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authorTravis Scrimshaw <tscrim at ucdavis.edu>2014-02-10 11:08:32 -0800
committerTravis Scrimshaw <tscrim at ucdavis.edu>2014-02-10 11:08:32 -0800
commit7f9b89ed07cb5053bce29a48748382da525f6d5c (patch)
treedf9f4d6e360787b8be1fd0ef43f0cac3b6d9ae93
parentWork on cleaning up documentation. (diff)
parentUpdated Sage version to 6.2.beta1 (diff)
Merge branch 'develop' into public/combinat/analytic-10519
-rw-r--r--README.txt23
-rw-r--r--VERSION.txt2
-rw-r--r--build/deps2
-rw-r--r--build/pkgs/configure/checksums.ini6
-rw-r--r--build/pkgs/configure/package-version.txt2
-rw-r--r--build/pkgs/flint/SPKG.txt223
-rw-r--r--build/pkgs/flint/checksums.ini8
-rw-r--r--build/pkgs/flint/package-version.txt2
-rw-r--r--build/pkgs/flint/patches/cflags.patch30
-rw-r--r--build/pkgs/flint/patches/dylib.patch17
-rw-r--r--build/pkgs/flint/patches/test_empty_string.patch19
-rw-r--r--build/pkgs/lcalc/SPKG.txt159
-rw-r--r--build/pkgs/lcalc/package-version.txt2
-rw-r--r--build/pkgs/lcalc/patches/init_stack.patch31
-rw-r--r--build/pkgs/lcalc/patches/pari-2.4.4.patch30
-rw-r--r--build/pkgs/ncurses/SPKG.txt17
-rw-r--r--build/pkgs/ncurses/patches/xopen_source.patch313
-rwxr-xr-xbuild/pkgs/pari/spkg-install2
-rw-r--r--build/pkgs/sagenb/checksums.ini6
-rw-r--r--build/pkgs/sagenb/package-version.txt2
-rw-r--r--src/bin/sage-banner2
-rwxr-xr-xsrc/bin/sage-spkg2
-rw-r--r--src/bin/sage-version.sh4
-rw-r--r--src/c_lib/SConstruct4
-rw-r--r--src/doc/en/bordeaux_2008/elliptic_curves.rst1
-rw-r--r--src/doc/en/reference/coercion/index.rst4
-rw-r--r--src/doc/en/reference/libs/index.rst1
-rw-r--r--src/doc/en/thematic_tutorials/coercion_and_categories.rst4
-rw-r--r--src/sage/algebras/group_algebra.py2
-rw-r--r--src/sage/algebras/hall_algebra.py4
-rw-r--r--src/sage/algebras/iwahori_hecke_algebra.py2
-rw-r--r--src/sage/all.py2
-rw-r--r--src/sage/categories/examples/finite_enumerated_sets.py2
-rw-r--r--src/sage/categories/facade_sets.py2
-rw-r--r--src/sage/categories/fields.py2
-rw-r--r--src/sage/categories/functor.pyx2
-rw-r--r--src/sage/categories/morphism.pyx2
-rw-r--r--src/sage/categories/quotient_fields.py42
-rw-r--r--src/sage/coding/binary_code.pyx2
-rw-r--r--src/sage/combinat/abstract_tree.py1233
-rw-r--r--src/sage/combinat/binary_tree.py2045
-rw-r--r--src/sage/combinat/cluster_algebra_quiver/mutation_class.py2
-rw-r--r--src/sage/combinat/cluster_algebra_quiver/quiver_mutation_type.py2
-rw-r--r--src/sage/combinat/composition.py86
-rw-r--r--src/sage/combinat/crystals/tensor_product.py2
-rw-r--r--src/sage/combinat/designs/block_design.py22
-rw-r--r--src/sage/combinat/designs/ext_rep.py2
-rw-r--r--src/sage/combinat/designs/incidence_structures.py104
-rw-r--r--src/sage/combinat/free_module.py8
-rw-r--r--src/sage/combinat/integer_vectors_mod_permgroup.py12
-rw-r--r--src/sage/combinat/kazhdan_lusztig.py2
-rw-r--r--src/sage/combinat/matrices/latin.py36
-rw-r--r--src/sage/combinat/ncsf_qsym/generic_basis_code.py65
-rw-r--r--src/sage/combinat/ncsf_qsym/ncsf.py1234
-rw-r--r--src/sage/combinat/ncsf_qsym/qsym.py489
-rw-r--r--src/sage/combinat/ncsf_qsym/tutorial.py22
-rw-r--r--src/sage/combinat/ordered_tree.py98
-rw-r--r--src/sage/combinat/partition.py239
-rw-r--r--src/sage/combinat/permutation.py17
-rw-r--r--src/sage/combinat/permutation_cython.pyx2
-rw-r--r--src/sage/combinat/posets/poset_examples.py2
-rw-r--r--src/sage/combinat/posets/posets.py2
-rw-r--r--src/sage/combinat/rigged_configurations/bij_type_B.py2
