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Update to sagemath 5.12

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This commit is contained in:
pcpa 2013-10-18 23:22:11 -03:00
parent 4f797f23e1
commit d4a07df7d0
37 changed files with 281 additions and 843 deletions
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1
.gitignore vendored
View file

@ -1,3 +1,4 @@
/sage-5.8.tar
/sage-5.9.tar
/sage-5.10.tar
/sage-5.12.tar

6
sagemath-4ti2.patch
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@ -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.
"""

8
sagemath-cbc.patch
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@ -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"])
)

6
sagemath-cremona.patch
View file

@ -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 \

8
sagemath-cryptominisat.patch
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@ -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'):
)

12
sagemath-ecl-unicode.patch
View file

@ -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.

8
sagemath-extensions.patch
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@ -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

8
sagemath-fes.patch
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@ -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

32
sagemath-flask.patch
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@ -1,32 +0,0 @@
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 2013-07-30 17:57:58.985060198 -0300
+++ sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/flask_version/base.py 2013-07-30 17:58:31.958061460 -0300
@@ -55,28 +55,6 @@ class SageNBFlask(Flask):
endpoint='/static'+base_url,
view_func=partial(self.static_view_func, root_path))
- def save_session(self, session, response):
- """
- This method needs to stay in sync with the version in Flask.
- The only modification made to it is the ``httponly=False``
- passed to ``save_cookie``.
-
- Saves the session if it needs updates. For the default
- implementation, check :meth:`open_session`.
-
- :param session: the session to be saved (a
- :class:`~werkzeug.contrib.securecookie.SecureCookie`
- object)
- :param response: an instance of :attr:`response_class`
- """
- expires = domain = None
- if session.permanent:
- expires = datetime.utcnow() + self.permanent_session_lifetime
- if self.config['SERVER_NAME'] is not None:
- domain = '.' + self.config['SERVER_NAME']
- session.save_cookie(response, self.session_cookie_name,
- expires=expires, httponly=False, domain=domain)
-
def message(self, msg, cont='/', username=None, **kwds):
"""Returns an error message to the user."""
template_dict = {'msg': msg, 'cont': cont, 'username': username}

