sagemath-7.1-4.parabola1: updating version

5 files changed, 423 insertions, 42 deletions

diff --git a/libre/sagemath/PKGBUILD b/libre/sagemath/PKGBUILD
index f1b948ccb..cb4e7432b 100644
--- a/libre/sagemath/PKGBUILD
+++ b/libre/sagemath/PKGBUILD
@@ -1,4 +1,4 @@
-# $Id: PKGBUILD 165384 2016-03-06 15:37:18Z arojas $
+# $Id: PKGBUILD 169479 2016-04-04 18:15:22Z 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>
@@ -10,13 +10,13 @@
 # Maintainer: André Silva <emulatorman@parabola.nu>
 
 pkgname=sagemath
-pkgver=7.0
-pkgrel=6.parabola1
-pkgdesc="Free Mathematics Software, free software replacement of Magma, Maple, Mathematica, and Matlab, without nonfree nauty recommendation"
+pkgver=7.1
+pkgrel=4.parabola1
+pkgdesc="Free Mathematics Software, free software replacement of Magma, Maple, Mathematica, and Matlab, without nonfree nauty support"
 arch=(i686 x86_64)
 url="http://www.sagemath.org"
 license=(GPL)
-depends=(ipython2 atlas-lapack ppl mpfi palp brial singular cliquer maxima-ecl gfan sympow tachyon python2-rpy2
+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 libgap flintqs lcalc lrcalc lrs 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)
@@ -26,31 +26,29 @@ 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'
-  'jupyter-notebook: Jupyter notebook interface')
-makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc
-  mcqd coxeter3 cryptominisat modular_decomposition bliss-graphs tdlib) # libfes
+  'jupyter-notebook: Jupyter notebook interface' 'atlas-lapack: improved performance for some linear algebra operations')
+makedepends=(cython2-devel boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc
+  mcqd coxeter3 cryptominisat modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
 conflicts=(sage-mathematics)
 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"
-	ntl-no-legacy-mulmod.patch::"http://git.sagemath.org/sage.git/patch/?id=0d8435cdf"
 	anal.h package.patch env.patch paths.patch clean.patch skip-check.patch
-	disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch contour.patch)
-md5sums=('34807a7cf5dd79c008abd377ba1427fa'
+	disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch gap-4.8.patch)
+md5sums=('c68e846444b9370fe79f43395cdc2725'
          'a346bb2c0350c1cb17d5325235c5e38a'
-         '8cd491caa5a574fb6348a02715151855'
          'a906a180d198186a39820b0a2f9a9c63'
          '9ba81f717ffd4e20b8b2f2a318307488'
-         'e1b1d0d2e6b187309ae2b74489356b9a'
-         'fd8e3e07f5b7318e6a7200a3c64f5bc2'
+         '21010618e80fc28582a84695a1fed0e5'
+         '0f746ed394fd7eb7a6b3963014976098'
          '6d9ae0978ce6a05a0da2cafdfb178a09'
          '5947a420a0b1483f0cbc74c76895789b'
          '4eb23a3c7363258bc9ba764d6e5512ba'
          '16b529194c6105c3364127bd8f1efa83'
          'cdcabd475b80afe0534a5621e972736e'
          'ef927896f2071b442b1d07d7e69f5f3a'
-         '930cb987f63fd465a3a7123b0f5c2b85')
+         '8f631f4132d3a97dade07e4c60044aed')
 
 prepare(){
   cd sage-$pkgver
@@ -83,16 +81,14 @@ prepare(){
   patch -p0 -i ../jupyter-path.patch
 # fix timeit with Python 2.7.11
   patch -p0 -i ../python-2.7.11.patch
-# fix contour plots with matplotlib 1.5.1
-  patch -p0 -i ../contour.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 away from deprecated NTL API http://trac.sagemath.org/19874
-  patch -p1 -i ../ntl-no-legacy-mulmod.patch
+# port to GAP 4.8 http://trac.sagemath.org/ticket/19911
+  patch -p1 -i ../gap-4.8.patch
 
 # use python2
   sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
@@ -139,7 +135,7 @@ package() {
 
   mkdir -p "$pkgdir"/usr/bin
   cp bin/sage "$pkgdir"/usr/bin
-  for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall CSI CSI-helper.py cython env eval grep grepdoc inline-fortran ipython \
+  for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipython \
     massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run run-cython runtests startuptime.py \
     sws2rst valgrind version.sh
   do
@@ -153,6 +149,9 @@ package() {
 # Create SAGE_SRC, needed for the notebook
   mkdir "$pkgdir"/usr/share/sage/source
 
+# Remove sage_setup
+  rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
 # install pexpect
   cd "$srcdir"/pexpect-*
   python2 setup.py install --root="$pkgdir" --optimize=1
diff --git a/libre/sagemath/contour.patch b/libre/sagemath/contour.patch
deleted file mode 100644
index f63955f8d..000000000
--- a/libre/sagemath/contour.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/sage/plot/contour_plot.py.orig	2016-01-20 15:01:00.077409793 +0100
-+++ src/sage/plot/contour_plot.py	2016-01-20 15:01:22.591370847 +0100
-@@ -568,7 +568,7 @@
-     g.add_primitive(ContourPlot(xy_data_array, xrange, yrange, options))
-     return g
- 
--@options(plot_points=150, contours=(0,0), fill=False, cmap=["blue"])
-+@options(plot_points=150, contours=(0,1e-20), fill=False, cmap=["blue"])
- def implicit_plot(f, xrange, yrange, **options):
-     r"""
-     ``implicit_plot`` takes a function of two variables, `f(x,y)`
diff --git a/libre/sagemath/env.patch b/libre/sagemath/env.patch
index e4a1be329..96d080e23 100644
--- a/libre/sagemath/env.patch
+++ b/libre/sagemath/env.patch
@@ -43,7 +43,7 @@
  
  # Don't execute the commands more than once for the same version of
  # sage-env.  Check this after checking the validity of SAGE_ROOT, but
-@@ -245,20 +211,12 @@
+@@ -245,21 +211,13 @@
  fi
  
  # Setting Sage-related location environment variables.
@@ -54,7 +54,8 @@
 -export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
 -export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
 -export SAGE_SRC="$SAGE_ROOT/src"
--export SAGE_DOC="$SAGE_SRC/doc"
+-export SAGE_DOC_SRC="$SAGE_SRC/doc"
+-export SAGE_DOC="$SAGE_SHARE/doc/sage"
 -
 -if [ -z "${SAGE_ORIG_PATH_SET}" ]; then 
 -    SAGE_ORIG_PATH=$PATH && export SAGE_ORIG_PATH 
@@ -66,6 +67,7 @@
 +export SAGE_SHARE="$SAGE_LOCAL/share/sage"
 +export SAGE_EXTCODE="$SAGE_SHARE/ext"
 +export SAGE_SRC="$SAGE_SHARE/source"
++export SAGE_DOC_SRC="$SAGE_SRC/doc"
 +export SAGE_DOC="/usr/share/doc/sage"
  
  # We offer a toolchain option, so if $SAGE_LOCAL/toolchain/toolchain-env exists source it.
@@ -80,10 +82,13 @@
  if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
      SAGE_REPO_ANONYMOUS="git://trac.sagemath.org/sage.git"
      export SAGE_REPO_ANONYMOUS
-@@ -363,30 +318,17 @@
+@@ -363,38 +318,33 @@
      export SAGE_STARTUP_FILE
  fi
  
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
++
 -IPYTHONDIR=`find "$SAGE_SPKG_INST" -name "ipython*"`
 -if [ -n "$IPYTHONDIR" ]; then
 -    export IPYTHONDIR="$DOT_SAGE/${IPYTHONDIR##*/}"
@@ -95,19 +100,27 @@
      export PYTHON_EGG_CACHE
  fi
  
+ # Set PYTHONUSERBASE to avoid picking up non-Sage versions of
+ # Matplotlib, numpy, etc. See http://trac.sagemath.org/ticket/19612.
+ #
+ # For more history (it used to be PYTHONNOUSERSITE=yes which killed
+ # the ability to do "sage -pip install PACKAGE --user"), see
+ # http://trac.sagemath.org/ticket/14243 and
+ # http://trac.sagemath.org/ticket/18955.
+ 
+ if [ "$PYTHONUSERBASE" = "" ]; then
+     PYTHONUSERBASE="$DOT_SAGE/local"
+     export PYTHONUSERBASE
+ fi
+ 
 -if [ -d "$SAGE_LOCAL/lib/python" ]; then
 -    PYTHONPATH="$SAGE_LOCAL/lib/python:$SAGE_LOCAL/lib/python/site_packages"
 -    if [ -n "$SAGE_PATH" ]; then
 -        PYTHONPATH="$SAGE_PATH:$PYTHONPATH"
 -    fi
 -    PYTHONHOME="$SAGE_LOCAL"
--    # Set PYTHONNOUSERSITE to avoid picking up non-Sage versions of
--    # Matplotlib, numpy, etc. See http://trac.sagemath.org/ticket/14243
--    # and http://trac.sagemath.org/ticket/18955.
--    PYTHONNOUSERSITE=yes
 -    export PYTHONPATH
 -    export PYTHONHOME
--    export PYTHONNOUSERSITE
 -fi
 +PYTHONPATH="/usr/lib/sage/site-packages:$PYTHONPATH"
 +PYTHONHOME="$SAGE_ROOT"
diff --git a/libre/sagemath/gap-4.8.patch b/libre/sagemath/gap-4.8.patch
new file mode 100644
index 000000000..af8ed5027
--- /dev/null
+++ b/libre/sagemath/gap-4.8.patch
@@ -0,0 +1,378 @@
+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/paths.patch b/libre/sagemath/paths.patch
index 2426c07ff..12922dcc3 100644
--- a/libre/sagemath/paths.patch
+++ b/libre/sagemath/paths.patch
@@ -1,6 +1,6 @@
 --- src/sage/env.py.orig	2014-06-25 10:47:25.827203554 +1200
 +++ src/sage/env.py	2014-06-25 10:49:07.667402821 +1200
-@@ -87,24 +87,21 @@
+@@ -87,25 +87,22 @@
  _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
  
  # bunch of sage directories and files
@@ -25,11 +25,13 @@
 -_add_variable_or_fallback('SAGE_EXTCODE',    opj('$SAGE_SHARE', 'sage', 'ext'))
 -_add_variable_or_fallback('SAGE_LOGS',       opj('$SAGE_ROOT', 'logs', 'pkgs'))
 -_add_variable_or_fallback('SAGE_SPKG_INST',  opj('$SAGE_LOCAL', 'var', 'lib', 'sage', 'installed'))
--_add_variable_or_fallback('SAGE_DOC',        opj('$SAGE_SRC', 'doc'))
+-_add_variable_or_fallback('SAGE_DOC_SRC',    opj('$SAGE_SRC', 'doc'))
+-_add_variable_or_fallback('SAGE_DOC',        opj('$SAGE_SHARE', 'doc', 'sage'))
 -_add_variable_or_fallback('DOT_SAGE',        opj(os.environ.get('HOME','$SAGE_ROOT'), '.sage'))
 -_add_variable_or_fallback('SAGE_DOT_GIT',    opj('$SAGE_ROOT', '.git'))
 +_add_variable_or_fallback('SAGE_EXTCODE',    opj('$SAGE_SHARE', 'ext'))
-+_add_variable_or_fallback('SAGE_DOC',        '/usr/share/doc/sage')
++_add_variable_or_fallback('SAGE_DOC_SRC',    opj('$SAGE_SRC', 'doc'))
++_add_variable_or_fallback('SAGE_DOC',        opj('/usr/share', 'doc', 'sage'))        
 +_add_variable_or_fallback('DOT_SAGE',        opj(os.environ.get('HOME'), '.sage'))
  _add_variable_or_fallback('SAGE_DISTFILES',  opj('$SAGE_ROOT', 'upstream'))