-rw-r--r--src/sage/combinat/root_system/branching_rules.py4
-rw-r--r--src/sage/combinat/root_system/cartan_matrix.py20
-rw-r--r--src/sage/combinat/root_system/cartan_type.py2
-rw-r--r--src/sage/combinat/root_system/dynkin_diagram.py30
-rw-r--r--src/sage/combinat/root_system/root_system.py2
-rw-r--r--src/sage/combinat/root_system/weyl_characters.py2
-rw-r--r--src/sage/combinat/root_system/weyl_group.py2
-rw-r--r--src/sage/combinat/sf/classical.py2
-rw-r--r--src/sage/combinat/sf/sfa.py440
-rw-r--r--src/sage/combinat/skew_partition.py129
-rw-r--r--src/sage/combinat/sloane_functions.py2
-rw-r--r--src/sage/combinat/species/series.py2
-rw-r--r--src/sage/combinat/species/stream.py2
-rw-r--r--src/sage/combinat/tableau.py10
-rw-r--r--src/sage/combinat/tools.py24
-rw-r--r--src/sage/combinat/words/alphabet.py154
-rw-r--r--src/sage/combinat/words/finite_word.py4
-rw-r--r--src/sage/combinat/words/morphism.py2
-rw-r--r--src/sage/combinat/words/shuffle_product.py124
-rw-r--r--src/sage/crypto/classical.py22
-rw-r--r--src/sage/crypto/classical_cipher.py2
-rw-r--r--src/sage/crypto/stream.py4
-rw-r--r--src/sage/databases/sql_db.py6
-rw-r--r--src/sage/doctest/control.py2
-rw-r--r--src/sage/doctest/reporting.py2
-rw-r--r--src/sage/functions/generalized.py10
-rw-r--r--src/sage/functions/orthogonal_polys.py4
-rw-r--r--src/sage/functions/special.py2
-rw-r--r--src/sage/graphs/base/c_graph.pyx27
-rw-r--r--src/sage/graphs/base/sparse_graph.pyx112
-rw-r--r--src/sage/graphs/bipartite_graph.py50
-rw-r--r--src/sage/graphs/digraph.py8
-rw-r--r--src/sage/graphs/dot2tex_utils.py2
-rw-r--r--src/sage/graphs/generators/random.py2
-rw-r--r--src/sage/graphs/generic_graph.py35
-rw-r--r--src/sage/graphs/graph.py4
-rw-r--r--src/sage/graphs/graph_latex.py4
-rw-r--r--src/sage/graphs/planarity.pyx10
-rw-r--r--src/sage/graphs/schnyder.py2
-rw-r--r--src/sage/groups/generic.py12
-rw-r--r--src/sage/groups/perm_gps/permgroup.py6
-rw-r--r--src/sage/gsl/ode.pyx4
-rw-r--r--src/sage/gsl/probability_distribution.pyx22
-rw-r--r--src/sage/homology/chain_complex.py2
-rw-r--r--src/sage/homology/simplicial_complex.py80
-rw-r--r--src/sage/interacts/debugger.py2
-rw-r--r--src/sage/interfaces/axiom.py2
-rw-r--r--src/sage/interfaces/expect.py6
-rw-r--r--src/sage/interfaces/giac.py2
-rw-r--r--src/sage/interfaces/interface.py4
-rw-r--r--src/sage/interfaces/macaulay2.py2
-rw-r--r--src/sage/interfaces/magma.py2
-rw-r--r--src/sage/interfaces/maple.py2
-rw-r--r--src/sage/interfaces/mathematica.py2
-rw-r--r--src/sage/interfaces/phc.py2
-rw-r--r--src/sage/interfaces/tests.py2
-rw-r--r--src/sage/lfunctions/lcalc.py3
-rw-r--r--src/sage/libs/lcalc/lcalc_Lfunction.pxd8
-rw-r--r--src/sage/libs/lcalc/lcalc_Lfunction.pyx408
-rw-r--r--src/sage/libs/ntl/ntl_lzz_p.pyx2
-rw-r--r--src/sage/libs/ntl/ntl_lzz_pX.pyx2
-rw-r--r--src/sage/libs/pari/gen.pyx78
-rw-r--r--src/sage/libs/polybori/pb_wrap.h (renamed from src/c_lib/include/pb_wrap.h)0
-rw-r--r--src/sage/matrix/constructor.py2
-rw-r--r--src/sage/matrix/matrix2.pyx56
-rw-r--r--src/sage/matrix/matrix_double_dense.pyx2
-rw-r--r--src/sage/matrix/operation_table.py6
-rw-r--r--src/sage/misc/attached_files.py4
-rw-r--r--src/sage/misc/explain_pickle.py2
-rw-r--r--src/sage/misc/functional.py13
-rw-r--r--src/sage/misc/getusage.py2
-rw-r--r--src/sage/misc/latex.py3
-rw-r--r--src/sage/misc/lazy_list.pyx12
-rw-r--r--src/sage/misc/log.py2
-rw-r--r--src/sage/misc/misc.py2