194
sagemath-fplll.patch
View file

@ -1,194 +0,0 @@
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 19:57:20.544060055 -0300
+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 19:57:33.521060552 -0300
@@ -638,6 +638,7 @@ ext_modules = [
libraries = ['gmp', 'mpfr', 'stdc++', 'fplll'],
language="c++",
include_dirs = [SAGE_INC + '/fplll'],
+ extra_compile_args=["-DFPLLL_V3_COMPAT"],
depends = [SAGE_INC + "/fplll/fplll.h"]),
Extension('sage.libs.linbox.linbox',
diff -up sage-5.10/spkg/build/sage-5.10/sage/libs/fplll/fplll.pxi.orig sage-5.10/spkg/build/sage-5.10/sage/libs/fplll/fplll.pxi
--- sage-5.10/spkg/build/sage-5.10/sage/libs/fplll/fplll.pxi.orig 2013-07-29 19:57:29.779060409 -0300
+++ sage-5.10/spkg/build/sage-5.10/sage/libs/fplll/fplll.pxi 2013-07-29 19:57:33.523060552 -0300
@@ -10,22 +10,22 @@ cdef extern from "fplll/fplll.h":
#
cdef extern from "fplll/nr.h":
- ctypedef struct Z_NR "Z_NR<mpz_t>":
+ ctypedef struct Z_NR "fplll::Z_NR<mpz_t>":
mpz_t (*GetData)()
void (*set_mpz_t "set")(mpz_t d)
- Z_NR *Z_NR_new "new Z_NR<mpz_t>"()
+ Z_NR *Z_NR_new "new fplll::Z_NR<mpz_t>"()
void Z_NR_delete "delete "(Z_NR *mem)
- Z_NR *Z_NR_construct "Construct< Z_NR<mpz_t> >"(void *mem)
- void Z_NR_destruct "Destruct< Z_NR<mpz_t> >"(Z_NR *mem)
+ Z_NR *Z_NR_construct "Construct< fplll::Z_NR<mpz_t> >"(void *mem)
+ void Z_NR_destruct "Destruct< fplll::Z_NR<mpz_t> >"(Z_NR *mem)
#
# matrices over the integers
#
cdef extern from "fplll/matrix.h":
- ctypedef struct ZZ_mat "ZZ_mat<mpz_t>":
+ ctypedef struct ZZ_mat "fplll::ZZ_mat<mpz_t>":
int (*GetNumCols)()
int (*GetNumRows)()
@@ -41,83 +41,83 @@ cdef extern from "fplll/matrix.h":
void (*gen_ntrulike2)(int bits,int q)
void (*gen_ajtai)(double alpha)
- ZZ_mat *ZZ_mat_new "new ZZ_mat<mpz_t>"(int r, int c)
+ ZZ_mat *ZZ_mat_new "new fplll::ZZ_mat<mpz_t>"(int r, int c)
void ZZ_mat_delete "delete "(ZZ_mat *mem)
#
# fastest LLL
#
-cdef extern from "fplll/fast.h":
- ctypedef struct fast_double "fast<mpz_t,double>":
+cdef extern from "fplll/fplllv31.h":
+ ctypedef struct fast_double "fplll::fast<mpz_t,double>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- fast_double *fast_double_new "new fast<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
+ fast_double *fast_double_new "new fplll::fast<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
void fast_double_delete "delete "(fast_double *mem)
#
# fastest LLL with early reduction
#
-cdef extern from "fplll/fast_earlyred.h":
- ctypedef struct fast_early_red_double "fast_early_red<mpz_t,double>":
+cdef extern from "fplll/fplllv31.h":
+ ctypedef struct fast_early_red_double "fplll::fast_early_red<mpz_t,double>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- fast_early_red_double *fast_early_red_double_new "new fast_early_red<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
+ fast_early_red_double *fast_early_red_double_new "new fplll::fast_early_red<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
void fast_early_red_double_delete "delete "(fast_early_red_double *mem)
#
# heuristic
#
-cdef extern from "fplll/heuristic.h":
- ctypedef struct heuristic_mpfr "heuristic<mpz_t,mpfr_t>":
+cdef extern from "fplll/fplllv31.h":
+ ctypedef struct heuristic_mpfr "fplll::heuristic<mpz_t,mpfr_t>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- heuristic_mpfr *heuristic_mpfr_new "new heuristic<mpz_t,mpfr_t>"(ZZ_mat *B,int precision, double eta, double delta)
+ heuristic_mpfr *heuristic_mpfr_new "new fplll::heuristic<mpz_t,mpfr_t>"(ZZ_mat *B,int precision, double eta, double delta)
void heuristic_mpfr_delete "delete "(heuristic_mpfr *mem)
- ctypedef struct heuristic_dpe "heuristic<mpz_t,dpe_t>":
+ ctypedef struct heuristic_dpe "fplll::heuristic<mpz_t,dpe_t>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- heuristic_dpe *heuristic_dpe_new "new heuristic<mpz_t,dpe_t>"(ZZ_mat *B,int precision, double eta, double delta)
+ heuristic_dpe *heuristic_dpe_new "new fplll::heuristic<mpz_t,dpe_t>"(ZZ_mat *B,int precision, double eta, double delta)
void heuristic_dpe_delete "delete "(heuristic_dpe *mem)
- ctypedef struct heuristic_double "heuristic<mpz_t,double>":
