diff options
| -rw-r--r-- | .SRCINFO | 108 | ||||
| -rw-r--r-- | PKGBUILD | 175 | ||||
| -rw-r--r-- | anal.h | 65 | ||||
| -rw-r--r-- | clean.patch | 23 | ||||
| -rw-r--r-- | disable-fes.patch | 19 | ||||
| -rw-r--r-- | env.patch | 132 | ||||
| -rw-r--r-- | extensions.patch | 12 | ||||
| -rw-r--r-- | ntl9.patch | 178 | ||||
| -rw-r--r-- | package.patch | 11 | ||||
| -rw-r--r-- | paths.patch | 33 | ||||
| -rw-r--r-- | pexpect-del.patch | 15 | ||||
| -rw-r--r-- | pexpect-env.patch | 32 | ||||
| -rw-r--r-- | skip-check.patch | 21 |
13 files changed, 824 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..2eae6857a715 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,108 @@ +pkgbase = sagemath-git + pkgdesc = Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab + pkgver = 6.8.beta3.r0.g336ae6c + pkgrel = 1 + url = http://www.sagemath.org + arch = i686 + arch = x86_64 + license = GPL + makedepends = cython2-devel + makedepends = boost + makedepends = ratpoints + makedepends = symmetrica + makedepends = fflas-ffpack + makedepends = python2-jinja + makedepends = coin-or-cbc + makedepends = mcqd + makedepends = coxeter3 + makedepends = cryptominisat + makedepends = arb + makedepends = modular_decomposition + makedepends = bliss-graphs + depends = ipython2 + depends = ppl + depends = glpk + depends = mpfi + depends = palp + depends = polybori + depends = singular + depends = libcliquer + depends = maxima-ecl + depends = gfan + depends = sympow + depends = tachyon + depends = python2-rpy2 + depends = python2-matplotlib + depends = python2-scipy + depends = python2-sympy + depends = python2-networkx + depends = libgap + depends = gap + depends = flintqs + depends = lcalc + depends = lrcalc + depends = eclib + depends = gmp-ecm + depends = zn_poly + depends = gd + depends = python2-cvxopt + depends = pynac + depends = linbox + depends = gsl + depends = rubiks + depends = pari-galdata + depends = pari-seadata-small + depends = planarity + depends = sage-data-combinatorial_designs + depends = sage-data-elliptic_curves + depends = sage-data-graphs + depends = sage-data-polytopes_db + depends = sage-data-conway_polynomials + optdepends = cython2: to compile cython code + optdepends = jmol: 3D plots + optdepends = sage-notebook: Browser-based (flask) notebook interface + optdepends = sagemath-doc: Documentation and inline help + optdepends = sagemath-src: source files needed to build cython code + optdepends = ipython2-notebook: IPython notebook interface + optdepends = mathjax: IPython notebook interface + optdepends = coin-or-cbc: COIN backend for numerical computations + optdepends = nauty: for generating some classes of graphs + optdepends = buckygen: for generating fullerene graphs + optdepends = plantri: for generating some classes of graphs + optdepends = benzene: for generating fusenes and benzenoids + optdepends = modular_decomposition: modular decomposition of graphs + optdepends = lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes + optdepends = imagemagick: to show animations + optdepends = coxeter3: Coxeter groups implementation + optdepends = cryptominisat: SAT solver + optdepends = arb: floating-point ball arithmetic + provides = sagemath + provides = sage-mathematics + conflicts = sagemath + source = git://git.sagemath.org/sage.git#branch=develop + source = http://mirrors.mit.edu/sage/spkg/upstream/pexpect/pexpect-2.0.tar.bz2 + source = anal.h + source = package.patch + source = env.patch + source = paths.patch + source = clean.patch + source = skip-check.patch + source = pexpect-env.patch + source = pexpect-del.patch + source = ntl9.patch + source = disable-fes.patch + md5sums = SKIP + md5sums = d9a3e113ed147dcee8f89962a8dccd43 + md5sums = a906a180d198186a39820b0a2f9a9c63 + md5sums = 0eb5ac1537aac93bd67a2925c0cfd84d + md5sums = a97ad60cca257b389f1e6e60eef2525f + md5sums = 020bdb34b6fc0f2c9f46341bdb79937a + md5sums = 46c212a3a6713b0f78c370c7186d0982 + md5sums = 5947a420a0b1483f0cbc74c76895789b + md5sums = a83a3b1bc7fcb7cbf752a83a8311fc42 + md5sums = f333939ea6c41377b66407c81016cee4 + md5sums = 308abbb1a49db9b8f0e088aff69567ff + md5sums = 4eb23a3c7363258bc9ba764d6e5512ba + +pkgname = sagemath-git + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..03ffa57d46a6 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,175 @@ +# $Id: PKGBUILD 118896 2014-09-13 07:12:02Z arcanis $ +# Maintainer: Evgeniy Alekseev <arcanis.arch at gmail dot com> +# Maintainer: Antonio Rojas <arojas@archlinux.org> +# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com> +# Contributor: Thomas Dziedzic <gostrc at gmail dot com> +# Contributor: Osman Ugus <ugus11 at yahoo dot com> +# Contributor: Stefan Husmann <stefan-husmann at t-online dot de> +# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD + +pkgname=sagemath-git +pkgver=6.8.beta3.r0.g336ae6c +pkgrel=1 +pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" +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' 'planarity' + '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' + 'nauty: for generating some classes of graphs' + 'buckygen: for generating fullerene graphs' + 'plantri: for generating some classes of graphs' + 'benzene: for generating fusenes and benzenoids' + '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' 'ratpoints' 'symmetrica' 'fflas-ffpack' 'python2-jinja' 'coin-or-cbc' + 'mcqd' 'coxeter3' 'cryptominisat' 'arb' 'modular_decomposition' 'bliss-graphs') +conflicts=('sagemath') +provides=('sagemath' 'sage-mathematics') +source=("git://git.sagemath.org/sage.git#branch=develop" +"http://mirrors.mit.edu/sage/spkg/upstream/pexpect/pexpect-2.0.tar.bz2" 'anal.h' +'package.patch' 'env.patch' 'paths.patch' 'clean.patch' 'skip-check.patch' +'pexpect-env.patch' 'pexpect-del.patch' 'ntl9.patch' 'disable-fes.patch') +md5sums=('SKIP' + 'd9a3e113ed147dcee8f89962a8dccd43' + 'a906a180d198186a39820b0a2f9a9c63' + '0eb5ac1537aac93bd67a2925c0cfd84d' + 'a97ad60cca257b389f1e6e60eef2525f' + '020bdb34b6fc0f2c9f46341bdb79937a' + '46c212a3a6713b0f78c370c7186d0982' + '5947a420a0b1483f0cbc74c76895789b' + 'a83a3b1bc7fcb7cbf752a83a8311fc42' + 'f333939ea6c41377b66407c81016cee4' + '308abbb1a49db9b8f0e088aff69567ff' + '4eb23a3c7363258bc9ba764d6e5512ba') + +pkgver() { + cd sage + git describe --long --tags | sed -r 's/([^-]*-g)/r\1/;s/-/./g' +} + + +prepare(){ + cd sage + +# Arch-specific patches +# assume all optional packages are installed + patch -p0 -i "$srcdir"/package.patch +# find L.h header + sed -e 's|libLfunction|Lfunction|' -i src/module_list.py +# don't try to link against libpng 1.2 + sed -e 's|png12|png|' -i src/module_list.py +# set env variables + patch -p0 -i "$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 "$srcdir"/skip-check.patch +# supress warning about GAP install dir + sed -e "s|gapdir = os.path.join(SAGE_LOCAL, 'gap', 'latest')|gapdir = '/usr/lib/gap'|" -i src/sage/libs/gap/util.pyx +# fix Cremona database detection + sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/sage/cremona/cremona.db')|" \ + -i src/sage/databases/cremona.py +# fix IPython kernel path + sed -e "s|os.path.join(SAGE_ROOT, 'sage')|'/usr/bin/sage'|" -i src/sage/repl/ipython_kernel/install.py +# find bliss headers + sed -e 's|graph.hh|bliss/graph.hh|' -i src/sage/graphs/bliss.pyx +# Rename class to fix conflicts with NTL + sed -e 's|WrappedPtr|SageWrappedPtr|' -i src/sage/libs/polybori/decl.pxd -i src/sage/libs/polybori/pb_wrap.h +# Disable fes module, broken upstream + patch -p0 -i "$srcdir"/disable-fes.patch + +# Upstream patches +# 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 "$srcdir"/pexpect-del.patch +} + + +build() { + cd sage/src + + export SAGE_LOCAL="/usr" + export SAGE_SRC="$PWD" + export CC=gcc + + make sage/libs/pari/auto_gen.pxi + make sage/ext/interpreters/__init__.py + + python2 setup.py build + +# build pexpect + pushd "$srcdir"/pexpect-2.0 + python2 setup.py build + popd +} + + +package() { + cd sage/src + + export