-rw-r--r--src/sage/misc/random_testing.py6
-rw-r--r--src/sage/misc/sage_extension.py4
-rw-r--r--src/sage/misc/sageinspect.py8
-rw-r--r--src/sage/modular/arithgroup/congroup_pyx.pyx2
-rw-r--r--src/sage/modular/modform/element.py6
-rw-r--r--src/sage/modules/vector_double_dense.pyx2
-rw-r--r--src/sage/monoids/string_monoid_element.py2
-rw-r--r--src/sage/plot/all.py2
-rw-r--r--src/sage/plot/animate.py470
-rw-r--r--src/sage/plot/graphics.py85
-rw-r--r--src/sage/plot/line.py1
-rw-r--r--src/sage/plot/matrix_plot.py2
-rw-r--r--src/sage/plot/plot3d/base.pyx22
-rw-r--r--src/sage/plot/plot3d/implicit_surface.pyx2
-rw-r--r--src/sage/plot/plot3d/tachyon.py77
-rw-r--r--src/sage/quadratic_forms/extras.py2
-rw-r--r--src/sage/quadratic_forms/quadratic_form.py14
-rw-r--r--src/sage/quadratic_forms/quadratic_form__automorphisms.py4
-rw-r--r--src/sage/quadratic_forms/quadratic_form__genus.py4
-rw-r--r--src/sage/quadratic_forms/quadratic_form__local_normal_form.py2
-rw-r--r--src/sage/quadratic_forms/quadratic_form__variable_substitutions.py2
-rw-r--r--src/sage/quadratic_forms/random_quadraticform.py4
-rw-r--r--src/sage/rings/complex_mpc.pyx2
-rw-r--r--src/sage/rings/finite_rings/integer_mod.pyx34
-rw-r--r--src/sage/rings/fraction_field_element.pyx2
-rw-r--r--src/sage/rings/homset.py8
-rw-r--r--src/sage/rings/integer.pyx2
-rw-r--r--src/sage/rings/morphism.pyx6
-rw-r--r--src/sage/rings/number_field/morphism.py2
-rw-r--r--src/sage/rings/number_field/totallyreal_rel.py6
-rw-r--r--src/sage/rings/polynomial/cyclotomic.pyx2
-rw-r--r--src/sage/rings/polynomial/groebner_fan.py4
-rw-r--r--src/sage/rings/polynomial/infinite_polynomial_element.py12
-rw-r--r--src/sage/rings/polynomial/infinite_polynomial_ring.py18
-rw-r--r--src/sage/rings/polynomial/multi_polynomial_ideal.py115
-rw-r--r--src/sage/rings/polynomial/multi_polynomial_libsingular.pyx290
-rw-r--r--src/sage/rings/polynomial/pbori.pyx8
-rw-r--r--src/sage/rings/polynomial/polynomial_ring.py10
-rw-r--r--src/sage/rings/polynomial/symmetric_ideal.py4
-rw-r--r--src/sage/rings/polynomial/term_order.py6
-rw-r--r--src/sage/rings/polynomial/toy_variety.py6
-rw-r--r--src/sage/rings/power_series_ring_element.pyx2
-rw-r--r--src/sage/rings/rational.pyx2
-rw-r--r--src/sage/rings/real_lazy.pyx2
-rw-r--r--src/sage/rings/residue_field.pyx11
-rw-r--r--src/sage/schemes/affine/affine_morphism.py2
-rw-r--r--src/sage/schemes/affine/affine_rational_point.py2
-rw-r--r--src/sage/schemes/elliptic_curves/ell_field.py6
-rw-r--r--src/sage/schemes/elliptic_curves/ell_finite_field.py2
-rw-r--r--src/sage/schemes/elliptic_curves/ell_point.py4
-rw-r--r--src/sage/schemes/elliptic_curves/ell_rational_field.py2
-rw-r--r--src/sage/schemes/elliptic_curves/ell_tate_curve.py2
-rw-r--r--src/sage/schemes/elliptic_curves/gal_reps.py2
-rw-r--r--src/sage/schemes/elliptic_curves/lseries_ell.py6
-rw-r--r--src/sage/schemes/projective/projective_space.py2
-rw-r--r--src/sage/server/support.py2
-rw-r--r--src/sage/sets/family.py166
-rw-r--r--src/sage/sets/totally_ordered_finite_set.py2
-rw-r--r--src/sage/structure/category_object.pyx2
-rw-r--r--src/sage/structure/coerce.pyx8
-rw-r--r--src/sage/structure/coerce_maps.pyx12
-rw-r--r--src/sage/structure/element.pyx2
-rw-r--r--src/sage/structure/factorization.py4
-rw-r--r--src/sage/structure/parent.pyx8
-rw-r--r--src/sage/structure/parent_old.pyx4
-rw-r--r--src/sage/structure/sage_object.pyx4
-rw-r--r--src/sage/symbolic/constants_c.pxd2
-rw-r--r--src/sage/symbolic/constants_c.pyx2