+ ctypedef struct heuristic_double "fplll::heuristic<mpz_t,double>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- heuristic_double *heuristic_double_new "new heuristic<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
+ heuristic_double *heuristic_double_new "new fplll::heuristic<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
void heuristic_double_delete "delete "(heuristic_double *mem)
#
# heuristic with early reduction
#
-cdef extern from "fplll/heuristic_early_red.h":
- ctypedef struct heuristic_early_red_mpfr "heuristic_early_red<mpz_t,mpfr_t>":
+cdef extern from "fplll/fplllv31.h":
+ ctypedef struct heuristic_early_red_mpfr "fplll::heuristic_early_red<mpz_t,mpfr_t>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- heuristic_early_red_mpfr *heuristic_early_red_mpfr_new "new heuristic_early_red<mpz_t,mpfr_t>"(ZZ_mat *B,int precision, double eta, double delta)
+ heuristic_early_red_mpfr *heuristic_early_red_mpfr_new "new fplll::heuristic_early_red<mpz_t,mpfr_t>"(ZZ_mat *B,int precision, double eta, double delta)
void heuristic_early_red_mpfr_delete "delete "(heuristic_early_red_mpfr *mem)
- ctypedef struct heuristic_early_red_dpe "heuristic_early_red<mpz_t,dpe_t>":
+ ctypedef struct heuristic_early_red_dpe "fplll::heuristic_early_red<mpz_t,dpe_t>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- heuristic_early_red_dpe *heuristic_early_red_dpe_new "new heuristic_early_red<mpz_t,dpe_t>"(ZZ_mat *B,int precision, double eta, double delta)
+ heuristic_early_red_dpe *heuristic_early_red_dpe_new "new fplll::heuristic_early_red<mpz_t,dpe_t>"(ZZ_mat *B,int precision, double eta, double delta)
void heuristic_early_red_dpe_delete "delete "(heuristic_early_red_dpe *mem)
- ctypedef struct heuristic_early_red_double "heuristic_early_red<mpz_t,double>":
+ ctypedef struct heuristic_early_red_double "fplll::heuristic_early_red<mpz_t,double>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- heuristic_early_red_double *heuristic_early_red_double_new "new heuristic_early_red<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
+ heuristic_early_red_double *heuristic_early_red_double_new "new fplll::heuristic_early_red<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
void heuristic_early_red_double_delete "delete "(heuristic_early_red_double *mem)
@@ -126,36 +126,36 @@ cdef extern from "fplll/heuristic_early
# provable LLL
#
-cdef extern from "fplll/proved.h":
- ctypedef struct proved_mpfr "proved<mpz_t,mpfr_t>":
+cdef extern from "fplll/fplllv31.h":
+ ctypedef struct proved_mpfr "fplll::proved<mpz_t,mpfr_t>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- proved_mpfr *proved_mpfr_new "new proved<mpz_t,mpfr_t>"(ZZ_mat *B,int precision, double eta, double delta)
+ proved_mpfr *proved_mpfr_new "new fplll::proved<mpz_t,mpfr_t>"(ZZ_mat *B,int precision, double eta, double delta)
void proved_mpfr_delete "delete "(proved_mpfr *mem)
- ctypedef struct proved_dpe "proved<mpz_t,dpe_t>":
+ ctypedef struct proved_dpe "fplll::proved<mpz_t,dpe_t>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- proved_dpe *proved_dpe_new "new proved<mpz_t,dpe_t>"(ZZ_mat *B,int precision, double eta, double delta)
+ proved_dpe *proved_dpe_new "new fplll::proved<mpz_t,dpe_t>"(ZZ_mat *B,int precision, double eta, double delta)
void proved_dpe_delete "delete "(proved_dpe *mem)
- ctypedef struct proved_double "proved<mpz_t,double>":
+ ctypedef struct proved_double "fplll::proved<mpz_t,double>":
int (*LLL)()
ZZ_mat* (*GetBase)()
- proved_double *proved_double_new "new proved<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
+ proved_double *proved_double_new "new fplll::proved<mpz_t,double>"(ZZ_mat *B,int precision, double eta, double delta)
void proved_double_delete "delete "(proved_double *mem)
#
# wrapper code which chooses a LLL sequence automatically
#
-cdef extern from "fplll/wrapper.h":
- ctypedef struct wrapper:
+cdef extern from "fplll/fplllv31.h":
+ ctypedef struct wrapper "fplll::wrapper":
int (*LLL)()
ZZ_mat* (*GetBase)()
- wrapper *wrapper_new "new wrapper"(ZZ_mat *B,int precision, double eta, double delta)
+ wrapper *wrapper_new "new fplll::wrapper"(ZZ_mat *B,int precision, double eta, double delta)
void wrapper_delete "delete "(wrapper *mem)

