%{?fedora} <= 19
+%patch17 -p1
+%patch18 -p1
%patch19 -p1
-%endif
%patch20 -p1
-
-%if 0%{?fedora} >= 18
-%if 0%{?fedora} < 20
%patch21 -p1
-%endif
-%endif
-
-%patch22 -p1
-%patch23 -p1
-%patch24 -p1
-%patch25 -p1
%if %{have_lrcalc}
-%patch26 -p1
+%patch22 -p1
%endif
# other coin-or packages are build requires or coin-or-Cbc
%if %{have_coin_or_Cbc}
-%patch27 -p1
+%patch23 -p1
%endif
-%if %{have_libgap}
-%patch28 -p1
-%else
-%patch29 -p1
-%endif
+%patch24 -p1
%if %{have_fes}
-%patch30 -p1
-%endif
-
-%patch31 -p1
-
-%if 0%{?fedora} >= 19
-%patch32 -p1
-%endif
-
-%if 0%{?fedora} == 19
-%patch33 -p1
+%patch25 -p1
%endif
-%if 0%{?fedora} <= 19
-%patch34 -p1
-%endif
+%patch26 -p1
+%patch27 -p1
+%patch28 -p1
-%if 0%{?fedora} >= 20
-%patch35 -p1
-%endif
+sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
+ -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
+ -i spkg/build/sage-%{version}/sage/env.py
#------------------------------------------------------------------------
# ensure proper/preferred libatlas is in linker path
@@ -738,6 +674,7 @@ 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
@@ -745,34 +682,27 @@ export CFLAGS="%{optflags}"
export CXXFLAGS="%{optflags}"
export SAGE_ROOT=%{buildroot}%{SAGE_ROOT}
export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL}
-export SAGE_SRC=%{buildroot}%{SAGE_SRC}
+# Avoid buildroot in gcc command line (use _builddir instead)
+export SAGE_SRC="$PWD/spkg/build/sage-%{version}"
export SAGE_FORTRAN=%{_bindir}/gfortran
export SAGE_FORTRAN_LIB=`gfortran --print-file-name=libgfortran.so`
-%if 0%{?fedora} > 20
-export SAGE_BLAS=satlas
-%endif
export DESTDIR=%{buildroot}
# Use file in /tmp because there are issues with long pathnames
export DOT_SAGE=/tmp/sage$$
mkdir -p $DOT_SAGE/tmp
# match system packages as sagemath packages
-export SAGE_ROOT=%{buildroot}%{SAGE_ROOT}
-export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL}
-export SAGE_SRC=%{buildroot}%{SAGE_SRC}
-mkdir -p $SAGE_ROOT $SAGE_LOCAL $SAGE_SRC
-ln -sf $PWD/spkg/build/sage-%{version}/sage $SAGE_SRC/sage
+mkdir -p $SAGE_ROOT $SAGE_LOCAL #%{buildroot}%{SAGE_SRC}
ln -sf %{_libdir} $SAGE_LOCAL/lib
ln -sf %{_includedir} $SAGE_LOCAL/include
ln -sf %{_datadir} $SAGE_LOCAL/share
+#ln -sf $SAGE_SRC/sage %{buildroot}%{SAGE_SRC}/sage
export PATH=%{buildroot}%{_bindir}:$PATH
export PYTHONPATH=%{buildroot}%{python_sitearch}:$PYTHONPATH
#------------------------------------------------------------------------
pushd spkg/build/sage-%{version}
- sed -e 's|@@libdir@@|%{_libdir}|g' \
- -i setup.py
pushd c_lib
# scons ignores most environment variables
# and does not have soname support
@@ -1036,11 +966,7 @@ export PATH=$SAGE_LOCAL/bin:\$PATH
export SINGULARPATH=%{_libdir}/Singular/LIB
export SINGULAR_BIN_DIR=%{_libdir}/Singular
##export PYTHONPATH="$SAGE_PYTHONPATH:\$SAGE_LOCAL/bin"
-%if 0%{?fedora} > 20
-export SAGE_CBLAS=satlas
-%else
export SAGE_CBLAS=cblas
-%endif
export SAGE_FORTRAN=%{_bindir}/gfortran
export SAGE_FORTRAN_LIB=\`gfortran --print-file-name=libgfortran.so\`
export SYMPOW_DIR="\$DOT_SAGE/sympow"
@@ -1186,23 +1112,19 @@ find %{buildroot}%{SAGE_DOC} -name .buildinfo -exec rm {} \;
rm -fr %{buildroot}%{SAGE_DOC}/output/inventory
find %{buildroot}%{SAGE_DOC} -type d -name _sources | xargs rm -fr
-rm %{buildroot}%{python_sitearch}/sagenb/data/mathjax/.gitignore \
- %{buildroot}%{python_sitearch}/sagenb/data/mathjax/docs/.gitignore
-
# remove bundles fonts
rm -r %{buildroot}%{python_sitearch}/sagenb/data/mathjax/fonts
# remove .po files
rm %{buildroot}%{python_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
-# remove zero length files
-rm %{buildroot}%{python_sitearch}/sage/server/notebook/compress/all.py* \
- %{buildroot}%{python_sitearch}/sage/misc/test_cpickle_sage.py*
-
%if !%{with_sage3d}
rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d
%endif
+# remove cache files
+rm -r %{buildroot}%{python_sitearch}/sagenb/data/.webassets-cache
+
# last install command
rm -fr $DOT_SAGE
@@ -1391,6 +1313,8 @@ exit 0
%{python_sitearch}/sagenb/data/json
# ASL 2.0
%{python_sitearch}/sagenb/data/mathjax
+# Empty (do not run doctests flag file)
+%{python_sitearch}/sagenb/data/nodoctest.py*
# BSD
%{python_sitearch}/sagenb/data/openid-realselector
# GPLv2+
@@ -1401,6 +1325,8 @@ exit 0
%endif
# LGPLv2+
%{python_sitearch}/sagenb/data/tiny_mce
+# Auto generated files
+%{python_sitearch}/sagenb/data/webassets_generated
# LGPLv2+
%{python_sitearch}/sagenb/data/zorn
# GPLv2+
@@ -1449,8 +1375,8 @@ exit 0
########################################################################
%changelog
-* Fri Oct 4 2013 pcpa <paulo.cesar.pereira.de.andrade at gmail.com> - 5.10-5
-- Rebuild with newer rawhide atlas.
+* Wed Oct 16 2013 pcpa <paulo.cesar.pereira.de.andrade at gmail.com> - 5.12-1
+- Update to sagemath 5.12.
* Sat Sep 14 2013 pcpa <paulo.cesar.pereira.de.andrade at gmail.com> - 5.10-4
- Do not hardcode SAGE_BROWSER (#967251)
diff --git a/sources b/sources
index 14b318a..7f08855 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-bfca3afc9030e63c7e7200287ee0135e sage-5.10.tar
+21d62a8a61e351c3c124167b3eead46f sage-5.12.tar
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