-rw-r--r--src/sage/symbolic/expression.pxd2
-rw-r--r--src/sage/symbolic/expression.pyx13
-rw-r--r--src/sage/symbolic/function.pyx4
-rw-r--r--src/sage/symbolic/getitem.pyx2
-rw-r--r--src/sage/symbolic/ginac.pxd (renamed from src/sage/libs/ginac.pxd)0
-rw-r--r--src/sage/symbolic/ginac_wrap.h (renamed from src/c_lib/include/ginac_wrap.h)0
-rw-r--r--src/sage/symbolic/pynac.pyx10
-rw-r--r--src/sage/symbolic/relation.py8
-rw-r--r--src/sage/symbolic/ring.pyx2
-rw-r--r--src/sage/version.py4
216 files changed, 8094 insertions, 2214 deletions
diff --git a/README.txt b/README.txt
index eb614bd..b4bbee9 100644
--- a/README.txt
+++ b/README.txt
@@ -75,12 +75,23 @@ Installation Guide:
"Precise"), you need the dpkg-dev package.
OS X: Xcode. Make sure you have installed the most recent version
- of Xcode. For pre-Lion versions of OS X, you can download Xcode
- from http://developer.apple.com/downloads/. For OS X Lion, you can
- install it using the App Store. With Xcode 4.3 or later, you need
- to install the "Command Line Tools": from the File menu, choose
- "Preferences", then the "Downloads" tab, and then "Install" the
- Command Line Tools.
+ of Xcode. With recent versions of OS X (OS X Lion or later), you
+ can install Xcode for free from the App Store. For pre-Lion
+ versions of OS X, you can download Xcode from
+ http://developer.apple.com/downloads/.
+
+ With OS X, you also need to install the "command line tools". When
+ using OS X Mavericks, after installing Xcode, run this command from
+ a terminal window:
+
+ xcode-select --install
+
+ Then click "Install" in the pop-up window.
+
+ When using OS X Mountain Lion or earlier, you need to install the
+ command line tools from Xcode: run Xcode; then from the File
+ menu, choose "Preferences", then the "Downloads" tab, and then
+ "Install" the Command Line Tools.
Other platforms: See detailed instructions below.
diff --git a/VERSION.txt b/VERSION.txt
index 1c3c3ec..0f3dc25 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-Sage version 6.2.beta0, released 2014-02-02
+Sage version 6.2.beta1, released 2014-02-07
diff --git a/build/deps b/build/deps
index aceb6da..b27ddb3 100644
--- a/build/deps
+++ b/build/deps
@@ -476,8 +476,6 @@ $(INST)/csage: $(INST)/$(SCONS) \
$(INST)/$(MPIR) \
$(INST)/$(NTL) \
$(INST)/$(PARI) \
- $(INST)/$(POLYBORI) \
- $(INST)/$(PYNAC) \
$(INST)/$(PYTHON)
if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
cd $(SAGE_SRC) && source bin/sage-env && cd c_lib && \
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
index 2018f8c..6f3ab7e 100644
--- a/build/pkgs/configure/checksums.ini
+++ b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
tarball=configure-VERSION.tar.gz
-sha1=fe9add8a54ba26a8073f083b53a381e205da52bd
-md5=9c311beb40f324c1f8d3fe681f8417e4
-cksum=3541167752
+sha1=e0f0951560918d79141995852f276ac3e99a42f4
+md5=33b6cac80bafecc0ad880fd68cf258e6
+cksum=3483617699
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
index ec63514..b4de394 100644
--- a/build/pkgs/configure/package-version.txt
+++ b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-9
+11
diff --git a/build/pkgs/flint/SPKG.txt b/build/pkgs/flint/SPKG.txt
index 6dca0b9..fdf022b 100644
--- a/build/pkgs/flint/SPKG.txt
+++ b/build/pkgs/flint/SPKG.txt
@@ -26,224 +26,7 @@ FLINT is licensed GPL v2+.
* MPFR
* NTL
-== Patches ==
-
- * dylib.patch: patch configure so that the shared library is called
- libflint.dylib on Darwin.
