sagemath: add new package to [libre]

12 files changed, 741 insertions, 0 deletions

diff --git a/libre/sagemath/PKGBUILD b/libre/sagemath/PKGBUILD
new file mode 100644
index 000000000..485f89544
--- /dev/null
+++ b/libre/sagemath/PKGBUILD
@@ -0,0 +1,169 @@
+# $Id: PKGBUILD 118896 2014-09-13 07:12:02Z arcanis $
+# 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>
+# Contributor (Arch): Thomas Dziedzic <gostrc at gmail dot com>
+# Contributor (Arch): Osman Ugus <ugus11 at yahoo dot com>
+# Contributor (Arch): Stefan Husmann <stefan-husmann at t-online dot de>
+# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
+# Maintainer: Omar Vega Ramos <ovruni@gnu.org.pe>
+
+pkgname=sagemath
+pkgver=6.7
+pkgrel=3.parabola1
+pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab, without nonfree nauty recommendation"
+arch=('i686' 'x86_64')
+url="http://www.sagemath.org"
+license=('GPL')
+depends=('ipython2' 'ppl' 'glpk' 'mpfi' 'palp' 'polybori' 'singular' 'libcliquer' 'maxima-ecl' 'gfan' 'sympow' 'tachyon' 'python2-rpy2'
+  'python2-matplotlib' 'python2-scipy' 'python2-sympy' 'python2-networkx' 'libgap' 'gap' 'flintqs' 'lcalc' 'lrcalc'
+  'eclib' 'gmp-ecm' 'zn_poly' 'gd' 'python2-cvxopt' 'pynac' 'linbox' 'gsl' 'rubiks' 'pari-galdata' 'pari-seadata-small'
+  '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'
+  'sagemath-doc: Documentation and inline help' 'sagemath-src: source files needed to build cython code'
+  'ipython2-notebook: IPython notebook interface' 'mathjax: IPython notebook interface'
+  'coin-or-cbc: COIN backend for numerical computations'
+  'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
+  'libfes: exhaustive search of solutions for boolean polynomial systems' 'modular_decomposition: modular decomposition of graphs'
+  'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes' 'imagemagick: to show animations'
+  'coxeter3: Coxeter groups implementation' 'cryptominisat: SAT solver' 'arb: floating-point ball arithmetic')
+makedepends=('cython2-devel' 'boost' 'scons' 'ratpoints' 'symmetrica' 'fflas-ffpack' 'python2-jinja' 'coin-or-cbc'
+  'mcqd' 'libfes' 'coxeter3' 'cryptominisat' 'arb' 'modular_decomposition' 'bliss-graphs')
+conflicts=('sage-mathematics')
+replaces=('sage-mathematics')
+provides=('sage-mathematics')
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" 
+# "http://www.sagemath.org/packages/upstream/pexpect/pexpect-2.0.tar.bz2" 
+"http://mirrors.mit.edu/sage/spkg/upstream/pexpect/pexpect-2.0.tar.bz2"
+'anal.h' 'package.patch' 'c_lib.patch' 'env.patch' 'paths.patch' 'clean.patch' 'skip-check.patch' 
+'pexpect-env.patch' 'pexpect-del.patch' 'fes02.patch' 'ntl9.patch')
+md5sums=('df744e882a4b25b42dd8347e202cd497'
+         'd9a3e113ed147dcee8f89962a8dccd43'
+         'a906a180d198186a39820b0a2f9a9c63'
+         '0eb5ac1537aac93bd67a2925c0cfd84d'
+         'c452558d3496b07be472dad57195d45d'
+         '3fc9a5bb250896533365c30c2b926e3c'
+         '020bdb34b6fc0f2c9f46341bdb79937a'
+         '46c212a3a6713b0f78c370c7186d0982'
+         '5947a420a0b1483f0cbc74c76895789b'
+         'a83a3b1bc7fcb7cbf752a83a8311fc42'
+         'f333939ea6c41377b66407c81016cee4'
+         '506944613082ba7f5b34360939ca90eb'
+         '308abbb1a49db9b8f0e088aff69567ff')
+
+prepare(){
+  cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+  patch -p0 -i "$srcdir"/package.patch
+# don't assume Sage is already available (Fedora)
+  patch -p0 -i "$srcdir"/c_lib.patch
+# find L.h header