8
sagemath-gap-hap.patch
View file

@ -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
"""

4
sagemath-gmp.patch
View file

@ -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/
****************************************************************************/

6
sagemath-jmol.patch
View file

@ -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")

6
sagemath-libgap.patch
View file

@ -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

65
sagemath-libmpc.patch
View file

@ -1,65 +0,0 @@
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 12:42:08.694809731 -0300
+++ sage-5.10/spkg/build/sage-5.10/c_lib/SConstruct 2013-02-23 12:43:00.412811711 -0300
@@ -145,7 +145,7 @@ soname = libname + "." + major
shlink_flags += [ '-Wl,-Bsymbolic', '-Wl,-soname=%s' % soname ]
lib = env.SharedLibrary( "csage", [ "src/" + x for x in srcFiles ],
- LIBS=['ntl', 'pari', 'gmp', 'python$PYV'],
+ LIBS=['ntl', 'pari', 'gmp', 'mpfr', 'python$PYV'],
LIBPATH=['@@libdir@@','@@libdir@@/python$PYV/config/'],
SHLIBSUFFIX=shlib_suffix,
SHLINKFLAGS=shlink_flags,
diff -up sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c.orig sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c
--- sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c.orig 2013-02-23 12:42:18.286810098 -0300
+++ sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c 2013-02-23 12:43:15.062812272 -0300
@@ -58,3 +58,49 @@ void init_csage_module() {
init_csage();
#endif
}
+
+#include <mpc.h>
+
+int
+mpc_div_2ui (mpc_ptr a, mpc_srcptr b, unsigned long int c, mpc_rnd_t rnd)
+{
+ int inex_re, inex_im;
+
+ inex_re = mpfr_div_2ui (mpc_realref(a), mpc_realref(b), c, MPC_RND_RE(rnd));
+ inex_im = mpfr_div_2ui (mpc_imagref(a), mpc_imagref(b), c, MPC_RND_IM(rnd));
+
+ return MPC_INEX(inex_re, inex_im);
+}
+
+int
+mpc_div_2si (mpc_ptr a, mpc_srcptr b, long int c, mpc_rnd_t rnd)
+{
+ int inex_re, inex_im;
+
+ inex_re = mpfr_div_2si (mpc_realref(a), mpc_realref(b), c, MPC_RND_RE(rnd));
+ inex_im = mpfr_div_2si (mpc_imagref(a), mpc_imagref(b), c, MPC_RND_IM(rnd));
+
+ return MPC_INEX(inex_re, inex_im);
+}
+
+int
+mpc_mul_2ui (mpc_ptr a, mpc_srcptr b, unsigned long int c, mpc_rnd_t rnd)
+{
+ int inex_re, inex_im;
+
+ inex_re = mpfr_mul_2ui (mpc_realref(a), mpc_realref(b), c, MPC_RND_RE(rnd));
+ inex_im = mpfr_mul_2ui (mpc_imagref(a), mpc_imagref(b), c, MPC_RND_IM(rnd));
+
+ return MPC_INEX(inex_re, inex_im);
+}
+
+int
+mpc_mul_2si (mpc_ptr a, mpc_srcptr b, long int c, mpc_rnd_t rnd)
+{
+ int inex_re, inex_im;
+
+ inex_re = mpfr_mul_2si (mpc_realref(a), mpc_realref(b), c, MPC_RND_RE(rnd));
+ inex_im = mpfr_mul_2si (mpc_imagref(a), mpc_imagref(b), c, MPC_RND_IM(rnd));
+
+ return MPC_INEX(inex_re, inex_im);
+}

8
sagemath-lrcalc.patch
View file

@ -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]
)

8
sagemath-lrslib.patch
View file

@ -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.
"""

62
sagemath-m4rie.patch
View file

@ -1,62 +0,0 @@
--- sage-5.10/spkg/build/sage-5.10/sage/libs/m4rie.pxd.orig 2013-05-07 08:12:27.137652862 -0600
+++ sage-5.10/spkg/build/sage-5.10/sage/libs/m4rie.pxd 2013-05-07 11:45:12.067923724 -0600
@@ -52,9 +52,9 @@ cdef extern from "m4rie/m4rie.h":
void mzed_add_elem(mzed_t *a, const_size_t row, const_size_t col, const_int elem)
- void mzed_add_multiple_of_row(mzed_t *A, size_t ar, mzed_t *B, size_t br, m4ri_word *X, size_t start_col)
+ void mzed_add_multiple_of_row(mzed_t *A, size_t ar, mzed_t *B, size_t br, m4ri_word x, size_t start_col)
- void mzed_rescale_row(mzed_t *A, size_t r, size_t c, m4ri_word *X)
+ void mzed_rescale_row(mzed_t *A, size_t r, size_t c, m4ri_word x)
void mzed_row_swap(mzed_t *M, const_size_t rowa, const_size_t rowb)
@@ -112,14 +112,12 @@ cdef extern from "m4rie/m4rie.h":
#cdef extern from "m4rie/mzd_slice.h":
- int __M4RIE_MAX_KARATSUBA_DEGREE
-
ctypedef struct mzd_slice_t:
mzd_t *x[16]
- gf2e *finite_field
int nrows
int ncols
int depth
+ gf2e *finite_field
mzd_slice_t *mzd_slice_init(gf2e *ff, size_t m, size_t n)
--- sage-5.10/spkg/build/sage-5.10/sage/matrix/matrix_mod2e_dense.pyx.orig 2013-05-07 08:12:27.139652859 -0600
+++ sage-5.10/spkg/build/sage-5.10/sage/matrix/matrix_mod2e_dense.pyx 2013-05-07 11:21:05.095668016 -0600
@@ -561,9 +561,6 @@ cdef class Matrix_mod2e_dense(matrix_den
if self._ncols != right._nrows:
raise ArithmeticError("left ncols must match right nrows")
- if self._entries.finite_field.degree > __M4RIE_MAX_KARATSUBA_DEGREE:
- raise NotImplementedError("Karatsuba multiplication is only implemented for matrices over GF(2^e) with e <= %d."%__M4RIE_MAX_KARATSUBA_DEGREE)
-
cdef Matrix_mod2e_dense ans
ans = self.new_matrix(nrows = self.nrows(), ncols = right.ncols())
@@ -1047,8 +1044,7 @@ cdef class Matrix_mod2e_dense(matrix_den
[ a a^2 + 1 a + 1]
"""
cdef m4ri_word x = <m4ri_word>(<M4RIE__FiniteField*>self.cc.objectptr).log2pol((<FiniteField_givaroElement>multiple).element)
- cdef m4ri_word *X = self._entries.finite_field.mul[x]
- mzed_rescale_row(self._entries, row, start_col, X)
+ mzed_rescale_row(self._entries, row, start_col, x)
cdef add_multiple_of_row_c(self, Py_ssize_t row_to, Py_ssize_t row_from, multiple, Py_ssize_t start_col):
@@ -1077,8 +1073,7 @@ cdef class Matrix_mod2e_dense(matrix_den
"""
cdef m4ri_word x = <m4ri_word>(<M4RIE__FiniteField*>self.cc.objectptr).log2pol((<FiniteField_givaroElement>multiple).element)
- cdef m4ri_word *X = self._entries.finite_field.mul[x]
- mzed_add_multiple_of_row(self._entries, row_to, self._entries, row_from, X, start_col)
+ mzed_add_multiple_of_row(self._entries, row_to, self._entries, row_from, x, start_col)
cdef swap_rows_c(self, Py_ssize_t row1, Py_ssize_t row2):

12
sagemath-maxima.patch
View file

@ -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>")

12
sagemath-maxima.system.patch
View file

@ -1,12 +0,0 @@
diff -up sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima_lib.py.orig sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima_lib.py
--- sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima_lib.py.orig 2012-12-29 15:42:54.811218546 -0200
+++ sage-5.10/spkg/build/sage-5.10/sage/interfaces/maxima_lib.py 2012-12-29 15:43:06.739219003 -0200
@@ -77,7 +77,7 @@ from maxima_abstract import (MaximaAbstr
## We begin here by initializing Maxima in library mode
## i.e. loading it into ECL
ecl_eval("(setf *load-verbose* NIL)")
-ecl_eval("(require 'maxima)")
+ecl_eval("(require 'maxima.system)")
ecl_eval("(in-package :maxima)")
ecl_eval("(setq $nolabels t))")
ecl_eval("(defvar *MAXIMA-LANG-SUBDIR* NIL)")

8
sagemath-nauty.patch
View file

@ -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

54
sagemath-nolibgap.patch
View file

@ -1,54 +0,0 @@
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 20:07:17.633082920 -0300
+++ sage-5.10/spkg/build/sage-5.10/module_list.py 2013-07-29 20:07:28.577083339 -0300
@@ -487,8 +487,8 @@ ext_modules = [
Extension('sage.groups.old',
sources = ['sage/groups/old.pyx']),
- Extension('sage.groups.libgap_wrapper',
- sources = ['sage/groups/libgap_wrapper.pyx']),
+# Extension('sage.groups.libgap_wrapper',
+# sources = ['sage/groups/libgap_wrapper.pyx']),
Extension('sage.groups.perm_gps.permgroup_element',
sources = ['sage/groups/perm_gps/permgroup_element.pyx']),
@@ -771,25 +771,25 @@ ext_modules = [
##
################################
- Extension('sage.libs.gap.util',
- sources = ["sage/libs/gap/util.pyx"],
- libraries = ['csage', 'gmp', 'gap', 'm'],
- include_dirs = [SAGE_INC]),
-
- Extension('sage.libs.gap.element',
- sources = ["sage/libs/gap/element.pyx"],
- libraries = ['csage', 'gmp', 'gap', 'm'],
- include_dirs = [SAGE_INC]),
+# Extension('sage.libs.gap.util',
+# sources = ["sage/libs/gap/util.pyx"],
+# libraries = ['csage', 'gmp', 'gap', 'm'],
+# include_dirs = [SAGE_INC]),
+#
+# Extension('sage.libs.gap.element',
+# sources = ["sage/libs/gap/element.pyx"],
+# libraries = ['csage', 'gmp', 'gap', 'm'],
+# include_dirs = [SAGE_INC]),
# Extension('sage.libs.gap.type',
# sources = ["sage/libs/gap/type.pyx"],
# libraries = ['csage', 'gmp', 'gap', 'm'],
# include_dirs = [SAGE_INC]),
-
- Extension('sage.libs.gap.libgap',
- sources = ["sage/libs/gap/libgap.pyx"],
- libraries = ['csage', 'gmp', 'gap', 'm'],
- include_dirs = [SAGE_INC]),
+#
+# Extension('sage.libs.gap.libgap',
+# sources = ["sage/libs/gap/libgap.pyx"],
+# libraries = ['csage', 'gmp', 'gap', 'm'],
+# include_dirs = [SAGE_INC]),
###################################
##

22
sagemath-nopari2.6.patch
View file

@ -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()

18
sagemath-ntl6.patch
View file

@ -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":

16
sagemath-pari.patch
View file

@ -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()!

12
sagemath-png.patch
View file

@ -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,

8
sagemath-readonly.patch
View file

@ -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::

14
sagemath-rh_bz_961372.patch
View file

@ -1,14 +0,0 @@
diff -up sage-5.10/spkg/build/sage-5.10/sage/ext/cdefs.pxi.orig sage-5.10/spkg/build/sage-5.10/sage/ext/cdefs.pxi
--- sage-5.10/spkg/build/sage-5.10/sage/ext/cdefs.pxi.orig 2013-07-29 20:12:52.183095731 -0300
+++ sage-5.10/spkg/build/sage-5.10/sage/ext/cdefs.pxi 2013-07-29 20:13:06.111096264 -0300
@@ -5,6 +5,9 @@
from libc.stdio cimport *
from libc.string cimport strlen, strcpy, memset, memcpy
-from libc.math cimport sqrt, frexp, ldexp
+cdef extern from "math.h":
+ cdef double sqrt "sqrt" (double)
+ cdef double frexp "frexp" (double, int*)
+ cdef double ldexp "ldexp" (double, int)
from sage.libs.gmp.all cimport *

29
sagemath-rpmbuild.patch
View file

@ -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:
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 = 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]

36
sagemath-sagedoc.patch
View file

@ -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) + ']'

89
sagemath-sagenb.patch
View file

@ -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 -->
@ -22,44 +22,9 @@ 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):
jmol_script = jmol_file.read()
jmol_file.close()
- jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "' + self.url_to_self() + '/')
+ jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "/home/' + self.worksheet_filename() + '/')
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
# 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
+sagenb_dir = os.path.join(os.environ['SAGE_ROOT'], 'src', 'sagenb')
+sys.path.append(sagenb_dir)
+import flask_version.base as flask_base
opts={}
startup_token = '{0:x}'.format(random.randint(0, 2**128))
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
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
@ -70,3 +35,35 @@ diff -up sage-5.10/spkg/build/sagenb-0.10.4/src/sagenb/sagenb/data/sage/js/jmol_
//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()
- jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "' + self.url_to_self() + '/')
+ jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "/home/' + self.worksheet_filename() + '/')
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
@@ -46,12 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
# Flask #
#########
import os, sys, random
-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
opts={}
startup_token = '{0:x}'.format(random.randint(0, 2**128))
if %(automatic_login)s:
opts['startup_token'] = startup_token
-flask_app = flask_base.create_app(%(notebook_opts)s, **opts)
+flask_app = flask_base.create_app(%(notebook_opts)s, startup_token=startup_token)
def save_notebook(notebook):
print "Quitting all running worksheets..."

6
sagemath-scons.patch
View file

@ -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

72
sagemath-scripts.patch
View file

@ -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"

6
sagemath-sympy.patch
View file

@ -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())

60
sagemath-unpatched_ntl.patch
View file

@ -1,60 +0,0 @@
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 2013-01-25 21:54:01.313110341 -0200
+++ sage-5.10/spkg/build/sage-5.10/c_lib/include/ntl_wrap.h 2013-01-25 21:54:13.153110794 -0200
@@ -35,8 +35,6 @@ using namespace NTL;
EXTERN void del_charstar(char*);
-EXTERN void setup_NTL_error_callback(void (*function)(const char*, void*), void* context);
-
//////// ZZ //////////
#ifndef __cplusplus
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 2013-01-25 21:53:32.800109249 -0200
+++ sage-5.10/spkg/build/sage-5.10/c_lib/src/ntl_wrap.cpp 2013-01-25 21:53:49.625109893 -0200
@@ -11,13 +11,6 @@ void del_charstar(char* a) {
delete[] a;
}
-
-void setup_NTL_error_callback(void (*function)(const char*, void*), void* context)
-{
- NTL::SetErrorCallbackFunction(function, context);
-}
-
-
//////// ZZ //////////
/* Return value is only valid if the result should fit into an int.
diff -up sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c.orig sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c
--- sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c.orig 2013-01-25 21:54:34.072111596 -0200
+++ sage-5.10/spkg/build/sage-5.10/c_lib/src/stdsage.c 2013-01-25 21:54:49.832112199 -0200
@@ -29,27 +29,12 @@ void init_global_empty_tuple(void) {
global_empty_tuple = PyTuple_New(0);
}
-
-/*
- This function gets called whenever NTL calls Error().
- s is the error message generated by NTL.
- We just copy the error message into a global buffer, and then abort() to run
- the usual interrupt machinery.
- */
-void global_NTL_error_callback(const char* s, void* context)
-{
- set_sage_signal_handler_message(s);
- abort();
-}
-
-
/* This is called once during Sage startup. On some platforms like
* Cygwin, this is also called from init_csage_module(). */
void init_csage() {
init_global_empty_tuple();
init_memory_functions();
setup_sage_signal_handler();
- setup_NTL_error_callback(global_NTL_error_callback, NULL);
}
/* This is called once for every single module that links in stdsage */

198
sagemath.spec
View file

@ -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
Patch27: %{name}-cryptominisat.patch
# Adapt to m4rie 20130416
Patch33: %{name}-m4rie.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
%patch25 -p1
%endif
%patch31 -p1
%patch26 -p1
%patch27 -p1
%patch28 -p1
%if 0%{?fedora} >= 19
%patch32 -p1
%endif
%if 0%{?fedora} == 19
%patch33 -p1
%endif
%if 0%{?fedora} <= 19
%patch34 -p1
%endif
%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@gmail.com> - 5.10-5
- Rebuild with newer rawhide atlas.
* Wed Oct 16 2013 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 5.12-1
- Update to sagemath 5.12.
* Sat Sep 14 2013 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 5.10-4
- Do not hardcode SAGE_BROWSER (#967251)

2
sources
View file

@ -1 +1 @@
bfca3afc9030e63c7e7200287ee0135e sage-5.10.tar
21d62a8a61e351c3c124167b3eead46f sage-5.12.tar