- * cflags.patch: patch configure so that "-m64" (and other potentially
- unwanted cflags) is not added on PowerPC G5. Also add -fno-common
- on Darwin, which is needed for OS X 10.4 and doesn't hurt on other
- systems.
-
-== Changelog ==
-
-=== flint-2.3.p1 (Jean-Pierre Flori, 8 May 2013) ===
- * Trac #12173: add dylib.patch and cflags.patch
-
-=== flint-2.3 (Mike Hansen, Fredrik Johansson, Jean-Pierre Flori, May 2012-March 2013) ===
- * Trac #12173: Update FLINT to version 2.3.
- * Removed obsolete patches.
- * Cleanup spkg-install and spkg-check scripts.
- * Removed Cygwin hack for libntl.a made useless by #9050.
- * Removed now useless patch --binary flag on Cygwin.
- * Only build shared library on Cygwin.
-
-=== flint-1.5.2.p3 (Timo Kluck, 7 March 2013) ===
- * #14241: Fix double // path separators in longlong.patch
-
-=== flint-1.5.2.p2 (Paul-Olivier Dehaye, 16 October 2012) ===
- * #9697: Remove the file 'src/zn_poly/demo/bernoulli/.DS_Store'
-
-=== flint-1.5.2.p1 (Jean-Pierre Flori, 3 August 2012) ===
- * #13330: Pass --binary flag to patch on Cygwin to deal with file terminators
- mess.
-
-=== flint-1.5.2.p0 (Dima Pasechnik, March 24th 2012) ===
- * bumped up the version to reflect the fact that we patch the source
-
-=== flint-1.5.2 (Julien Puydt, William Stein, December 21st 2011) ===
- * #10328: enable ARM support; longlong.patch removes non-working
- asm code for 32-bit ARM
-
-=== flint-1.5.0.p10 (Leif Leonhardy, October 11th 2011) ===
- * #9858: Add an upstream patch from FLINT 1.5.2 to make FLINT's test suite
- build (when `SAGE_CHECK=yes`) with MPIR 1.3.x, 2.x (cf. #8664) and GMP 5.x.
- The patch just substitutes deprecated random functions in one file
- (`fmpz-test.c`) which have been removed from the mentioned GMP / MPIR
- versions.
-
-=== flint-1.5.0.p9 (Karl-Dieter Crisman, Dima Pasechnik, 25 August 2011) ===
- * Fix DOS file endings introduced in p7 which made patch fail on some systems
-
-=== flint-1.5.0.p8 (Karl-Dieter Crisman, 12th July 2011) ===
- * Enable both libflint.dll and .so on Cygwin (see Trac 11547).
- * Use 'cp' rather than '$CP' (affects only Cygwin).
- * Remove '.svn' directories from upstream.
-
-=== flint-1.5.0.p7 (Jeroen Demeyer, 6 July 2011) ===
- * Trac #11246: remove check for gcc version since we require gcc >= 4.0.1
- for Sage anyway.
- * Use `patch` instead of `cp` for patching the makefile
- * Remove test_gcc_version.sh and the horrible makepatchfiles
- * Check that `patch` succeeded in spkg-install, apply patches at -p1 level
- * Remove obsolete dist/debian directory
-
-=== flint-1.5.0.p6 (Dima Pasechnik, 25th April 2011) ===
- * removed extraneous #include statements in ZmodF_mul.c, ZmodF_poly.c, and, mpn_extras.h, which
- triggered a clash of typedef for ulong in sys/types.h and #define ulong in flint.h
- on Cygwin (trac ticket 11246).
-
-=== flint-1.5.0.p5 (David Kirkby, 19th June 2010) ===
- * #9277 Add -m64 flag when building the Flint test suite
- if SAGE64 is set to "yes". Otherwise it builds 32-bit
- objects and so the test files are not built, but instead
- generating the usual "WRONG ELF CLASS" error.
- * Remove a couple of lines which call spkg-check from
- spkg-install if SAGE_CHECK is set to "yes". Otherwise,
- spkg-check gets called twice, which is a waste of time.
- I'm afraid to say it was probably me that put those couple
- of lines in a year or two ago, before I realised how
- spkg-check was supposed to be called.
-
-=== flint-1.5.0.p4 (Jaap Spies, Feb 23th, 2010) ===
- * #8112 Pass CFLAG64 to FLINT_TUNE if set for a 64 bit build.
-
-=== flint-1.5.0.p3 (David Kirkby, January 2nd, 2010) ===
- * #7815 Changed makes and spkg-install so that the flag -m64 got
- added with a 64-bit build.
-
-=== flint-1.5.0.p1 (William Stein, September 25th, 2009) ===
- * Included a cygwin fix that involves naming the library .dll instead of .so.
-
-=== flint-1.5.0.p0 (Mike Hansen, September 25th, 2009) ===
- * Updated to 1.5.0.