SAGE_ROOT="/usr" + export SAGE_LOCAL="$SAGE_ROOT" + export SAGE_SRC="$PWD" + + python2 setup.py install --root="$pkgdir" --optimize=1 + + mkdir -p "$pkgdir"/usr/bin + cp bin/sage "$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/anal.h b/anal.h new file mode 100644 index 000000000000..f77d47025c97 --- /dev/null +++ b/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/clean.patch b/clean.patch new file mode 100644 index 000000000000..c577d3d42114 --- /dev/null +++ b/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/disable-fes.patch b/disable-fes.patch new file mode 100644 index 000000000000..873a6a663cfb --- /dev/null +++ b/disable-fes.patch @@ -0,0 +1,19 @@ +--- src/module_list.py.orig 2015-06-07 11:29:30.710612146 +0200 ++++ src/module_list.py 2015-06-07 11:30:21.877506106 +0200 +@@ -685,11 +685,11 @@ + include_dirs = [SAGE_INC + '/ecl'], + depends = [SAGE_INC + '/ecl/ecl.h']), + +- OptionalExtension("sage.libs.fes", +- ["sage/libs/fes.pyx"], +- language = "c", +- libraries = ['fes'], +- package = 'fes'), ++# OptionalExtension("sage.libs.fes", ++# ["sage/libs/fes.pyx"], ++# language = "c", ++# libraries = ['fes'], ++# package = 'fes'), + + Extension('sage.libs.flint.flint', + sources = ["sage/libs/flint/flint.pyx"], diff --git a/env.patch b/env.patch new file mode 100644 index 000000000000..430823ca1f40 --- /dev/null +++ b/env.patch @@ -0,0 +1,132 @@ +--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 ++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 +@@ -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 $SAGE_LOCAL/toolchain/toolchain-env exists source it. + # Since the user might do something crazy we do not do any checks, but hope for the best. +@@ -309,9 +267,6 @@ + GIT_TEMPLATE_DIR="$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 +@@ -363,25 +318,17 @@ + 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_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" +- 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 +@@ -431,8 +378,6 @@ + R_MAKEVARS_SITE="$SAGE_LOCAL/lib/R/share/Makevars.site" && export R_MAKEVARS_SITE + R_MAKEVARS_USER="$SAGE_LOCAL/lib/R/share/Makevars.user" && export R_MAKEVARS_USER + +-MAXIMA_PREFIX="$SAGE_ROOT/local" && export MAXIMA_PREFIX +- + ############ architecture flags + + # Support flags to change the build architecture. Currently, this is +@@ -602,9 +547,6 @@ + LD_LIBRARY_PATH="$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/extensions.patch b/extensions.patch new file mode 100644 index 000000000000..802155d974f9 --- /dev/null +++ b/extensions.patch @@ -0,0 +1,12 @@ +--- src/module_list.py.orig 2015-01-02 01:37:15.614093528 +0100 ++++ src/module_list.py 2015-01-02 01:37:26.140827483 +0100 +@@ -2126,7 +2126,8 @@ + # These extensions are to be compiled only if the + # corresponding packages have been installed + +-from sage.misc.package import is_package_installed ++def is_package_installed(name): ++ return False + + if is_package_installed('fes'): + ext_modules.extend([ diff --git a/ntl9.patch b/ntl9.patch new file mode 100644 index 000000000000..191491826e8e --- /dev/null +++ b/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/package.patch b/package.patch new file mode 100644 index 000000000000..08ab8a8bde66 --- /dev/null +++ b/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/paths.patch b/paths.patch new file mode 100644 index 000000000000..4691c8af94ef --- /dev/null +++ b/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/pexpect-del.patch b/pexpect-del.patch new file mode 100644 index 000000000000..3019968d2fc5 --- /dev/null +++ b/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/pexpect-env.patch b/pexpect-env.patch new file mode 100644 index 000000000000..99cf44885b9c --- /dev/null +++ b/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/skip-check.patch b/skip-check.patch new file mode 100644 index 000000000000..dae5f7277312 --- /dev/null +++ b/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" |