+  sed -e 's|libLfunction|Lfunction|' -i src/module_list.py
+# don't try to link against libpng 1.2
+  sed -e 's|png12|png|' -i src/module_list.py
+# set env variables
+  patch -p0 -i "$srcdir"/env.patch
+# fix paths in python imports
+  patch -p0 -i "$srcdir"/paths.patch
+# fix cython linking
+  sed -e "s| atlas(),||" -i src/sage/misc/cython.py
+# don't try to remove installed files
+  patch -p0 -i "$srcdir"/clean.patch
+# skip checking build status
+  patch -p0 -i "$srcdir"/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
+# fix IPython kernel path
+  sed -e "s|os.path.join(SAGE_ROOT, 'sage')|'/usr/bin/sage'|" -i src/sage/repl/ipython_kernel/install.py
+# find bliss headers
+  sed -e 's|graph.hh|bliss/graph.hh|' -i src/sage/graphs/bliss.pyx
+# Rename class to fix conflicts with NTL
+  sed -e 's|WrappedPtr|SageWrappedPtr|' -i src/sage/libs/polybori/decl.pxd -i src/sage/libs/polybori/pb_wrap.h  
+
+# Upstream patches  
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+  patch -p0 -i "$srcdir"/fes02.patch
+# fix build aginst NTL 9 (Fedora)
+  patch -p0 -i "$srcdir"/ntl9.patch
+
+# use python2
+  sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
+  sed -e 's|cython %s %s|cython2 %s %s|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
+  sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|' -i src/bin/sage
+  sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+  sed -e 's|python -c|python2 -c|' -i src/Makefile
+
+# copy required private PARI header
+  mkdir -p src/pari
+  cp "$srcdir"/anal.h src/pari/anal.h
+
+# remove developer interface
+  rm -r src/sage/dev
+
+  cd "$srcdir"/pexpect-2.0
+# fix env in pexpect
+  patch -p1 -i "$srcdir"/pexpect-env.patch
+# hide exceptions in pexpect
+  patch -p1 -i "$srcdir"/pexpect-del.patch
+}
+
+
+build() {
+  cd sage-$pkgver/src
+
+  export SAGE_LOCAL="/usr"
+  export SAGE_SRC="$PWD"
+  export CC=gcc
+
+  pushd c_lib
+    CXX=g++ UNAME=Linux SAGE64=auto scons
+  popd
+
+  make sage/libs/pari/auto_gen.pxi
+  make sage/ext/interpreters/__init__.py
+
+  python2 setup.py build
+
+# build pexpect
+  pushd "$srcdir"/pexpect-2.0
+    python2 setup.py build
+  popd
+}
+
+package() {
+  cd sage-$pkgver/src
+
+  export SAGE_ROOT="/usr"
+  export SAGE_LOCAL="$SAGE_ROOT"
+  export SAGE_SRC="$PWD"
+
+  python2 setup.py install --root="$pkgdir" --optimize=1
+
+  mkdir -p "$pkgdir"/usr/{bin,lib}
+  cp c_lib/libcsage.so "$pkgdir"/usr/lib
+  cp bin/sage "$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 \
+    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
+    cp bin/sage-$_i "$pkgdir"/usr/bin
+  done
+  cp bin/math-readline "$pkgdir"/usr/bin
+  
+  mkdir -p "$pkgdir"/usr/share/sage
+  cp -r ext "$pkgdir"/usr/share/sage
+  
+# Create SAGE_SRC, needed for the notebook
+  mkdir "$pkgdir"/usr/share/sage/src
+
+# Install Sage's own pexpect
+  cd "$srcdir"/pexpect-2.0
+  python2 setup.py install --root="$pkgdir" --optimize=1
+  mkdir -p "$pkgdir"/usr/lib/sage/site-packages/
+  mv "$pkgdir"/usr/lib/python2.7/site-packages/pexpect* "$pkgdir"/usr/lib/sage/site-packages/
+}
diff --git a/libre/sagemath/anal.h b/libre/sagemath/anal.h
new file mode 100644
index 000000000..f77d47025
--- /dev/null
+++ b/libre/sagemath/anal.h
@@ -0,0 +1,65 @@
+/* Copyright (C) 2000  The PARI group.
+
+This file is part of the PARI/GP package.
+
+PARI/GP is free software; you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free Software
+Foundation. It is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY WHATSOEVER.
+
+Check the License for details. You should have received a copy of it, along
+with the package; see the file 'COPYING'. If not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. */
+
+/*************************************************************************/
+/*                                                                       */
+/*                 Declarations specific to the analyzer                 */
+/*                                                                       */
+/*************************************************************************/
+BEGINEXTERN
+/* GP control structures */
+#define EXPR_WRAP(code, call) \
+{ GEN z; GEN __E = code; \
+  push_lex(gen_0, __E); z = call; pop_lex(1); return z; }
+#define EXPR_ARG __E, &gp_eval
+#define EXPR_ARGUPTO __E, &gp_evalupto
+#define EXPR_ARGBOOL __E, &gp_evalbool
+
+/* functions */
+void   changevalue(entree *ep, GEN val);
+void    freeep(entree *ep);
+void   pari_fill_hashtable(entree **table, entree *ep);
+
+void compile_err(const char *msg, const char *str);
+void compile_varerr(const char *str);
+
+#ifdef STACK_CHECK
+extern THREAD void *PARI_stack_limit;
+#endif
+
+extern entree  **varentries;
+
+struct node_loc
+{
+  const char *start,*end;
+};
+
+union token_value { long val; };
+
+int pari_lex(union token_value *yylval, struct node_loc *yylloc, char **lex);
+int pari_parse(char **lex);
+entree* fetch_entry(const char *s, long len);
+entree* fetch_member(const char *s, long len);
+void pari_close_parser(void);
+void pari_close_compiler(void);
+void pari_close_evaluator(void);
+void pari_init_parser(void);
+void pari_init_compiler(void);
+void pari_init_evaluator(void);
+void optimizenode(long n);
+void push_frame(GEN C, long lpc, long flag);
+const char * closure_func_err(void);
+GEN  gp_closure(long n);
+long eval_mnemonic(GEN str, const char *tmplate);
+
+ENDEXTERN
diff --git a/libre/sagemath/c_lib.patch b/libre/sagemath/c_lib.patch
new file mode 100644
index 000000000..6df7b8efa
--- /dev/null
+++ b/libre/sagemath/c_lib.patch
@@ -0,0 +1,17 @@
+--- src/setup.py.orig	2014-11-01 23:49:10.000000000 +0100
++++ src/setup.py	2014-11-07 00:40:58.414838636 +0100
+@@ -171,10 +171,12 @@
+     m.libraries = ['csage'] + m.libraries
+     if m.language == 'c++':
+         m.libraries.append('stdc++')
++        m.libraries.append('ntl')
++    m.libraries = m.libraries + ['gmp', 'm', 'dl']
+ 
+     m.extra_compile_args = m.extra_compile_args + extra_compile_args
+     m.extra_link_args = m.extra_link_args + extra_link_args
+-    m.library_dirs = m.library_dirs + [os.path.join(SAGE_LOCAL, "lib")]
++    m.library_dirs += ['c_lib', '%s/lib' % SAGE_LOCAL]
+     m.include_dirs = m.include_dirs + include_dirs
+
+ 
+ 
diff --git a/libre/sagemath/clean.patch b/libre/sagemath/clean.patch
new file mode 100644
index 000000000..c577d3d42
--- /dev/null
+++ b/libre/sagemath/clean.patch
@@ -0,0 +1,23 @@
+--- src/setup.py.orig	2014-11-16 10:34:05.521441703 +0100
++++ src/setup.py	2014-11-16 10:34:16.054812569 +0100
+@@ -581,20 +581,6 @@
+ 
+ 
+ #########################################################
+-### Clean
+-#########################################################
+-
+-print('Cleaning up stale installed files....')
+-t = time.time()
+-from sage_setup.clean import clean_install_dir
+-output_dirs = SITE_PACKAGES + glob.glob(os.path.join(SAGE_SRC, 'build', 'lib*'))
+-for output_dir in output_dirs:
+-    print('- cleaning {0}'.format(output_dir))
+-    clean_install_dir(output_dir, python_packages, python_modules, ext_modules)
+-print('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
+-
+-
+-#########################################################
+ ### Distutils
+ #########################################################
+ 
diff --git a/libre/sagemath/env.patch b/libre/sagemath/env.patch
new file mode 100644
index 000000000..9ad163262
--- /dev/null
+++ b/libre/sagemath/env.patch
@@ -0,0 +1,132 @@
+--- src/bin/sage-env.orig	2015-05-15 11:32:42.546800174 +0200
++++ src/bin/sage-env	2015-04-29 15:12:46.000000000 +0200
+@@ -110,41 +110,7 @@
+ }
+ 
+ 
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$SAGE_ROOT" ]; then
+-    NEW_SAGE_ROOT="$SAGE_ROOT"
+-elif [ -f sage -a -d build ]; then
+-    NEW_SAGE_ROOT="."
+-elif [ -f ../../sage -a -d ../../build ]; then
+-    NEW_SAGE_ROOT="../.."
+-else
+-    # No idea what SAGE_ROOT should be...
+-    echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
+-    echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
+-    return 1
+-fi
+-
+-# Make NEW_SAGE_ROOT absolute
+-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
+-
+-# Sanity check NEW_SAGE_ROOT
+-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
+-    :
+-else
+-    echo >&2 "Error: SAGE_ROOT is set to a bad value:"
+-    echo >&2 "SAGE_ROOT=$SAGE_ROOT"
+-    echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
+-    echo >&2 "or SAGE_ROOT/local/bin/ directory."
+-    return 1
+-fi
+-
+-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
+-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
+-    echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
+-    echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
+-    echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+ 
+ # 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 @@
+ fi
+ 
+ # Setting Sage-related location environment variables.
+-export SAGE_LOCAL="$SAGE_ROOT/local"
+-export SAGE_ETC="$SAGE_LOCAL/etc"
+-export SAGE_SHARE="$SAGE_LOCAL/share"
+-export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
+-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"
+-
+-if [ -z "${SAGE_ORIG_PATH_SET}" ]; then 
+-    SAGE_ORIG_PATH=$PATH && export SAGE_ORIG_PATH 
+-    SAGE_ORIG_PATH_SET=True && export SAGE_ORIG_PATH_SET 
+-fi 
+-export PATH="$SAGE_SRC/bin:$SAGE_LOCAL/bin:$PATH"
++export SAGE_LOCAL="$SAGE_ROOT"
++export SAGE_ETC="/etc/sage"
++export SAGE_SHARE="$SAGE_LOCAL/share/sage"
++export SAGE_EXTCODE="$SAGE_SHARE/ext"
++export SAGE_SRC="$SAGE_SHARE/src"
++export SAGE_DOC="/usr/share/doc/sage"
+ 
+ # We offer a toolchain option, so if $SAGE_LOCAL/toolchain/toolchain-env exists source it.
+ # Since the user might do something crazy we do not do any checks, but hope for the best.
+@@ -309,9 +267,7 @@
+ GIT_TEMPLATE_DIR="$SAGE_LOCAL"/share/git-core/templates && export GIT_TEMPLATE_DIR
+ GIT_EXEC_PATH="$SAGE_LOCAL"/libexec/git-core && export GIT_EXEC_PATH
+ 
+-SINGULARPATH="$SAGE_LOCAL/share/singular" && export SINGULARPATH
+-SINGULAR_EXECUTABLE="$SAGE_LOCAL/bin/Singular" && export SINGULAR_EXECUTABLE
+ 
+ if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
+     SAGE_REPO_ANONYMOUS="git://trac.sagemath.org/sage.git"
+     export SAGE_REPO_ANONYMOUS
+@@ -346,25 +310,17 @@
+     export SAGE_STARTUP_FILE
+ fi
+ 
+-IPYTHONDIR=`find "$SAGE_SPKG_INST" -name "ipython*"`
+-if [ -n "$IPYTHONDIR" ]; then
+-    export IPYTHONDIR="$DOT_SAGE/${IPYTHONDIR##*/}"
+-fi
++export IPYTHONDIR="$DOT_SAGE/ipython"
+ 
+ if [ "$PYTHON_EGG_CACHE" = "" ]; then
+     PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
+     export PYTHON_EGG_CACHE
+ fi
+ 
+-if [ -d "$SAGE_ROOT/local/lib/python" ]; then
+-    PYTHONPATH="$SAGE_ROOT/local/lib/python"
+-    if [ -n "$SAGE_PATH" ]; then
+-        PYTHONPATH="$SAGE_PATH:$PYTHONPATH"
+-    fi
+-    PYTHONHOME="$SAGE_ROOT/local"
+-    export PYTHONPATH
+-    export PYTHONHOME
+-fi
++PYTHONPATH="/usr/lib/sage/site-packages:$PYTHONPATH"
++PYTHONHOME="$SAGE_ROOT"
++export PYTHONPATH
++export PYTHONHOME
+ 
+ if [ -z "${SAGE_ORIG_LD_LIBRARY_PATH_SET}" ]; then
+     SAGE_ORIG_LD_LIBRARY_PATH=$LD_LIBRARY_PATH && export SAGE_ORIG_LD_LIBRARY_PATH
+@@ -412,8 +368,6 @@
+ unset R_HOME
+ unset R_PROFILE
+ 
+-MAXIMA_PREFIX="$SAGE_ROOT/local" && export MAXIMA_PREFIX
+-
+ ############ architecture flags
+ 
+ # Support flags to change the build architecture.  Currently, this is
+@@ -585,9 +539,6 @@
+     LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
+ fi
+ 
+-# See trac 7186 -- this is needed if ecl is moved
+-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
+-
+ # Handle parallel building/testing/...
+ # See Trac Ticket #12016
+ # First, figure out the right values for SAGE_NUM_THREADS (default
diff --git a/libre/sagemath/fes02.patch b/libre/sagemath/fes02.patch
new file mode 100644
index 000000000..b0cfda79f
--- /dev/null
+++ b/libre/sagemath/fes02.patch
@@ -0,0 +1,45 @@
+diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
+index 40b9c23..d188cf0 100644
+--- src/sage/libs/fes.pyx
++++ src/sage/libs/fes.pyx
+@@ -1,17 +1,19 @@
+ """
+-Binding for the FES library.
++Binding for the libFES library.
+ 
+ Finding solutions of systems of boolean equations by exhaustive
+ search, via the fes library. This is usually (much) faster than
+ computing a Groebner basis, except in special cases where the latter
+ is particularly easy.
+ 
+-The FES library is presently only able to deal with polynomials in 64
++More information is available at [http://www.lifl.fr/~bouillag/fes].
++
++The libFES library is presently only able to deal with polynomials in 64
+ variables. Performing a full exhaustive search over 64 variables will
+ take a **long** time. The number of variables can be artificially
+ reduced to 64 by specializing some of them.
+ 
+-Note that the FES library **requires** at least of the equations to be
++Note that the libFES library **requires** at least of the equations to be
+ non-linear.
+ 
+ AUTHORS:
+@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
+ cdef extern from "fes_interface.h":
+     ctypedef int (*solution_callback_t)(void *, uint64_t)
+ 
+-    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
++    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
+ 
+ 
+ include 'sage/ext/interrupt.pxi'  #sig_on(), sig_off()
+@@ -219,7 +221,7 @@ def exhaustive_search(eqs,  max_sols=Infinity, verbose=False):
+ 
+     # ------- runs the library
+     sig_on()
+-    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose)
++    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0)
+     sig_off()
+ 
+     # ------- frees memory occupied by the dense representation of the equations
diff --git a/libre/sagemath/ntl9.patch b/libre/sagemath/ntl9.patch
new file mode 100644
index 000000000..191491826
--- /dev/null
+++ b/libre/sagemath/ntl9.patch
@@ -0,0 +1,178 @@
+--- ./src/sage/rings/bernmm/bernmm-test.cpp.orig	2015-02-16 17:15:12.000000000 -0700
++++ ./src/sage/rings/bernmm/bernmm-test.cpp	2015-05-07 21:39:58.565251320 -0600
+@@ -70,7 +70,7 @@ void bern_naive(mpq_t* res, long n)
+ */
+ int testcase__bern_modp_powg(long p, long k, mpq_t b)
+ {
+-   double pinv = 1 / ((double) p);
++   wide_double pinv = wide_double(1) / wide_double(p);
+ 
+    // compute B_k mod p using _bern_modp_powg()
+    long x = _bern_modp_powg(p, pinv, k);
+@@ -147,7 +147,7 @@ int test__bern_modp_powg()
+ */
+ int testcase__bern_modp_pow2(long p, long k)
+ {
+-   double pinv = 1 / ((double) p);
++   wide_double pinv = wide_double(1) / wide_double(p);
+ 
+    if (PowerMod(2, k, p, pinv) == 1)
+       return 1;
+--- ./src/sage/rings/bernmm/bern_modp.cpp.orig	2015-02-16 17:15:12.000000000 -0700
++++ ./src/sage/rings/bernmm/bern_modp.cpp	2015-05-07 20:17:37.680381004 -0600
+@@ -43,14 +43,14 @@ namespace bernmm {
+       pinv = 1 / ((double) p)
+       g = a multiplicative generator of GF(p), in [0, p)
+ */
+-long bernsum_powg(long p, double pinv, long k, long g)
++long bernsum_powg(long p, wide_double pinv, long k, long g)
+ {
+    long half_gm1 = (g + ((g & 1) ? 0 : p) - 1) / 2;    // (g-1)/2 mod p
+    long g_to_jm1 = 1;
+    long g_to_km1 = PowerMod(g, k-1, p, pinv);
+    long g_to_km1_to_j = g_to_km1;
+    long sum = 0;
+-   double g_pinv = ((double) g) / ((double) p);
++   wide_double g_pinv = wide_double(g) / wide_double(p);
+    mulmod_precon_t g_to_km1_pinv = PrepMulModPrecon(g_to_km1, p, pinv);
+ 
+    for (long j = 1; j <= (p-1)/2; j++)
+@@ -224,7 +224,7 @@ public:
+ #error Number of bits in a long must be divisible by TABLE_LG_SIZE
+ #endif
+ 
+-long bernsum_pow2(long p, double pinv, long k, long g, long n)
++long bernsum_pow2(long p, wide_double pinv, long k, long g, long n)
+ {
+    // In the main summation loop we accumulate data into the _tables_ array;
+    // tables[y][z] contributes to the final answer with a weight of
+@@ -481,7 +481,7 @@ long PrepRedc(long n)
+    (See bernsum_pow2() for code comments; we only add comments here where
+    something is different from bernsum_pow2())
+ */
+-long bernsum_pow2_redc(long p, double pinv, long k, long g, long n)
++long bernsum_pow2_redc(long p, wide_double pinv, long k, long g, long n)
+ {
+    long pinv2 = PrepRedc(p);
+    long F = (1L << (ULONG_BITS/2)) % p;
+@@ -655,7 +655,7 @@ long bernsum_pow2_redc(long p, double pi
+ 
+    Algorithm: uses bernsum_powg() to compute the main sum.
+ */
+-long _bern_modp_powg(long p, double pinv, long k)
++long _bern_modp_powg(long p, wide_double pinv, long k)
+ {
+    Factorisation F(p-1);
+    long g = primitive_root(p, pinv, F);
+@@ -685,7 +685,7 @@ long _bern_modp_powg(long p, double pinv
+    Algorithm: uses bernsum_pow2() (or bernsum_pow2_redc() if p is small
+    enough) to compute the main sum.
+ */
+-long _bern_modp_pow2(long p, double pinv, long k)
++long _bern_modp_pow2(long p, wide_double pinv, long k)
+ {
+    Factorisation F(p-1);
+    long g = primitive_root(p, pinv, F);
+@@ -717,7 +717,7 @@ long _bern_modp_pow2(long p, double pinv
+       2 <= k <= p-3, k even
+       pinv = 1 / ((double) p)
+ */
+-long _bern_modp(long p, double pinv, long k)
++long _bern_modp(long p, wide_double pinv, long k)
+ {
+    if (PowerMod(2, k, p, pinv) != 1)
+       // 2^k != 1 mod p, so we use the faster version
+@@ -765,7 +765,7 @@ long bern_modp(long p, long k)
+    if (m == 0)
+       return -1;
+ 
+-   double pinv = 1 / ((double) p);
++   wide_double pinv = wide_double(1) / wide_double (p);
+    long x = _bern_modp(p, pinv, m);    // = B_m/m mod p
+    return MulMod(x, k, p, pinv);
+ }
+--- ./src/sage/rings/bernmm/bern_modp.h.orig	2015-02-16 17:15:12.000000000 -0700
++++ ./src/sage/rings/bernmm/bern_modp.h	2015-05-09 08:06:39.732529882 -0600
+@@ -12,6 +12,7 @@
+ #ifndef BERNMM_BERN_MODP_H
+ #define BERNMM_BERN_MODP_H
+ 
++#include <NTL/ZZ.h>
+ 
+ namespace bernmm {
+ 
+@@ -29,8 +30,8 @@ long bern_modp(long p, long k);
+ /*
+    Exported for testing.
+ */
+-long _bern_modp_powg(long p, double pinv, long k);
+-long _bern_modp_pow2(long p, double pinv, long k);
++long _bern_modp_powg(long p, NTL::wide_double pinv, long k);
++long _bern_modp_pow2(long p, NTL::wide_double pinv, long k);
+ 
+ 
+ };
+--- ./src/sage/rings/bernmm/bern_modp_util.cpp.orig	2015-02-16 17:15:12.000000000 -0700
++++ ./src/sage/rings/bernmm/bern_modp_util.cpp	2015-05-07 21:38:06.662182003 -0600
+@@ -20,7 +20,7 @@ NTL_CLIENT;
+ namespace bernmm {
+ 
+ 
+-long PowerMod(long a, long ee, long n, double ninv)
++long PowerMod(long a, long ee, long n, wide_double ninv)
+ {
+    long x, y;
+ 
+@@ -89,7 +89,7 @@ PrimeTable::PrimeTable(long bound)
+ }
+ 
+ 
+-long order(long x, long p, double pinv, const Factorisation& F)
++long order(long x, long p, wide_double pinv, const Factorisation& F)
+ {
+    // in the loop below, m is always some multiple of the order of x
+    long m = p - 1;
+@@ -113,7 +113,7 @@ long order(long x, long p, double pinv,
+ 
+ 
+ 
+-long primitive_root(long p, double pinv, const Factorisation& F)
++long primitive_root(long p, wide_double pinv, const Factorisation& F)
+ {
+    if (p == 2)
+       return 1;
+--- ./src/sage/rings/bernmm/bern_modp_util.h.orig	2015-02-16 17:15:12.000000000 -0700
++++ ./src/sage/rings/bernmm/bern_modp_util.h	2015-05-09 08:58:22.618458475 -0600
+@@ -17,6 +17,7 @@
+ #include <vector>
+ #include <cassert>
+ #include <climits>
++#include <NTL/ZZ.h>
+ 
+ 
+ #if ULONG_MAX == 4294967295U
+@@ -39,7 +40,7 @@ namespace bernmm {
+ 
+    (Implementation is adapted from ZZ.c in NTL 5.4.1.)
+ */
+-long PowerMod(long a, long ee, long n, double ninv);
++long PowerMod(long a, long ee, long n, NTL::wide_double ninv);
+ 
+ 
+ /*
+@@ -123,13 +124,13 @@ long next_prime(long p);
+ /*
+    Computes order of x mod p, given the factorisation F of p-1.
+ */
+-long order(long x, long p, double pinv, const Factorisation& F);
++long order(long x, long p, NTL::wide_double pinv, const Factorisation& F);
+ 
+ 
+ /*
+    Finds the smallest primitive root mod p, given the factorisation F of p-1.
+ */
+-long primitive_root(long p, double pinv, const Factorisation& F);
++long primitive_root(long p, NTL::wide_double pinv, const Factorisation& F);
+ 
+ 
+ };    // end namespace
diff --git a/libre/sagemath/package.patch b/libre/sagemath/package.patch
new file mode 100644
index 000000000..08ab8a8bd
--- /dev/null
+++ b/libre/sagemath/package.patch
@@ -0,0 +1,11 @@
+--- src/sage/misc/package.py.orig	2014-11-23 15:58:13.000000000 +0100
++++ src/sage/misc/package.py	2015-01-22 20:32:25.651383902 +0100
+@@ -194,7 +194,7 @@
+         sage: is_package_installed('sage')
+         True
+     """
+-    return any(p.startswith(package) for p in install_package())
++    return True
+ 
+ def standard_packages():
+     """
diff --git a/libre/sagemath/paths.patch b/libre/sagemath/paths.patch
new file mode 100644
index 000000000..4691c8af9
--- /dev/null
+++ b/libre/sagemath/paths.patch
@@ -0,0 +1,33 @@
+--- 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
+@@ -86,21 +86,18 @@
+ _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
+ 
+ # bunch of sage directories and files
+-_add_variable_or_fallback('SAGE_ROOT',       None)
+-_add_variable_or_fallback('SAGE_LOCAL',      opj('$SAGE_ROOT', 'local'))
+-_add_variable_or_fallback('SAGE_ETC',        opj('$SAGE_LOCAL', 'etc'))
+-_add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share'))
++_add_variable_or_fallback('SAGE_ROOT',       '/usr')
++_add_variable_or_fallback('SAGE_LOCAL',      '/usr')
++_add_variable_or_fallback('SAGE_ETC',        '/etc/sage')
++_add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share', 'sage'))
+ 
+ _add_variable_or_fallback('SAGE_SRC',        opj('$SAGE_ROOT', 'src'))
+-_add_variable_or_fallback('SITE_PACKAGES',   site.getsitepackages())
++_add_variable_or_fallback('SITE_PACKAGES',   site.getsitepackages()+['/usr/lib/sage/site-packages'])
+ _add_variable_or_fallback('SAGE_LIB',        SITE_PACKAGES[0])
+ 
+-_add_variable_or_fallback('SAGE_EXTCODE',    opj('$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('$SAGE_SRC', 'doc'))
+-_add_variable_or_fallback('DOT_SAGE',        opj(os.environ.get('HOME','$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('DOT_SAGE',        opj(os.environ.get('HOME'), '.sage'))
+ _add_variable_or_fallback('SAGE_DISTFILES',  opj('$SAGE_ROOT', 'upstream'))
+ 
+ # misc
+
diff --git a/libre/sagemath/pexpect-del.patch b/libre/sagemath/pexpect-del.patch
new file mode 100644
index 000000000..3019968d2
--- /dev/null
+++ b/libre/sagemath/pexpect-del.patch
@@ -0,0 +1,15 @@
+diff -ru src/pexpect.py src.del/pexpect.py
+--- src/pexpect.py	2005-11-17 15:36:09.000000000 +0100
++++ src.del/pexpect.py	2012-01-13 10:24:01.000000000 +0100
+@@ -341,7 +341,10 @@
+         """
+         if self.closed:
+             return
+-        self.close()
++        try:
++            self.close()
++        except:
++            pass
+ 
+     def __str__(self):
+         """This returns the current state of the pexpect object as a string.
diff --git a/libre/sagemath/pexpect-env.patch b/libre/sagemath/pexpect-env.patch
new file mode 100644
index 000000000..99cf44885
--- /dev/null
+++ b/libre/sagemath/pexpect-env.patch
@@ -0,0 +1,32 @@
+diff -ru src.p4/pexpect.py src.new/pexpect.py
+--- src.p4/pexpect.py	2009-01-23 11:01:57.000000000 +0100
++++ src.new/pexpect.py	2012-01-12 13:38:06.000000000 +0100
+@@ -209,7 +209,7 @@
+     Use this class to start and control child applications.
+     """
+ 
+-    def __init__(self, command, args=[], timeout=30, maxread=2000, searchwindowsize=None, logfile=None):
++    def __init__(self, command, args=[], timeout=30, maxread=2000, searchwindowsize=None, logfile=None, env=None):
+         """This is the constructor. The command parameter may be a string
+         that includes a command and any arguments to the command. For example:
+             p = pexpect.spawn ('/usr/bin/ftp')
+@@ -302,6 +302,7 @@
+         self.child_fd = -1 # initially closed
+         self.timeout = timeout
+         self.delimiter = EOF
++        self.env = env    
+         self.logfile = logfile    
+         self.maxread = maxread # Max bytes to read at one time into buffer.
+         self.buffer = '' # This is the read buffer. See maxread.
+@@ -421,7 +422,10 @@
+             # (specifically, Tomcat).
+             signal.signal(signal.SIGHUP, signal.SIG_IGN)
+ 
+-            os.execv(self.command, self.args)
++            if self.env is None:
++                os.execv(self.command, self.args)
++            else:
++                os.execve(self.command, self.args, self.env)
+ 
+         # Parent
+         self.terminated = 0
diff --git a/libre/sagemath/skip-check.patch b/libre/sagemath/skip-check.patch
new file mode 100644
index 000000000..dae5f7277
--- /dev/null
+++ b/libre/sagemath/skip-check.patch
@@ -0,0 +1,21 @@
+--- src/bin/sage.orig	2014-12-18 09:47:27.354829070 +0100
++++ src/bin/sage	2014-12-18 09:48:00.041563401 +0100
+@@ -286,18 +286,6 @@
+ 
+ # 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).
+-    if [ ! -d "$SAGE_LOCAL/lib/python/site-packages/sage" ]; then
+-        echo >&2 '************************************************************************'
+-        echo >&2 'It seems that you are attempting to run Sage from an unpacked source'
+-        echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
+-        echo >&2 'finished). You should run `make` in the Sage root directory first.'
+-        echo >&2 'If you did not intend to build Sage from source, you should download'
+-        echo >&2 'a binary tarball instead. Read README.txt for more information.'
+-        echo >&2 '************************************************************************'
+-        exit 1
+-    fi
+-
+     # Display the startup banner
+     if [ "$SAGE_BANNER" != "no" ]; then
+         cat "$SAGE_LOCAL/bin/sage-banner"