-
-=== flint-1.3.0p3 (Ondrej Certik, September 20th, 2009) ===
- * Move libntl.a out of the way temporarily on CYGWIN (this makes the package
- built, because it will link to the .so lib instead)
-
-=== flint-1.3.0p2 (David Kirkby, June 30th, 2009) ===
- * Change '-a' to '-p' option spkg-install so flint installs
- on Solaris too. The usual GNUism. Only one byte is changed!
-
-=== flint-1.3.0 (Nick Alexander, June 9th, 2009) ===
- * Update to latest upstream FLINT, 1.3.0.
-
-=== flint-1.3.0 (Nick Alexander, June 9th, 2009) ===
- * Update to latest upstream FLINT, 1.3.0.
-
-=== flint-1.2.5.p0 (Mike Hansen, June 4th, 2009) ===
- * Fix build issues found in #6209.
-
-=== flint-1.2.5 (Michael Abshoff, April 29th, 2009) ===
- * Update to latest upstream FLINT with reenabled znpoly 0.9.
-
-=== flint-1.2.4.p1 (William Stein, April 8th, 2009) ===
- * Disable znpoly.
-
-=== flint-1.2.4.p0 (Michael Abshoff, April 5th, 2009) ===
- * Build the OSX dylibs with CPP instead of CC
-
-=== flint-1.2.4 (Michael Abshoff, April 3rd, 2009) ===
- * Upgraded to newest stable version
- * remove soname hack on Linux
- * build all tests with CPP since otherwise linker failures due to the NTL interface happen on OSX
-
-=== flint-1.2.3 (Michael Abshoff, April 2nd, 2009) ===
- * Upgraded to newest stable version
-
-=== flint-1.2.2 (Burcin Erocal, March 31st, 2009) ===
- * Upgraded to newest stable version
-
-=== flint-1.2.1 (Burcin Erocal, March 15th, 2009) ===
- * Upgraded to newest stable version
- * delay deleting library in local/lib until build is complete
- * added zmod_mat-test and NTL-interface-test to spkg-check
- * spkg-check now exits on error
- * enabled tests
-
-=== flint-1.1.2 (William Stein, March 1st, 2009) ===
- * Upgraded to newest stable version
-
-=== flint-1.1.1 (William Stein, February 28th, 2009) ===
- * Upgraded to newest stable version
-
-=== flint-1.0.21.0 (Michael Abshoff, January 2nd, 2009) ===
- * do not run the test suite automatically
-
-=== flint-1.0.21 (Michael Abshoff, December 23rd, 2008) ===
- * Upgrade to latest upstream (#4879)
-
-=== flint-1.0.20 (Michael Abshoff, December 23rd, 2008) ===
- * Upgrade to latest upstream (#4861)
- * clean up SPKG.txt
-
-=== flint-1.0.13.p0 (Michael Abshoff, August 18th, 2008) ===
- * Add 64 bit OSX support
-
-=== flint-1.0.13 (Michael Abshoff, July 21st, 2008) ===
- * Update FLINT to 1.0.13 release
-
-=== flint-1.011.p0 (William Stein, July 9th, 2008) ===
- * Fixed trac #3627: another FLINT BUG (in in ZmodF_poly_pointwise_mul): illegal instruction on modular/modsym/subspace.py on P4 3.4Ghz with 3.0.4.rc0
-
-=== flint-1.011 (Michael Abshoff, July 9th, 2008) ===
- * update FLINT to 1.0.11 release (fixes a critical Itanium bug - thanks to Bill Hart)
- * turn on spkg-check per default
- * add additional tests to spkg-check as instructed by Bill Hart
-
-=== flint-1.010.p0 (Michael Abshoff, July 6th, 2008) ===
- * Only check major and minor gcc release number, not tiny (fixes #3528)
-
-=== flint-1.010 (William Stein and Craig Citro, June 30, 2008) ===
- * upgrade to version 1.0.10
-
-=== flint-1.06.p3 (Michael Abshoff, April 1st, 2008) ===
- * import shared library versioning for flint (Tim Abbott, #3259)
- * create proper link, fix bash shebang
- * make sure $SAGE_LOCAL is defined (#633)
-
-=== flint-1.06.p2 (Michael Abshoff, April 1st, 2008) ===
- * Debian amd64 fixes for FLINT (Tim Abbott, #2762)
- * Debian Copyright patch for FLINT (Tim Abbott, #2199)
-
-=== flint-1.06.p0 (Michael Abshoff, February 2nd, 2008) ===
- * disable mandatory check
-
-=== flint-1.06 (Michael Abshoff, January 19th, 2008) ===
- * update to FLINT 1.0.6 release
- * turn make check on again per default
-
-=== flint-1.05.p0 (Michael Abshoff, January 17th, 2008) ===
- * disable mandatory check
-
-=== flint-1.05 (Michael Abshoff) ===
- * update to FLINT 1.05
-
-2007-12-19 (Michael Abshoff):
- + update to FLINT 1.03
- + reenable mandatory "make check"
-
-2007-12-16 (Michael Abshoff):
- + disable mandatory "make check"
- + remove -B flag in make check since it breaks make 2.79 and earlier
-
-2007-12-10 (Michael Abshoff): Update to FLINT 1.02
-
-2007-12-08 (Michael Abshoff): Update to FLINT 1.01
-
-2007-12-06 (Michael Abshoff): Update to FLINT 1.00
-
-2007-11-25 (Michael Abshoff): add "flint_stack_release();" in fmpz_poly.c:1485
- to avoid a memory leak. Deteced and fixed by Bill Hart
-
-2007-11-24 (Michael Abshoff): upgraded to svn r1075
-
-2007-10-02 (William Stein): upgraded to svn 1012
-
-2007-10-02 (Robert Bradshaw): upgraded to svn r1068
-
-Obtained from:
- svn export https://flint.svn.sourceforge.net/svnroot/flint/trunk
-
+== Special Update/Build Instructions ==
+=== Patches ===
+ * test_empty_string.patch: fix test for empty string in Makefile.in.
diff --git a/build/pkgs/flint/checksums.ini b/build/pkgs/flint/checksums.ini
index 825e003..ce64bd5 100644
--- a/build/pkgs/flint/checksums.ini
+++ b/build/pkgs/flint/checksums.ini
@@ -1,4 +1,4 @@
-tarball=flint-VERSION.tar.bz2
-sha1=03cb7f95b960cb64693d01a8c0b6243e64aca74c
-md5=932e1c8790b3c761eb0bc058cfdcc50b
-cksum=970975353
+tarball=flint-VERSION.tar.gz
+sha1=b506c3870a3d976796ec0b6224659e9c82dcceae
+md5=3b9bc754ef9e974ad4d0cf808d9809df
+cksum=1290600232
diff --git a/build/pkgs/flint/package-version.txt b/build/pkgs/flint/package-version.txt
index 3b11617..2cf4320 100644
--- a/build/pkgs/flint/package-version.txt
+++ b/build/pkgs/flint/package-version.txt
@@ -1 +1 @@
-2.3.p1
+2.4.1.p0
diff --git a/build/pkgs/flint/patches/cflags.patch b/build/pkgs/flint/patches/cflags.patch
deleted file mode 100644
index 55ce02a..00000000
--- a/build/pkgs/flint/patches/cflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -ru src/configure b/configure
---- src/configure 2012-11-09 21:42:47.000000000 +0100
-+++ b/configure 2013-05-08 12:12:08.233238871 +0200
-@@ -262,13 +262,7 @@
- #various tuning parameters
-
- if [ -z "$FLINT_TUNE" ]; then
-- if [ "$KERNEL" = "Linux" -a "$ARCH" = "x86_64" ]; then
-- FLINT_TUNE="-funroll-loops"
-- elif [ "$KERNEL" = "Darwin" -a "$ARCH" = "ppc" ]; then
-- FLINT_TUNE=" -funroll-loops"
-- elif [ "`uname -p`" = "powerpc" ]; then
-- FLINT_TUNE="-m64 -mcpu=970 -mtune=970 -mpowerpc64 -falign-loops=16 -falign-functions=16 -falign-labels=16 -falign-jumps=16"
-- elif [ "$ARCH" = "ia64" ]; then
-+ if [ "$ARCH" = "ia64" ]; then
- # -funroll-loops crashes the build on itanium under GCC-4.2.1, as reported by
- # Kate Minola.
- FLINT_TUNE=""
-@@ -325,6 +319,11 @@
- CFLAGS="-O2 -g -ansi -pedantic -Wall $POPCNT_FLAG $ABI_FLAG"
- fi
-
-+# Old Darwin versions (OS X 10.4) require -fno-common
-+if [ "$KERNEL" = Darwin ]; then
-+ CFLAGS="-fno-common $CFLAGS"
-+fi
-+
- #add tuning parameters to CFLAGS
-
- CFLAGS="$CFLAGS $FLINT_TUNE"
diff --git a/build/pkgs/flint/patches/dylib.patch b/build/pkgs/flint/patches/dylib.patch
deleted file mode 100644
index b7be024..00000000
--- a/build/pkgs/flint/patches/dylib.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff -druN src.orig/configure src/configure
---- src.orig/configure 2012-11-09 21:42:47.000000000 +0100
-+++ src/configure 2013-03-06 18:21:03.644037750 +0100
-@@ -225,12 +225,7 @@
- if [ -z "$FLINT_LIB" ]; then
- case $OS in
- Darwin)
-- case $MACHINE in
-- *64)
-- FLINT_LIB="libflint.dylib64";;
-- *)
-- FLINT_LIB="libflint.dylib";;
-- esac;;
-+ FLINT_LIB="libflint.dylib";;
- CYGWIN | MINGW*)
- FLINT_LIB="libflint.dll";;
- *)
diff --git a/build/pkgs/flint/patches/test_empty_string.patch b/build/pkgs/flint/patches/test_empty_string.patch
new file mode 100644
index 00000000..b407392
--- /dev/null
+++ b/build/pkgs/flint/patches/test_empty_string.patch
@@ -0,0 +1,19 @@
+commit 81c820b73dc0208f107629d7658f4f0642ca64e8
+Author: Jean-Pierre Flori <jean-pierre.flori@ssi.gouv.fr>
+Date: Mon Feb 3 15:02:22 2014 +0100
+
+ Fix test for empty string in install target.
+
+diff --git a/Makefile.in b/Makefile.in
+index 0fa717b..19caed2 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -178,7 +178,7 @@ install: library
+ cp libflint.a $(DESTDIR)$(PREFIX)/lib; \
+ fi
+ cp $(HEADERS) $(DESTDIR)$(PREFIX)/include/flint
+- $(AT)if [ ! -z $(EXT_HEADERS) ]; then \
++ $(AT)if [ ! -z "$(EXT_HEADERS)" ]; then \
+ cp $(EXT_HEADERS) $(DESTDIR)$(PREFIX)/include/flint; \
+ fi
+ mkdir -p $(DESTDIR)$(FLINT_CPIMPORT_DIR)
diff --git a/build/pkgs/lcalc/SPKG.txt b/build/pkgs/lcalc/SPKG.txt
index 8c70e38..67f8dd8 100644
--- a/build/pkgs/lcalc/SPKG.txt
+++ b/build/pkgs/lcalc/SPKG.txt
@@ -81,162 +81,13 @@ http://code.google.com/p/l-calc/
to not redefine the double() cast, thats just fragile and will sooner or
later again fail inside some system headers.
* pari-2.4.4.patch:
- (Patches src/src/Lcommandline.cc and src/src/Lcommandline_elliptic.cc)
- Use allocatemem() instead of allocatemoremem() which the new PARI no
- longer supports. Also replace lgeti() by (long)cgeti().
+ Replace obsolete lgeti() by (long)cgeti().
+ * init_stack.patch:
+ Replace obsolete allocatemoremem() by a direct call to the private
+ function pari_init_stack(). The public function allocatemem() prints
+ useless warnings and is by definition treated as an error.
* time.h.patch:
(Patches src/include/Lcommandline_numbertheory.h)
Include also <time.h> in Lcommandline_numbertheory.h (at least required
on Cygwin, cf. #9845).
This should get reported upstream.
-
-== Changelog ==
-
-=== lcalc-1.23.p11 (Jean-Pierre Flori, 8 August 2012) ===
- * #13351: modify Makefile to define binaries and libraries extension
- according to host system. As a side effect, this let
- sage.libs.lcalc.lcal_Lfunction be imported on Cygwin.
-
-=== lcalc-1.23.p10 (Leif Leonhardy, March 17th 2012) ===
- * #12681: Fix hard-coded 'g++'.
- The (patched) Makefile now uses $(CXX) (which *defaults* to 'g++')
- for compiling and linking C++, $(CC) (which *defaults* to 'gcc') for
- compiling C, although the latter is [currently] hardly used.
- See also "Special Update/Build Instructions" above. (We could now also
- set `INSTALL_DIR` and use 'make install'...)
-
-=== lcalc-1.23.p9 (Jeroen Demeyer, Leif Leonhardy, 6 October 2011) ===
- * Trac #11321: Add a patch for PARI-2.4.4 (use allocatemem() instead of
- allocatemoremem())
- * Remove unused patch Lcommandline_elliptic.cc.cygwin.diff
- * Use `patch` for patching instead of `cp`.
- * Restore upstream sources (src/src/Makefile was edited) but remove
- garbage files mentioned above.
- * Remove date from spkg version string
- * Various clean-up in spkg-install
-
-=== lcalc-20100428-1.23.p6 (Volker Braun, March 8, 2011) ===
- * upstream commented out lcalc_to_double(long double), but this is
- now required with gcc-4.6. Comment back in!
-
-=== lcalc-20100428-1.23.p5 (Jeroen Demeyer, September 19, 2010) ===
- * Remove dist directory
- * Put back SAGE_LOCAL sanity check in spkg-install
- * Change "make" to "$MAKE"
-
-=== lcalc-20100428-1.23.p4 (Mike Hansen, William Stein, September 2, 2010) ===
- * