sagemath-7.2-2.parabola1: updating version

6 files changed, 956 insertions, 394 deletions

diff --git a/libre/sagemath/PKGBUILD b/libre/sagemath/PKGBUILD
index 292176d53..e074b7bc0 100644
--- a/libre/sagemath/PKGBUILD
+++ b/libre/sagemath/PKGBUILD
@@ -1,4 +1,4 @@
-# $Id: PKGBUILD 171916 2016-04-26 17:25:19Z arojas $
+# $Id: PKGBUILD 175566 2016-05-17 19:19:04Z arojas $
 # Maintainer (Arch): Evgeniy Alekseev <arcanis.arch at gmail dot com>
 # Maintainer (Arch): Antonio Rojas <arojas@archlinux.org>
 # Contributor (Arch): Daniel Wallace <danielwallace at gtmanfred dot com>
@@ -10,14 +10,14 @@
 # Maintainer: André Silva <emulatorman@parabola.nu>
 
 pkgname=sagemath
-pkgver=7.1
-pkgrel=9.parabola1
+pkgver=7.2
+pkgrel=2.parabola1
 pkgdesc="Free Mathematics Software, free software replacement of Magma, Maple, Mathematica, and Matlab, without nonfree nauty support"
 arch=(i686 x86_64 armv7h)
 url="http://www.sagemath.org"
 license=(GPL)
 depends=(ipython2 cysignals ppl mpfi palp brial singular cliquer maxima-ecl gfan sympow tachyon python2-rpy2
-  python2-matplotlib python2-scipy python2-sympy python2-networkx python2-igraph python2-pillow libgap flintqs lcalc lrcalc lrs arb
+  python2-matplotlib python2-scipy python2-sympy python2-networkx python2-igraph python2-pillow libgap flintqs lcalc lrcalc arb
   eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox gsl rubiks pari-galdata pari-seadata-small planarity rankwidth
   sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
 optdepends=('cython2: to compile cython code' 'jmol: 3D plots' 'sage-notebook: Browser-based (flask) notebook interface'
@@ -26,6 +26,7 @@ optdepends=('cython2: to compile cython code' 'jmol: 3D plots' 'sage-notebook: B
   'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
   'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
   'coxeter3: Coxeter groups implementation' 'cryptominisat: SAT solver' 'gap-data: for computing Galois groups'
+  'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
   'jupyter-notebook: Jupyter notebook interface' 'atlas-lapack: improved performance for some linear algebra operations')
 makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc
   mcqd coxeter3 cryptominisat modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
@@ -34,22 +35,24 @@ replaces=(sage-mathematics)
 provides=(sage-mathematics)
 source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
         pexpect.zip::"https://github.com/pexpect/pexpect/archive/524495960dd8898ddd30f7ba37298de51beee773.zip"
-        anal.h package.patch env.patch paths.patch clean.patch skip-check.patch cython-sys-path.patch
-        disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch gap-4.8.patch)
-md5sums=('c68e846444b9370fe79f43395cdc2725'
+        anal.h env.patch paths.patch clean.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch
+        disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch linbox-1.4.patch ecm-7.patch)
+md5sums=('2afeb8f75a33107fef5d509698c0eabc'
          'a346bb2c0350c1cb17d5325235c5e38a'
          'a906a180d198186a39820b0a2f9a9c63'
-         '9ba81f717ffd4e20b8b2f2a318307488'
          'f6c62f0ccc168c5e6e3dd9d6f73f6389'
-         '0f746ed394fd7eb7a6b3963014976098'
+         '52d30e91110183489f66d7bf73c36c64'
          '6d9ae0978ce6a05a0da2cafdfb178a09'
          '5947a420a0b1483f0cbc74c76895789b'
          'a1bcdd3fe620dbae60ed8b0e98b2ece7'
+         '541988696465f204235d595a349017f3'
+         '9ba81f717ffd4e20b8b2f2a318307488'
          '4eb23a3c7363258bc9ba764d6e5512ba'
          '16b529194c6105c3364127bd8f1efa83'
          'cdcabd475b80afe0534a5621e972736e'
          'ef927896f2071b442b1d07d7e69f5f3a'
-         '8f631f4132d3a97dade07e4c60044aed')
+         '9f1cef3e477bafebe2ad301db56db8a2'
+         '0c9a57d35de80c2cd418ebec912efbbb')
 
 prepare(){
   cd sage-$pkgver
@@ -71,9 +74,6 @@ prepare(){
   patch -p0 -i ../skip-check.patch
 # supress warning about GAP install dir
   sed -e "s|gapdir = os.path.join(SAGE_LOCAL, 'gap', 'latest')|gapdir = '/usr/lib/gap'|" -i src/sage/libs/gap/util.pyx 
-# fix Cremona database detection
-  sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/sage/cremona/cremona.db')|" \
-   -i src/sage/databases/cremona.py
 # find bliss headers
   sed -e 's|graph.hh|bliss/graph.hh|' -i src/sage/graphs/bliss.pyx
 # don't list optional packages when running tests
@@ -84,14 +84,18 @@ prepare(){
   patch -p0 -i ../python-2.7.11.patch
 # search system paths for cython includes
   patch -p1 -i ../cython-sys-path.patch
+# fix regressions with ECM 7
+  patch -p1 -i ../ecm-7.patch
 
 # Upstream patches  
 # fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
 #  patch -p0 -i ../fes02.patch
 # disable fes module, fails to compile
   patch -p0 -i ../disable-fes.patch
-# port to GAP 4.8 http://trac.sagemath.org/ticket/19911
-  patch -p1 -i ../gap-4.8.patch
+# port to new givaro/fflas-ffpack/linbox http://trac.sagemath.org/ticket/17635
+  patch -p1 -i ../linbox-1.4.patch
+# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
+  patch -p1 -i ../is-package-installed.patch
 
 # use python2
   sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
diff --git a/libre/sagemath/ecm-7.patch b/libre/sagemath/ecm-7.patch
new file mode 100644
index 000000000..617e18d98
--- /dev/null
+++ b/libre/sagemath/ecm-7.patch
@@ -0,0 +1,79 @@
+--- a/src/sage/interfaces/ecm.py.orig	2016-05-16 22:18:03.894827738 +0200
++++ b/src/sage/interfaces/ecm.py	2016-05-16 22:19:14.674904932 +0200
+@@ -140,9 +140,6 @@
+         - ``ve`` -- integer `n`. Verbosely show short (`< n`
+           character) expressions on each loop
+ 
+-        - ``cofdec`` -- boolean. Force cofactor output in decimal
+-          (even if expressions are used )
+-
+         - ``B2scale`` -- integer. Multiplies the default B2 value
+ 
+         - ``go`` -- integer. Preload with group order val, which can
+@@ -395,15 +392,15 @@
+             if m is not None:
+                 factor = m.group('factor')
+                 primality = m.group('primality')
+-                assert primality in ['probable prime', 'composite']
+-                result += [(ZZ(factor), primality == 'probable prime')]
++                assert primality in ['prime', 'composite']
++                result += [(ZZ(factor), primality == 'prime')]
+                 continue  # cofactor on the next line
+             m = self._found_cofactor_re.match(line)
+             if m is not None:
+                 cofactor = m.group('cofactor')
+                 primality = m.group('primality')
+-                assert primality in ['Probable prime', 'Composite']
+-                result += [(ZZ(cofactor), primality == 'Probable prime')]
++                assert primality in ['Prime', 'Composite']
++                result += [(ZZ(cofactor), primality == 'Prime')]
+                 # assert len(result) == 2
+                 return result
+         raise ValueError('failed to parse ECM output')
+@@ -501,7 +498,6 @@
+         if factor_digits is not None:
+             B1 = self.recommended_B1(factor_digits)
+         kwds['one'] = True
+-        kwds['cofdec'] = True
+         cmd = self._make_cmd(B1, None, kwds)
+         out = self._run_ecm(cmd, n)
+         return self._parse_output(n, out)
+@@ -828,8 +828,8 @@
+ Step 1 took 12ms
+ Step 2 took 17ms
+ ********** Factor found in step 2: 79792266297612017
+-Found probable prime factor of 17 digits: 79792266297612017
+-Probable prime cofactor 6366805760909027985741435139224233 has 34 digits
++Found prime factor of 17 digits: 79792266297612017
++Prime cofactor 6366805760909027985741435139224233 has 34 digits
+ """
+ 
+ TEST_ECM_OUTPUT_2 = """
+@@ -839,8 +839,8 @@
+ Step 1 took 2ms
+ Step 2 took 3ms
+ ********** Factor found in step 2: 179424673
+-Found probable prime factor of  9 digits: 179424673
+-Probable prime cofactor 179424673 has 9 digits
++Found prime factor of  9 digits: 179424673
++Prime cofactor 179424673 has 9 digits
+ """
+ 
+ TEST_ECM_OUTPUT_3 = """
+@@ -858,7 +858,7 @@
+ Step 1 took 5ms
+ Step 2 took 4ms
+ ********** Factor found in step 2: 197002597249
+-Found probable prime factor of 12 digits: 197002597249
++Found prime factor of 12 digits: 197002597249
+ Composite cofactor 339872432034468861533158743041639097889948066859 has 48 digits
+ """
+ 
+@@ -870,5 +870,5 @@
+ Step 2 took 2ms
+ ********** Factor found in step 2: 265748496095531068869578877937
+ Found composite factor of 30 digits: 265748496095531068869578877937
+-Probable prime cofactor 251951573867253012259144010843 has 30 digits
++Prime cofactor 251951573867253012259144010843 has 30 digits
+ """
+
diff --git a/libre/sagemath/gap-4.8.patch b/libre/sagemath/gap-4.8.patch
deleted file mode 100644
index af8ed5027..000000000
--- a/libre/sagemath/gap-4.8.patch
+++ /dev/null
@@ -1,378 +0,0 @@
-diff --git a/src/ext/gap/console.g b/src/ext/gap/console.g
-index 57043ff..db8b925 100644
---- a/src/ext/gap/console.g
-+++ b/src/ext/gap/console.g
-@@ -1,6 +1,6 @@
--# If we are loaded with a workspace then $SAGE will be defined and in
-+# If we are loaded with a workspace then \$SAGE will be defined and in
- # that case we need to call StartInteract so that the pager will be
- # set correctly.  See trac #5043.
--if IsBound($SAGE) then
--    $SAGE.StartInteract();
-+if IsBound(\$SAGE) then
-+    \$SAGE.StartInteract();
- fi;
-diff --git a/src/ext/gap/sage.g b/src/ext/gap/sage.g
-index 8535b7d..2216fda 100644
---- a/src/ext/gap/sage.g
-+++ b/src/ext/gap/sage.g
-@@ -2,15 +2,15 @@
- #
- # SAGE support utilities to read into the GAP session.
- #
--$SAGE := rec();
-+\$SAGE := rec();
- 
--$SAGE.OldPager := Pager;
-+\$SAGE.OldPager := Pager;
- 
- 
--$SAGE.NewPager :=
-+\$SAGE.NewPager :=
-           function( data )
-     local   str,  lines,  line, fn, start;
--    str := OutputTextFile($SAGE.tempfile,false);
-+    str := OutputTextFile(\$SAGE.tempfile,false);
-     start := 1;
-     if IsRecord(data) then
-         lines := data.lines;
-@@ -30,38 +30,38 @@ $SAGE.NewPager :=
-     Print("Page from ",start,"\n");
- end;
- 
--$SAGE.StartInteract := function()
-+\$SAGE.StartInteract := function()
-     MakeReadWriteGlobal("Pager");
--    Pager := $SAGE.OldPager;
--    HELP_VIEWER_INFO.screen.show := $SAGE.OldPager;
-+    Pager := \$SAGE.OldPager;
-+    HELP_VIEWER_INFO.screen.show := \$SAGE.OldPager;
-     MakeReadOnlyGlobal("Pager");
- end;
- 
- 
--$SAGE.StopInteract := function()
-+\$SAGE.StopInteract := function()
-     MakeReadWriteGlobal("Pager");
--    Pager := $SAGE.NewPager;
--    HELP_VIEWER_INFO.screen.show := $SAGE.NewPager;
-+    Pager := \$SAGE.NewPager;
-+    HELP_VIEWER_INFO.screen.show := \$SAGE.NewPager;
-     MakeReadOnlyGlobal("Pager");
- end;
- 
- 
--$SAGE.StopInteract();
-+\$SAGE.StopInteract();
- 
--#$SAGE.ErrorHandler := function(m,a,m2,mode)
-+#\$SAGE.ErrorHandler := function(m,a,m2,mode)
- #    PrintTo("*errout*", m);
- #    if a <> fail then
- #        PrintTo("*errout*",a);
- #    fi;
--#    SetErrorHandler($SAGE.ErrorHandler);
-+#    SetErrorHandler(\$SAGE.ErrorHandler);
- #    return true;
- #end;
- 
--#SetErrorHandler($SAGE.ErrorHandler);
-+#SetErrorHandler(\$SAGE.ErrorHandler);
- 
- SetAllInfoLevels(0);
- 
--$SAGE.OperationsAdmittingFirstArgument := function(obj)
-+\$SAGE.OperationsAdmittingFirstArgument := function(obj)
-     local   hits,  myflags,  i,  flagss,  flags;
-     hits := [];
-     myflags := FlagsType(TypeObj(obj));
-@@ -78,7 +78,7 @@ $SAGE.OperationsAdmittingFirstArgument := function(obj)
- end;
- 
- 
--$SAGE.CleanOperationName := function(name)
-+\$SAGE.CleanOperationName := function(name)
-     local   lt,  ls;
-     lt := Length("Tester(");
-     if Length(name) > lt and name{[1..lt]} = "Tester(" then
-@@ -91,7 +91,7 @@ $SAGE.CleanOperationName := function(name)
-     return name;
- end;
- 
--$SAGE.HasAtLeastOneMethodAsFirstArgument := function(op,obj)
-+\$SAGE.HasAtLeastOneMethodAsFirstArgument := function(op,obj)
-     local   t,  f,  n,  meths,  i;
-     t := TypeObj(obj);
-     f := FlagsType(t);
-@@ -107,11 +107,11 @@ $SAGE.HasAtLeastOneMethodAsFirstArgument := function(op,obj)
- end;
- 
- 
--$SAGE.PlausibleTabCompletionsForSage := function(o)
-+\$SAGE.PlausibleTabCompletionsForSage := function(o)
-     local   ops,  opnames;
--    ops := Filtered($SAGE.OperationsAdmittingFirstArgument(o), op ->
--                   $SAGE.HasAtLeastOneMethodAsFirstArgument(op,o));
--    opnames := List(ops, op -> $SAGE.CleanOperationName(NameFunction(op)));
-+    ops := Filtered(\$SAGE.OperationsAdmittingFirstArgument(o), op ->
-+                   \$SAGE.HasAtLeastOneMethodAsFirstArgument(op,o));
-+    opnames := List(ops, op -> \$SAGE.CleanOperationName(NameFunction(op)));
-     return Concatenation(opnames, GLOBAL_FUNCTION_NAMES);
- end;
- 
-diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 92a4393..fd856ef 100644
---- a/src/sage/groups/finitely_presented.py
-+++ b/src/sage/groups/finitely_presented.py
-@@ -1168,9 +1168,7 @@ class FinitelyPresentedGroup(GroupMixinLibGAP, UniqueRepresentation,
-         You can attempt to reduce the presentation of the output group::
- 
-             sage: D = C2.semidirect_product(C8, hom); D
--            Finitely presented group < a, b, c, d |
--             a^2, b^-1*a^-1*b*a*d^-1*c^-1, c^-1*a^-1*c*a*d^-1, d^-1*a^-1*d*a,
--             b^2*c^-1, c^-1*b^-1*c*b, d^-1*b^-1*d*b, c^2*d^-1, d^-1*c^-1*d*c, d^2 >
-+            Finitely presented group < a, b | a^2, b^8, a^-1*b*a*b >
-             sage: D = C2.semidirect_product(C8, hom, reduced=True); D
-             Finitely presented group < a, b | a^2, (a*b)^2, b^8 >
- 
-@@ -1178,10 +1176,9 @@ class FinitelyPresentedGroup(GroupMixinLibGAP, UniqueRepresentation,
-             sage: C4 = groups.presentation.Cyclic(4)
-             sage: hom = (C3.gens(), [(C4.gens(), C4.gens())])
-             sage: C3.semidirect_product(C4, hom)
--            Finitely presented group < a, b, c |
--             a^3, b^-1*a^-1*b*a, c^-1*a^-1*c*a, b^2*c^-1, c^-1*b^-1*c*b, c^2 >
-+            Finitely presented group < a, b | a^3, b^4, a^-1*b*a*b^-1 >
-             sage: D = C3.semidirect_product(C4, hom, reduced=True); D
--            Finitely presented group < a, b | a^3, b^4, b^-1*a^-1*b*a >
-+            Finitely presented group < a, b | a^3, b^4, a^-1*b*a*b^-1 >
-             sage: D.as_permutation_group().is_cyclic()
-             True
- 
-@@ -1193,9 +1190,7 @@ class FinitelyPresentedGroup(GroupMixinLibGAP, UniqueRepresentation,
-             sage: C12 = groups.presentation.Cyclic(12)
-             sage: hom = (C5.gens(), [(C12.gens(), C12.gens())])
-             sage: sp = C5.semidirect_product(C12, hom, check=False); sp
--            Finitely presented group < a, b, c, d |
--             a^5, b^-1*a^-1*b*a, c^-1*a^-1*c*a, d^-1*a^-1*d*a, b^2*d^-1,
--             c^-1*b^-1*c*b, d^-1*b^-1*d*b, c^3, d^-1*c^-1*d*c, d^2 >
-+            Finitely presented group < a, b | a^5, b^12, a^-1*b*a*b^-1 >
-             sage: sp.as_permutation_group().is_cyclic(), sp.order()
-             (True, 60)
- 
-diff --git a/src/sage/groups/matrix_gps/matrix_group.py b/src/sage/groups/matrix_gps/matrix_group.py
-index 698a587..3e200e6 100644
---- a/src/sage/groups/matrix_gps/matrix_group.py
-+++ b/src/sage/groups/matrix_gps/matrix_group.py
-@@ -584,19 +584,19 @@ class MatrixGroup_gap(GroupMixinLibGAP, MatrixGroup_generic, ParentLibGAP):
-             sage: i = iter(GL(6,5))
-             sage: [ next(i) for j in range(8) ]
-             [
--            [1 0 0 0 0 0]  [4 0 0 0 0 1]  [0 4 0 0 0 0]  [0 4 0 0 0 0]
--            [0 1 0 0 0 0]  [4 0 0 0 0 0]  [0 0 4 0 0 0]  [0 0 4 0 0 0]
--            [0 0 1 0 0 0]  [0 4 0 0 0 0]  [0 0 0 4 0 0]  [0 0 0 4 0 0]
--            [0 0 0 1 0 0]  [0 0 4 0 0 0]  [0 0 0 0 4 0]  [0 0 0 0 4 0]
--            [0 0 0 0 1 0]  [0 0 0 4 0 0]  [0 0 0 0 0 4]  [0 0 0 0 0 4]
--            [0 0 0 0 0 1], [0 0 0 0 4 0], [1 4 0 0 0 0], [2 4 0 0 0 0],
-+            [1 0 0 0 0 0]  [2 0 0 0 0 0]  [3 0 0 0 0 0]  [3 2 0 0 0 0]
-+            [0 1 0 0 0 0]  [0 1 0 0 0 0]  [0 1 0 0 0 0]  [0 1 0 0 0 0]
-+            [0 0 1 0 0 0]  [0 0 1 0 0 0]  [0 0 1 0 0 0]  [0 0 1 0 0 0]
-+            [0 0 0 1 0 0]  [0 0 0 1 0 0]  [0 0 0 1 0 0]  [0 0 0 1 0 0]
-+            [0 0 0 0 1 0]  [0 0 0 0 1 0]  [0 0 0 0 1 0]  [0 0 0 0 1 0]
-+            [0 0 0 0 0 1], [0 0 0 0 0 1], [0 0 0 0 0 1], [0 0 0 0 0 1],
-             <BLANKLINE>
--            [3 0 0 0 0 1]  [4 0 0 1 3 3]  [0 0 0 2 0 0]  [1 0 0 0 4 4]
--            [3 0 0 0 0 0]  [4 0 0 0 3 3]  [0 0 0 0 4 0]  [1 0 0 0 0 4]
--            [0 4 0 0 0 0]  [3 0 0 0 0 1]  [2 2 0 0 0 2]  [1 0 0 0 0 0]
--            [0 0 4 0 0 0]  [3 0 0 0 0 0]  [1 4 0 0 0 0]  [0 1 0 0 0 0]
--            [0 0 0 4 0 0]  [0 4 0 0 0 0]  [0 2 4 0 0 0]  [0 0 1 0 0 0]
--            [4 0 0 0 2 3], [2 0 3 4 4 4], [0 0 1 4 0 0], [0 0 0 1 0 0]
-+            [2 1 0 0 0 0]  [3 3 0 2 3 0]  [2 4 0 1 4 0]  [1 2 4 1 0 3]
-+            [0 1 0 0 0 0]  [0 1 0 0 0 0]  [0 1 0 0 0 0]  [0 1 0 0 0 0]
-+            [0 0 1 0 0 0]  [0 0 1 0 0 0]  [0 0 1 0 0 0]  [0 0 1 0 0 0]
-+            [0 0 0 1 0 0]  [0 0 0 1 0 0]  [0 0 0 1 0 0]  [0 0 0 1 0 0]
-+            [0 0 0 0 1 0]  [0 0 0 0 1 0]  [0 0 0 0 1 0]  [0 0 0 0 1 0]
-+            [0 0 0 0 0 1], [0 0 0 0 0 1], [0 0 0 0 0 1], [0 0 0 0 0 1]
-             ]
- 
-         This is the direct computation in GAP, which will just run
-diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
-index 2a426f1..5295949 100644
---- a/src/sage/groups/perm_gps/permgroup.py
-+++ b/src/sage/groups/perm_gps/permgroup.py
-@@ -1548,18 +1548,23 @@ class PermutationGroup_generic(group.FiniteGroup):
- 
-         EXAMPLES::
- 
--            sage: SymmetricGroup(10).stabilizer(4)._order()
-+            sage: G = SymmetricGroup(10).subgroup([(i, 10) for i in range(1, 10) if i != 4])
-+            sage: G._order()
-             362880
--            sage: SymmetricGroup(10).stabilizer(4).stabilizer(5)._order()
--            40320
--            sage: SymmetricGroup(200).stabilizer(100)._order() == factorial(199) # this should be very fast
--            True
- 
-         TESTS::
- 
-             sage: [SymmetricGroup(n).stabilizer(1)._gap_().Size() for n in [4..10]]
-             [6, 24, 120, 720, 5040, 40320, 362880]
--            sage: [SymmetricGroup(n).stabilizer(1)._order() for n in [4..10]]
-+            sage: special_gens = [
-+            ....:     [(3,4), (2,4)],
-+            ....:     [(4,5), (3,5), (2,5)],
-+            ....:     [(5,6), (4,6), (3,6), (2,6)],
-+            ....:     [(6,7), (5,7), (4,7), (3,7), (2,7)],
-+            ....:     [(7,8), (6,8), (5,8), (4,8), (3,8), (2,8)],
-+            ....:     [(8,9), (7,9), (6,9), (5,9), (4,9), (3,9), (2,9)],
-+            ....:     [(9,10), (8,10), (7,10), (6,10), (5,10), (4,10), (3,10), (2,10)]]
-+            sage: [SymmetricGroup(n).subgroup(gen)._order() for gen in special_gens]
-             [6, 24, 120, 720, 5040, 40320, 362880]
-         """
-         gens = self.gens()
-diff --git a/src/sage/interfaces/expect.py b/src/sage/interfaces/expect.py
-index 756f701..88dbf82 100644
---- a/src/sage/interfaces/expect.py
-+++ b/src/sage/interfaces/expect.py
-@@ -1423,13 +1423,13 @@ class StdOutContext:
-         return self.interface
- 
-     def __exit__(self, typ, value, tb):
--        """
-+        r"""
-         EXAMPLE::
- 
-             sage: from sage.interfaces.expect import StdOutContext
-             sage: with StdOutContext(gap):
-             ....:     gap('1+1')
--            $sage...
-+            \$sage...
-         """
-         if self.silent:
-             return
-diff --git a/src/sage/interfaces/gap.py b/src/sage/interfaces/gap.py
-index 1f446aa..198fe84 100644
---- a/src/sage/interfaces/gap.py
-+++ b/src/sage/interfaces/gap.py
-@@ -716,7 +716,7 @@ class Gap_generic(ExtraTabCompletion, Expect):
-             sage: gap.eval('quit;')
-             ''
-             sage: a = gap(3)
--            ** Gap crashed or quit executing '$sage...:=3;;' **
-+            ** Gap crashed or quit executing '\$sage...:=3;;' **
-             Restarting Gap and trying again
-             sage: a
-             3
-@@ -858,7 +858,7 @@ class Gap_generic(ExtraTabCompletion, Expect):
-         EXAMPLES::
- 
-             sage: print gap.version()
--            4.7...
-+            4.8...
-         """
-         return self.eval('VERSION')[1:-1]
- 
-@@ -1162,25 +1162,29 @@ class Gap(Gap_generic):
-         return reduce_load_GAP, tuple([])
- 
-     def _next_var_name(self):
--        """
-+        r"""
-         Returns the next unused variable name.
- 
-+        Note that names starting with dollar signs are valid GAP
-+        identifiers, but need to be escaped with a backslash starting
-+        with GAP-4.8.
-+
-         EXAMPLES::
- 
-             sage: g = Gap()
-             sage: g._next_var_name()
--            '$sage1'
-+            '\\$sage1'
-             sage: g(2)^2
-             4
-             sage: g._next_var_name()
--            '$sage...'
-+            '\\$sage...'
-         """
-         if len(self._available_vars) != 0:
-             v = self._available_vars[0]
-             del self._available_vars[0]
-             return v
-         self.__seq += 1
--        return '$sage%s'%self.__seq
-+        return r'\$sage%s'%self.__seq
- 
-     def _start(self):
-         """
-@@ -1324,7 +1328,7 @@ class Gap(Gap_generic):
-         else:
-             tmp_to_use = self._local_tmpfile()
-         self.eval('SetGAPDocTextTheme("none")')
--        self.eval('$SAGE.tempfile := "%s";'%tmp_to_use)
-+        self.eval(r'\$SAGE.tempfile := "%s";'%tmp_to_use)
-         line = Expect.eval(self, "? %s"%s)
-         Expect.eval(self, "? 1")
-         match = re.search("Page from (\d+)", line)
-@@ -1384,7 +1388,7 @@ class Gap(Gap_generic):
-             sage: gap._pre_interact()
-             sage: gap._post_interact()
-         """
--        self._eval_line("$SAGE.StartInteract();")
-+        self._eval_line(r'\$SAGE.StartInteract();')
- 
-     def _post_interact(self):
-         """
-@@ -1393,7 +1397,7 @@ class Gap(Gap_generic):
-             sage: gap._pre_interact()
-             sage: gap._post_interact()
-         """
--        self._eval_line("$SAGE.StopInteract();")
-+        self._eval_line(r'\$SAGE.StopInteract();')
- 
-     def _eval_line_using_file(self, line):
-         i = line.find(':=')
-@@ -1641,7 +1645,7 @@ class GapElement(GapElement_generic):
-         """
-         from sage.misc.misc import uniq
-         P = self.parent()
--        v = P.eval('$SAGE.OperationsAdmittingFirstArgument(%s)'%self.name())
-+        v = P.eval(r'\$SAGE.OperationsAdmittingFirstArgument(%s)'%self.name())
-         v = v.replace('Tester(','').replace('Setter(','').replace(')','').replace('\n', '')
-         v = v.split(',')
-         v = [ oper.split('"')[1] for oper in v ]
-diff --git a/src/sage/libs/gap/gap_includes.pxd b/src/sage/libs/gap/gap_includes.pxd
-index bd945c7..fa23ba5 100644
---- a/src/sage/libs/gap/gap_includes.pxd
-+++ b/src/sage/libs/gap/gap_includes.pxd
-@@ -131,7 +131,7 @@ cdef extern from "gap/objects.h":
-     cdef int libGAP_LAST_TESTING_TNUM
- 
- cdef extern from "gap/read.h":
--    void* libGAP_ReadEvalCommand(libGAP_Obj context)
-+    void* libGAP_ReadEvalCommand(libGAP_Obj context, libGAP_UInt *dualSemicolon)
-     void* libGAP_ReadEvalFile()
-     void* libGAP_ReadEvalResult
-     bint libGAP_READ_ERROR()
-diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx
-index 52a75be..d62b8e9 100644
---- a/src/sage/libs/gap/util.pyx
-+++ b/src/sage/libs/gap/util.pyx
-@@ -280,7 +280,7 @@ cdef libGAP_Obj gap_eval(str gap_string) except? NULL:
-         libgap_start_interaction(cmd)
-         try:
-             sig_on()
--            status = libGAP_ReadEvalCommand(libGAP_BottomLVars)
-+            status = libGAP_ReadEvalCommand(libGAP_BottomLVars, NULL)
-             if status != libGAP_STATUS_END:
-                 libgap_call_error_handler()
-             sig_off()
-@@ -464,7 +464,7 @@ def command(command_string):
-         libgap_start_interaction(cmd)
-         try:
-             sig_on()
--            status = libGAP_ReadEvalCommand(libGAP_BottomLVars)
-+            status = libGAP_ReadEvalCommand(libGAP_BottomLVars, NULL)
-             if status != libGAP_STATUS_END:
-                 libgap_call_error_handler()
-             sig_off()
diff --git a/libre/sagemath/is-package-installed.patch b/libre/sagemath/is-package-installed.patch
new file mode 100644
index 000000000..3b6efc22b
--- /dev/null
+++ b/libre/sagemath/is-package-installed.patch
@@ -0,0 +1,387 @@
+diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
+index 0a5f794..2969d92 100644
+--- a/src/sage/databases/cremona.py
++++ b/src/sage/databases/cremona.py
+@@ -52,7 +52,6 @@ from sage.misc.prandom import randint
+ 
+ import sage.schemes.elliptic_curves.constructor as elliptic
+ from sql_db import SQLDatabase, verify_column
+-from sage.misc.package import is_package_installed
+ from sage.env import SAGE_SHARE
+ from sage.misc.all import walltime
+ 
+@@ -827,7 +826,7 @@ class MiniCremonaDatabase(SQLDatabase):
+             if N < self.largest_conductor():
+                 message = "There is no elliptic curve with label " + label \
+                     + " in the database"
+-            elif is_package_installed('database_cremona_ellcurve'):
++            elif os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+                 message = "There is no elliptic curve with label " + label \
+                     + " in the currently available databases"
+             else:
+@@ -1676,7 +1675,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+     if name is None and not set_global:
+         return _db
+     if set_global and name is None:
+-        if is_package_installed('database_cremona_ellcurve'):
++        if os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+             name = 'cremona'
+         else:
+             name = 'cremona mini'
+diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
+index b917d2a..80fb20c 100644
+--- a/src/sage/game_theory/normal_form_game.py
++++ b/src/sage/game_theory/normal_form_game.py
+@@ -612,8 +612,9 @@ from sage.rings.all import QQ
+ from sage.structure.sage_object import SageObject
+ from sage.matrix.constructor import matrix
+ from sage.matrix.constructor import vector
+-from sage.misc.package import is_package_installed
+ from sage.misc.temporary_file import tmp_filename
++import os
++from sage.env import SAGE_LOCAL
+ 
+ try:
+     from gambit import Game
+@@ -1315,13 +1316,13 @@ class NormalFormGame(SageObject, MutableMapping):
+             raise ValueError("utilities have not been populated")
+ 
+         if not algorithm:
+-            if is_package_installed('lrslib'):
++            if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+                 algorithm = "lrs"
+             else:
+                 algorithm = "enumeration"
+ 
+         if algorithm == "lrs":
+-            if not is_package_installed('lrslib'):
++            if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+                 raise NotImplementedError("lrslib is not installed")
+ 
+             return self._solve_lrs(maximization)
+diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
+index 2f58d8b..eb519a2 100644
+--- a/src/sage/geometry/polyhedron/base.py
++++ b/src/sage/geometry/polyhedron/base.py
+@@ -20,7 +20,6 @@ import six
+ from sage.structure.element import Element, coerce_binop, is_Vector
+ 
+ from sage.misc.all import cached_method, prod
+-from sage.misc.package import is_package_installed
+ 
+ from sage.rings.all import QQ, ZZ
+ from sage.rings.real_double import RDF
+@@ -3690,7 +3689,9 @@ class Polyhedron_base(Element):
+ 
+              David Avis's lrs program.
+         """
+-        if not is_package_installed('lrslib'):
++        import os
++        from sage.env import SAGE_LOCAL
++        if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')) != True:
+             raise NotImplementedError('You must install the optional lrslib package '
+                                        'for this function to work')
+ 
+diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
+index e80f2a5..04cd9ce 100644
+--- a/src/sage/graphs/generators/classical_geometries.py
++++ b/src/sage/graphs/generators/classical_geometries.py
+@@ -1287,10 +1287,9 @@ def CossidentePenttilaGraph(q):
+         raise ValueError('q(={}) must be an odd prime power'.format(q))
+ 
+     from sage.libs.gap.libgap import libgap
+-    from sage.misc.package import is_package_installed, PackageNotFoundError
++    from sage.interfaces.gap import gap
+ 
+-    if not is_package_installed('gap_packages'):
+-        raise PackageNotFoundError('gap_packages')
++    gap.load_package("grape")
+ 
+     adj_list=libgap.function_factory("""function(q)
+         local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -7833,7 +7833,6 @@ class GenericGraph(GenericGraph_pyx):
+            sage: abs(flow_ff-flow_igraph) < 0.00001         # optional python_igraph
+            True
+         """
+-        from sage.misc.package import is_package_installed
+         self._scream_if_not_simple(allow_loops=True)
+         if vertex_bound and algorithm in ["FF", "igraph"]:
+             raise ValueError("This method does not support both " +
+@@ -7851,10 +7850,12 @@ class GenericGraph(GenericGraph_pyx):
+         if algorithm is None:
+             if vertex_bound:
+                 algorithm = "LP"
+-            elif is_package_installed("python_igraph"):
+-                algorithm = "igraph"
+             else:
+-                algorithm = "FF"
++                algorithm = "igraph"
++                try:
++                    import igraph
++                except ImportError:
++                    algorithm = "FF"
+ 
+         if (algorithm == "FF"):
+             return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+@@ -20134,17 +20135,22 @@ class GenericGraph(GenericGraph_pyx):
+             Subgroup of (Permutation Group with generators [(0,7)(1,4)(2,3)(6,8)]) generated by [(0,7)(1,4)(2,3)(6,8)]]
+ 
+         """
+-        from sage.misc.package import is_package_installed
++        has_bliss=True
++        try:
++            from sage.graphs.bliss import automorphism_group
++        except ImportError:
++            has_bliss=False
++
+         if (algorithm == 'bliss'           or   # explicit choice from the user; or
+             (algorithm is None             and  # by default
+              not edge_labels               and
+-             is_package_installed('bliss'))):
++             has_bliss)):
++
++            if (not has_bliss):
++                raise NotImplementedError("you need to install bliss or set algorithm=sage to use this command")
++
+             if edge_labels:
+                 raise ValueError("bliss cannot be used when edge_labels is True")
+-            try:
+-                from sage.graphs.bliss import automorphism_group
+-            except ImportError:
+-                raise ImportError("You must install the 'bliss' package to run this command.")
+ 
+             A = automorphism_group(self, partition)
+ 
+@@ -20786,17 +20792,22 @@ class GenericGraph(GenericGraph_pyx):
+             True
+ 
+         """
+-        from sage.misc.package import is_package_installed
++        has_bliss=True
++        try:
++            from sage.graphs.bliss import canonical_form
++        except ImportError:
++            has_bliss=False
++
+         if (algorithm == 'bliss'           or  # explicit request; or
+             (algorithm is None             and # default choice
+-             is_package_installed('bliss') and
++	     has_bliss                     and
+              not edge_labels)):
++
++            if (not has_bliss):
++                raise NotImplementedError("you need to install bliss or set algorithm=sage to use this command")
++
+             if edge_labels:
+                 raise ValueError("bliss cannot be used when edge_labels is True")
+-            try:
+-                from sage.graphs.bliss import canonical_form
+-            except ImportError:
+-                raise ImportError("You must install the 'bliss' package to run this command.")
+             return canonical_form(self, partition, return_graph, certify)
+ 
+         if (algorithm is not None and
+diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
+index 5919ab3..1766796 100644
+--- a/src/sage/graphs/graph_generators.py
++++ b/src/sage/graphs/graph_generators.py
+@@ -1192,8 +1192,9 @@ class GraphGenerators():
+         .. [buckygen] \G. Brinkmann, J. Goedgebeur and B.D. McKay, Generation of Fullerenes,
+           Journal of Chemical Information and Modeling, 52(11):2910-2918, 2012.
+         """
+-        from sage.misc.package import is_package_installed
+-        if not is_package_installed("buckygen"):
++        import os
++        from sage.env import SAGE_LOCAL
++        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'buckygen')):
+             raise TypeError("the optional buckygen package is not installed")
+ 
+         # number of vertices should be positive
+@@ -1277,8 +1278,9 @@ class GraphGenerators():
+         .. [benzene] \G. Brinkmann, G. Caporossi and P. Hansen, A Constructive Enumeration of Fusenes and Benzenoids,
+           Journal of Algorithms, 45:155-166, 2002.
+         """
+-        from sage.misc.package import is_package_installed
+-        if not is_package_installed("benzene"):
++        import os
++        from sage.env import SAGE_LOCAL
++        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'benzene')):
+             raise TypeError("the optional benzene package is not installed")
+ 
+         # number of hexagons should be positive
+@@ -1430,8 +1432,9 @@ class GraphGenerators():
+         .. [plantri] \G. Brinkmann and B.D. McKay, Fast generation of planar graphs,
+            MATCH-Communications in Mathematical and in Computer Chemistry, 58(2):323-357, 2007.
+         """
+-        from sage.misc.package import is_package_installed
+-        if not is_package_installed("plantri"):
++        import os
++        from sage.env import SAGE_LOCAL
++        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+             raise TypeError("the optional plantri package is not installed")
+ 
+         # number of vertices should be positive
+@@ -1629,8 +1632,9 @@ class GraphGenerators():
+             sage: [g.size() for g in graphs.triangulations(6, minimum_connectivity=3)] # optional plantri
+             [12, 12]
+         """
+-        from sage.misc.package import is_package_installed
+-        if not is_package_installed("plantri"):
++        import os
++        from sage.env import SAGE_LOCAL
++        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+             raise TypeError("the optional plantri package is not installed")
+ 
+         # number of vertices should be positive
+@@ -1783,8 +1787,9 @@ class GraphGenerators():
+             sage: [len(g) for g in graphs.quadrangulations(12, no_nonfacial_quadrangles=True, dual=True)]  # optional plantri
+             [10, 10]
+         """
+-        from sage.misc.package import is_package_installed
+-        if not is_package_installed("plantri"):
++        import os
++        from sage.env import SAGE_LOCAL
++        if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+             raise TypeError("the optional plantri package is not installed")
+ 
+         # number of vertices should be positive
+diff --git a/src/sage/graphs/lovasz_theta.py b/src/sage/graphs/lovasz_theta.py
+index 0d345c9..60948d2 100644
+--- a/src/sage/graphs/lovasz_theta.py
++++ b/src/sage/graphs/lovasz_theta.py
+@@ -65,10 +65,9 @@ def lovasz_theta(graph):
+     from sage.misc.temporary_file import tmp_filename
+     import os, subprocess
+     from sage.env import SAGE_LOCAL
+-    from sage.misc.package import is_package_installed, PackageNotFoundError
+ 
+-    if not is_package_installed('csdp'):
+-        raise PackageNotFoundError("csdp")
++    if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'theta')):
++        raise NotImplementedError("You must install csdp before using this function")
+ 
+     g = graph.relabel(inplace=False, perm=range(1,n+1)).networkx_graph()
+     tf_name = tmp_filename()
+diff --git a/src/sage/groups/generic.py b/src/sage/groups/generic.py
+index c801636..f43e6d9 100644
+--- a/src/sage/groups/generic.py
++++ b/src/sage/groups/generic.py
+@@ -1396,15 +1396,15 @@ def structure_description(G, latex=False):
+         sage: groups.matrix.GL(4,2).structure_description() # optional - database_gap
+         'A8'
+     """
+-    import re
+-    from sage.misc.package import is_package_installed
++    import re, os
++    from sage.env import SAGE_LOCAL
+     def correct_dihedral_degree(match):
+         return "%sD%d" % (match.group(1), int(match.group(2))/2)
+ 
+     try:
+         description = str(G._gap_().StructureDescription())
+     except RuntimeError:
+-        if not is_package_installed('database_gap'):
++	if not os.path.isfile(os.path.join(SAGE_LOCAL, "gap", "latest", "small", "readsml.g")):
+             raise RuntimeError("You must install the optional database_gap package first.")
+         raise
+ 
+diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
+index e42db61..d4d5684 100644
+--- a/src/sage/groups/perm_gps/permgroup.py
++++ b/src/sage/groups/perm_gps/permgroup.py
+@@ -143,7 +143,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
+ from sage.groups.abelian_gps.abelian_group import AbelianGroup
+ from sage.misc.cachefunc import cached_method
+ from sage.groups.class_function import ClassFunction
+-from sage.misc.package import is_package_installed
+ from sage.sets.finite_enumerated_set import FiniteEnumeratedSet
+ from sage.categories.all import FiniteEnumeratedSets
+ from sage.groups.conjugacy_classes import ConjugacyClassGAP
+@@ -188,8 +187,6 @@ def hap_decorator(f):
+     """
+     @wraps(f)
+     def wrapped(self, n, p=0):
+-        if not is_package_installed('gap_packages'):
+-            raise RuntimeError("You must install the optional gap_packages package.")
+         load_hap()
+         from sage.arith.all import is_prime
+         if not (p == 0 or is_prime(p)):
+@@ -1681,9 +1678,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+         try:
+             return [Integer(n) for n in self._gap_().IdGroup()]
+         except RuntimeError:
+-            if not is_package_installed('database_gap'):
+-                raise RuntimeError("You must install the optional database_gap package first.")
+-            raise
++            raise RuntimeError("You must install the optional gap_packages package.")
+ 
+     def id(self):
+         """
+@@ -1734,9 +1729,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+         try:
+             return Integer(self._gap_().PrimitiveIdentification())
+         except RuntimeError:
+-            if not is_package_installed('database_gap'):
+-                raise RuntimeError("You must install the optional database_gap package first.")
+-            raise
++            raise RuntimeError("You must install the optional gap_packages package.")
+ 
+     def center(self):
+         """
+@@ -4112,8 +4105,6 @@ class PermutationGroup_generic(group.FiniteGroup):
+         - David Joyner and Graham Ellis
+ 
+         """
+-        if not is_package_installed('gap_packages'):
+-            raise RuntimeError("You must install the optional gap_packages package.")
+         load_hap()
+         from sage.arith.all import is_prime
+         if not (p == 0 or is_prime(p)):
+diff --git a/src/sage/misc/all.py b/src/sage/misc/all.py
+index 90e6985..21daeb0 100644
+--- a/src/sage/misc/all.py
++++ b/src/sage/misc/all.py
+@@ -52,11 +52,6 @@ from fpickle import pickle_function, unpickle_function
+ 
+ from dist import install_scripts
+ 
+-from package import (install_package,
+-        installed_packages, is_package_installed,
+-        standard_packages, optional_packages, experimental_packages,
+-        upgrade, package_versions)
+-
+ from pager import pager
+ 
+ lazy_import('sage.misc.sagedoc', ['browse_sage_doc',
+diff --git a/src/sage/rings/polynomial/multi_polynomial_sequence.py b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+index da41cb0..49cae0b 100644
+--- a/src/sage/rings/polynomial/multi_polynomial_sequence.py
++++ b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+@@ -158,7 +158,6 @@ from sage.misc.cachefunc import cached_method
+ 
+ from types import GeneratorType
+ from sage.misc.converting_dict import KeyConvertingDict
+-from sage.misc.package import is_package_installed
+ 
+ from sage.structure.sequence import Sequence, Sequence_generic
+ 
+@@ -1428,10 +1427,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
+ 
+         if S != []:
+             if algorithm == "exhaustive_search":
+-                if not is_package_installed('fes'):
+-                    from sage.misc.package import PackageNotFoundError
+-                    raise PackageNotFoundError("fes")
+-                from sage.libs.fes import exhaustive_search
++                try:
++                    from sage.libs.fes import exhaustive_search
++                except ImportError:
++                    raise RuntimeError("You must install the optional fes package.")
++
+                 solutions = exhaustive_search(S, max_sols=n, verbose=verbose, **kwds)
+ 
+             elif algorithm == "polybori":
diff --git a/libre/sagemath/linbox-1.4.patch b/libre/sagemath/linbox-1.4.patch
new file mode 100644
index 000000000..5897df763
--- /dev/null
+++ b/libre/sagemath/linbox-1.4.patch
@@ -0,0 +1,470 @@
+diff --git a/src/module_list.py b/src/module_list.py
+index a49ed36..7798cb8 100644
+--- a/src/module_list.py
++++ b/src/module_list.py
+@@ -27,6 +27,18 @@ lapack_libs = list(lapack_pc['libraries'])
+ lapack_library_dirs = list(lapack_pc['library_dirs'])
+ lapack_include_dirs = list(lapack_pc['include_dirs'])
+ 
++# FFLAS-FFPACK
++fflas_ffpack_pc = pkgconfig.parse('fflas-ffpack')
++fflas_ffpack_libs = list(fflas_ffpack_pc['libraries'])
++fflas_ffpack_library_dirs = list(fflas_ffpack_pc['library_dirs'])
++fflas_ffpack_cflags = pkgconfig.cflags('fflas-ffpack').split()
++
++# Givaro
++givaro_pc = pkgconfig.parse('givaro')
++givaro_libs = list(givaro_pc['libraries'])
++givaro_library_dirs = list(givaro_pc['library_dirs'])
++givaro_cflags = pkgconfig.cflags('givaro').split()
++
+ # GNU Scientific Library
+ # Note we replace the built-in gslcblas with the above cblas
+ gsl_pc = pkgconfig.parse('gsl')
+@@ -40,6 +52,12 @@ gd_libs = list(gd_pc['libraries'])
+ gd_library_dirs = list(gd_pc['library_dirs'])
+ gd_include_dirs = list(gd_pc['include_dirs'])
+ 
++# LinBox
++linbox_pc = pkgconfig.parse('linbox')
++linbox_libs = list(linbox_pc['libraries'])
++linbox_library_dirs = list(linbox_pc['library_dirs'])
++linbox_cflags = pkgconfig.cflags('linbox').split()
++
+ # PNG image library
+ png_pc = pkgconfig.parse('libpng')
+ png_libs = list(png_pc['libraries'])
+@@ -58,9 +76,18 @@ zlib_include_dirs = list(zlib_pc['include_dirs'])
+ #########################################################
+ 
+ aliases = dict(
++    FFLASFFPACK_CFLAGS=fflas_ffpack_cflags,
++    FFLASFFPACK_LIBRARIES=fflas_ffpack_libs,
++    FFLASFFPACK_LIBDIR=fflas_ffpack_library_dirs,
++    GIVARO_CFLAGS=givaro_cflags,
++    GIVARO_LIBRARIES=givaro_libs,
++    GIVARO_LIBDIR=givaro_library_dirs,
+     GSL_LIBRARIES=gsl_libs,
+     GSL_LIBDIR=gsl_library_dirs,
+     GSL_INCDIR=gsl_include_dirs,
++    LINBOX_CFLAGS=linbox_cflags,
++    LINBOX_LIBRARIES=linbox_libs,
++    LINBOX_LIBDIR=linbox_library_dirs,
+ )
+ 
+ #########################################################
+@@ -85,12 +112,6 @@ except ValueError:
+ singular_libs = ['singular', 'flint', 'ntl', 'gmpxx', 'gmp', 'readline', 'm']
+ 
+ #########################################################
+-### Givaro flags
+-#########################################################
+-
+-givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+-
+-#########################################################
+ ### Library order
+ #########################################################
+ 
+@@ -105,8 +126,7 @@ givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+ # at the very end of the list.
+ library_order_list = [
+     "singular", "ec", "ecm",
+-    "linboxsage", "ntl", "iml", "linbox", "givaro",
+-] + gsl_libs + [
++] + linbox_libs  + gsl_libs + [
+     "pari", "flint", "ratpoints", "ecl", "glpk", "ppl",
+     "arb", "fplll", "mpfi", "mpfr", "mpc", "gmp", "gmpxx",
+     "polybori",
+@@ -593,13 +613,10 @@ ext_modules = [
+ 
+     Extension('sage.libs.linbox.linbox',
+               sources = ['sage/libs/linbox/linbox.pyx'],
+-              libraries = ['linboxsage', 'ntl', 'iml', 'linbox',
+-                           'givaro', 'mpfr', 'gmp', 'gmpxx'] + cblas_libs,
++              libraries = linbox_libs,
+               language = 'c++',
+               library_dirs = cblas_library_dirs,
+-              include_dirs = cblas_include_dirs,
+-              extra_compile_args = givaro_extra_compile_args,
+-              depends = [os.path.join(SAGE_INC, 'givaro', 'givconfig.h')]),
++              include_dirs = cblas_include_dirs),
+ 
+     Extension('sage.libs.lcalc.lcalc_Lfunction',
+               sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
+@@ -645,9 +662,8 @@ ext_modules = [
+ 
+     Extension('sage.libs.singular.singular',
+               sources = ['sage/libs/singular/singular.pyx'],
+-              libraries = ['givaro'] + singular_libs,
+-              language="c++",
+-              extra_compile_args = givaro_extra_compile_args),
++              libraries = singular_libs,
++              language="c++"),
+ 
+     Extension('sage.libs.singular.polynomial',
+               sources = ['sage/libs/singular/polynomial.pyx'],
+@@ -667,8 +683,7 @@ ext_modules = [
+     Extension('sage.libs.singular.function',
+               sources = ['sage/libs/singular/function.pyx'],
+               libraries = singular_libs,
+-              language="c++",
+-              extra_compile_args = givaro_extra_compile_args),
++              language="c++"),
+ 
+     Extension('sage.libs.singular.option',
+               sources = ['sage/libs/singular/option.pyx'],
+@@ -923,19 +938,17 @@ ext_modules = [
+     Extension('sage.matrix.matrix_modn_dense_float',
+               sources = ['sage/matrix/matrix_modn_dense_float.pyx'],
+               language="c++",
+-              libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
++              libraries = linbox_libs + cblas_libs,
+               library_dirs = cblas_library_dirs,
+-              include_dirs = cblas_include_dirs,
+-              extra_compile_args = ['-DDISABLE_COMMENTATOR'] + givaro_extra_compile_args),
++              include_dirs = cblas_include_dirs),
+ 
+     Extension('sage.matrix.matrix_modn_dense_double',
+               sources = ['sage/matrix/matrix_modn_dense_double.pyx'],
+               language="c++",
+-              libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
++              libraries = linbox_libs + cblas_libs,
+               library_dirs = cblas_library_dirs,
+               include_dirs = cblas_include_dirs,
+-              extra_compile_args = ["-D_XPG6", "-DDISABLE_COMMENTATOR"]
+-                    + m4ri_extra_compile_args + givaro_extra_compile_args),
++              extra_compile_args = ["-D_XPG6"]),
+ 
+     Extension('sage.matrix.matrix_modn_sparse',
+               sources = ['sage/matrix/matrix_modn_sparse.pyx']),
+@@ -1374,8 +1387,7 @@ ext_modules = [
+     Extension('sage.rings.finite_rings.element_givaro',
+               sources = ["sage/rings/finite_rings/element_givaro.pyx"],
+               libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
+-              language='c++',
+-              extra_compile_args = givaro_extra_compile_args),
++              language='c++'),
+ 
+     Extension('sage.rings.finite_rings.element_ntl_gf2e',
+               sources = ['sage/rings/finite_rings/element_ntl_gf2e.pyx'],
+@@ -1395,8 +1407,7 @@ ext_modules = [
+               sources = ["sage/rings/finite_rings/hom_finite_field_givaro.pyx"],
+               # this order is needed to compile under windows.
+               libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
+-              language='c++',
+-              extra_compile_args = givaro_extra_compile_args),
++              language='c++'),
+ 
+     ################################
+     ##
+@@ -1548,8 +1559,7 @@ ext_modules = [
+     Extension('sage.rings.polynomial.plural',
+               sources = ['sage/rings/polynomial/plural.pyx'],
+               libraries = ['m', 'readline', 'singular', 'givaro', 'gmpxx', 'gmp'],
+-              language="c++",
+-              extra_compile_args = givaro_extra_compile_args),
++              language="c++"),
+ 
+     Extension('sage.rings.polynomial.multi_polynomial_libsingular',
+               sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx'],
+diff --git a/src/sage/libs/linbox/echelonform.pxd b/src/sage/libs/linbox/echelonform.pxd
+index 3097c8b..cf4902d 100644
+--- a/src/sage/libs/linbox/echelonform.pxd
++++ b/src/sage/libs/linbox/echelonform.pxd
+@@ -1,23 +1,27 @@
++# distutils: extra_compile_args = LINBOX_CFLAGS
++# distutils: libraries = LINBOX_LIBRARIES
++# distutils: library_dirs = LINBOX_LIBDIR
++
+ from sage.libs.linbox.modular cimport ModDoubleField, ModDoubleFieldElement, ModFloatField, ModFloatFieldElement
+ from libc.stdint cimport uint64_t
+ 
+-cdef extern from "linbox/matrix/blas-matrix.h" namespace "LinBox":
+-    cdef cppclass BlasMatrixDouble "LinBox::BlasMatrix<LinBox::Modular<double> >":
++cdef extern from "linbox/matrix/dense-matrix.h" namespace "LinBox":
++    cdef cppclass BlasMatrixDouble "LinBox::DenseMatrix<Givaro::Modular<double> >":
+         BlasMatrixDouble(ModDoubleField F, uint64_t nrows, uint64_t ncols)
+         void setEntry(size_t i, size_t j, ModDoubleFieldElement t)
+         ModDoubleFieldElement &getEntry(size_t i, size_t j)
+ 
+-    cdef cppclass BlasMatrixFloat "LinBox::BlasMatrix<LinBox::Modular<float> >":
++    cdef cppclass BlasMatrixFloat "LinBox::DenseMatrix<Givaro::Modular<float> >":
+         BlasMatrixFloat(ModFloatField F, uint64_t nrows, uint64_t ncols)
+         void setEntry(size_t i, size_t j, ModFloatFieldElement t)
+         ModFloatFieldElement &getEntry(size_t i, size_t j)
+ 
+ cdef extern from "linbox/algorithms/echelon-form.h":
+-    cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<LinBox::Modular<double> >":
++    cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<Givaro::Modular<double> >":
+         EchelonFormDomainDouble(ModDoubleField)
+         int rowReducedEchelon(BlasMatrixDouble, BlasMatrixDouble)
+ 
+-    cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<LinBox::Modular<float> >":
++    cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<Givaro::Modular<float> >":
+         EchelonFormDomainFloat(ModFloatField)
+         int rowReducedEchelon(BlasMatrixFloat, BlasMatrixFloat)
+ 
+diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd
+index e102004..01ab1b1 100644
+--- a/src/sage/libs/linbox/fflas.pxd
++++ b/src/sage/libs/linbox/fflas.pxd
+@@ -1,3 +1,7 @@
++# distutils: extra_compile_args = FFLASFFPACK_CFLAGS
++# distutils: libraries = FFLASFFPACK_LIBRARIES
++# distutils: library_dirs = FFLASFFPACK_LIBDIR
++
+ from modular cimport ModDoubleField, ModFloatField, ModDoubleFieldElement, ModFloatFieldElement
+ 
+ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std":
+diff --git a/src/sage/libs/linbox/linbox.pyx b/src/sage/libs/linbox/linbox.pyx
+index e932347..a9bd6d1 100644
+--- a/src/sage/libs/linbox/linbox.pyx
++++ b/src/sage/libs/linbox/linbox.pyx
+@@ -1,3 +1,7 @@
++# distutils: extra_compile_args = LINBOX_CFLAGS
++# distutils: libraries = LINBOX_LIBRARIES
++# distutils: library_dirs = LINBOX_LIBDIR
++
+ r"""
+ Linbox interface
+ """
+diff --git a/src/sage/libs/linbox/modular.pxd b/src/sage/libs/linbox/modular.pxd
+index 7ef204c..ea5fb29 100644
+--- a/src/sage/libs/linbox/modular.pxd
++++ b/src/sage/libs/linbox/modular.pxd
+@@ -1,10 +1,10 @@
+-cdef extern from "linbox/field/modular.h":
++cdef extern from "givaro/modular.h":
+     # double
+ 
+-    cdef cppclass ModDoubleFieldElement "LinBox::Modular<double>::Element":
++    cdef cppclass ModDoubleFieldElement "Givaro::Modular<double>::Element":
+         pass
+ 
+-    cdef cppclass ModDoubleField "LinBox::Modular<double>":
++    cdef cppclass ModDoubleField "Givaro::Modular<double>":
+         ModDoubleField(int modulus)
+         ModDoubleFieldElement init(ModDoubleFieldElement res, int v)
+         ModDoubleFieldElement init(ModDoubleFieldElement res, double v)
+@@ -20,10 +20,10 @@ cdef extern from "linbox/field/modular.h":
+ 
+ 
+     # float
+-    cdef cppclass ModFloatFieldElement "LinBox::Modular<float>::Element":
++    cdef cppclass ModFloatFieldElement "Givaro::Modular<float>::Element":
+         pass
+ 
+-    cdef cppclass ModFloatField "LinBox::Modular<float>":
++    cdef cppclass ModFloatField "Givaro::Modular<float>":
+         ModFloatField(int modulus)
+         ModFloatFieldElement init(ModFloatFieldElement res, int v)
+         ModFloatFieldElement init(ModFloatFieldElement res, double v)
+diff --git a/src/sage/libs/singular/singular.pyx b/src/sage/libs/singular/singular.pyx
+index 33d7f7ec..77f6e0a 100644
+--- a/src/sage/libs/singular/singular.pyx
++++ b/src/sage/libs/singular/singular.pyx
+@@ -22,6 +22,7 @@ cdef extern from "limits.h":
+ 
+ import os
+ 
++from libc.stdint cimport int64_t
+ from sage.libs.singular.decl cimport intvec
+ from sage.libs.singular.decl cimport SR_HDL, SR_INT, SR_TO_INT
+ from sage.libs.singular.decl cimport singular_options, singular_verbose_options
+@@ -155,7 +156,7 @@ cdef FFgivE si2sa_GFqGivaro(number *n, ring *_ring, Cache_givaro cache):
+     order = cache.objectptr.cardinality() - 1
+ 
+     while z:
+-        c = cache.objectptr.initi(c, <long>napGetCoeff(z))
++        c = cache.objectptr.initi(c, <int64_t>napGetCoeff(z))
+         e = napGetExpFrom(z,1, _ring)
+         if e == 0:
+             ret = cache.objectptr.add(ret, c, ret)
+diff --git a/src/sage/rings/finite_rings/element_givaro.pxd b/src/sage/rings/finite_rings/element_givaro.pxd
+index 68def46..91c4ed7 100644
+--- a/src/sage/rings/finite_rings/element_givaro.pxd
++++ b/src/sage/rings/finite_rings/element_givaro.pxd
+@@ -1,9 +1,15 @@
+-from sage.structure.element cimport Element, RingElement, ModuleElement
+-from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
++# distutils: extra_compile_args = GIVARO_CFLAGS
++
++from libcpp.vector cimport vector
++ctypedef vector[int] intvec
++
++from libc.stdint cimport int64_t
+ 
+-from sage.structure.parent  cimport Parent
++from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
++from sage.structure.parent cimport Parent
+ from sage.structure.sage_object cimport SageObject
+ 
++
+ cdef extern from "givaro/givconfig.h":
+     pass
+ 
+@@ -13,16 +19,7 @@ cdef extern from "givaro/givrandom.h":
+ 
+     GivRandom GivRandomSeeded  "Givaro::GivRandom"(unsigned long seed)
+ 
+-cdef extern from "givaro/givgfq.h":
+-    ctypedef struct intvec "std::vector<unsigned int>":
+-        void (* push_back)(int elem)
+-
+-    ctypedef struct constintvec "const std::vector<unsigned int>"
+-
+-    intvec intvec_factory "std::vector<unsigned int>"(int len)
+-
+-cdef extern from "givaro/givgfq.h":
+-
++cdef extern from "givaro/gfq.h":
+     ctypedef struct GivaroGfq "Givaro::GFqDom<int>":
+         #attributes
+         unsigned int one
+@@ -40,10 +37,10 @@ cdef extern from "givaro/givgfq.h":
+         unsigned int (* cardinality)()
+         int (* exponent)()
+         int (* random)(GivRandom gen, int res)
+-        int (* initi "init")(int res, int e)
++        int (* initi "init")(int res, int64_t e)
+         int (* initd "init")(int res, double e)
+         int (* indeterminate)()
+-        int (* convert)(int r, int p)
++        int (* convert)(int64_t r, int p)
+         int (* read)(int r, int p)
+         int (* axpyin)(int r, int a, int x)
+         int (* axpy)(int r, int a, int b, int c)
+@@ -60,7 +57,12 @@ cdef extern from "givaro/givgfq.h":
+     void delete "delete "(void *o)
+     int gfq_element_factory "Givaro::GFqDom<int>::Element"()
+ 
+-cdef class FiniteField_givaroElement(FinitePolyExtElement) #forward declaration
++
++cdef class FiniteField_givaroElement(FinitePolyExtElement):
++    cdef int element
++    cdef Cache_givaro _cache
++    cdef object _multiplicative_order
++    cdef FiniteField_givaroElement _new_c(self, int value)
+ 
+ cdef class Cache_givaro(SageObject):
+     cdef GivaroGfq *objectptr # C++ object
+@@ -85,11 +87,4 @@ cdef class FiniteField_givaro_iterator:
+     cdef int iterator
+     cdef Cache_givaro _cache
+ 
+-cdef class FiniteField_givaroElement(FinitePolyExtElement):
+-    cdef int element
+-    cdef Cache_givaro _cache
+-    cdef object _multiplicative_order
+-    cdef FiniteField_givaroElement _new_c(self, int value)
+-
+-
+ cdef inline FiniteField_givaroElement make_FiniteField_givaroElement(Cache_givaro cache, int x)
+diff --git a/src/sage/rings/finite_rings/element_givaro.pyx b/src/sage/rings/finite_rings/element_givaro.pyx
+index d32b5cf..f2afa44 100644
+--- a/src/sage/rings/finite_rings/element_givaro.pyx
++++ b/src/sage/rings/finite_rings/element_givaro.pyx
+@@ -58,8 +58,9 @@ from sage.misc.randstate cimport randstate, current_randstate
+ from sage.rings.finite_rings.finite_field_base cimport FiniteField
+ from sage.rings.ring cimport Ring
+ from element_ext_pari import FiniteField_ext_pariElement
+-from element_pari_ffelt import FiniteFieldElement_pari_ffelt
++from element_pari_ffelt cimport FiniteFieldElement_pari_ffelt
+ from sage.structure.sage_object cimport SageObject
++from sage.structure.element cimport Element, ModuleElement, RingElement
+ import operator
+ import sage.arith.all
+ import finite_field_constructor as finite_field
+@@ -373,18 +374,16 @@ cdef class Cache_givaro(SageObject):
+         elif isinstance(e, int) or \
+              isinstance(e, Integer) or \
+              isinstance(e, long) or is_IntegerMod(e):
+-            try:
+-                e_int = e
+-            except OverflowError:
+-                e_int = e % self.characteristic()
++            e_int = e % self.characteristic()
+             res = self.objectptr.initi(res, e_int)
+ 
+         elif e is None:
+             e_int = 0
+-            res = self.objectptr.initi(res,e_int)
++            res = self.objectptr.initi(res, e_int)
+ 
+         elif isinstance(e, float):
+-            res = self.objectptr.initd(res,e)
++            e_int = int(e) % self.characteristic()
++            res = self.objectptr.initd(res, e_int)
+ 
+         elif isinstance(e, str):
+             return self.parent(eval(e.replace("^","**"),self.parent.gens_dict()))
+@@ -394,8 +393,8 @@ cdef class Cache_givaro(SageObject):
+                 raise TypeError, "e.parent must match self.vector_space"
+             ret = self._zero_element
+             for i in range(len(e)):
+-                e_entry = e[i] % self.characteristic()
+-                res = self.objectptr.initi(res, int(e_entry))
++                e_int = e[i] % self.characteristic()
++                res = self.objectptr.initi(res, e_int)
+                 to_add = make_FiniteField_givaroElement(self, res)
+                 ret = ret + to_add*self.parent.gen()**i
+             return ret
+@@ -434,8 +433,8 @@ cdef class Cache_givaro(SageObject):
+                 raise ValueError, "list is too long"
+             ret = self._zero_element
+             for i in range(len(e)):
+-                e_entry = e[i] % self.characteristic()
+-                res = self.objectptr.initi(res, int(e_entry))
++                e_int = e[i] % self.characteristic()
++                res = self.objectptr.initi(res, e_int)
+                 to_add = make_FiniteField_givaroElement(self, res)
+                 ret = ret + to_add*self.parent.gen()**i
+             return ret
+@@ -572,19 +571,17 @@ cdef class Cache_givaro(SageObject):
+         cdef int ret = k.zero
+         cdef int a = k.indeterminate()
+         cdef int at = k.one
+-        cdef unsigned int ch = k.characteristic()
+-        cdef int _n, t, i
++        cdef int ch = k.characteristic()
++        cdef int t, i
+ 
+         if n<0 or n>k.cardinality():
+             raise TypeError, "n must be between 0 and self.order()"
+ 
+-        _n = n
+-
+         for i from 0 <= i < k.exponent():
+-            t = k.initi(t, _n%ch)
++            t = k.initi(t, n % ch)
+             ret = k.axpy(ret, t, at, ret)
+             at = k.mul(at,at,a)
+-            _n = _n/ch
++            n //= ch
+         return make_FiniteField_givaroElement(self, ret)
+ 
+     def _element_repr(self, FiniteField_givaroElement e):
+diff --git a/src/sage/rings/finite_rings/finite_field_givaro.py b/src/sage/rings/finite_rings/finite_field_givaro.py
+index adbaab3..c431f6d 100644
+--- a/src/sage/rings/finite_rings/finite_field_givaro.py
++++ b/src/sage/rings/finite_rings/finite_field_givaro.py
+@@ -269,7 +269,8 @@ class FiniteField_givaro(FiniteField):
+             sage: k(2) # indirect doctest
+             0
+ 
+-            Floats coerce in:
++        Floats are converted like integers::
++
+             sage: k(float(2.0))
+             0
+ 
+@@ -343,7 +344,7 @@ class FiniteField_givaro(FiniteField):
+             sage: k(pari('Mod(1,2)'))
+             1
+             sage: k(pari('Mod(2,3)'))
+-            0
++            a
+             sage: k(pari('Mod(1,3)*a^20'))
+             a^7 + a^5 + a^4 + a^2
+ 
diff --git a/libre/sagemath/paths.patch b/libre/sagemath/paths.patch
index 12922dcc3..c8afe39bb 100644
--- a/libre/sagemath/paths.patch
+++ b/libre/sagemath/paths.patch
@@ -12,7 +12,7 @@
 +_add_variable_or_fallback('SAGE_ROOT',       '/usr')
 +_add_variable_or_fallback('SAGE_LOCAL',      '/usr')
 +_add_variable_or_fallback('SAGE_ETC',        '/etc/sage')
-+_add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include', 'sage'))
++_add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
 +_add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share', 'sage'))
  
  _add_variable_or_fallback('SAGE_SRC',        opj('$SAGE_ROOT', 'src'))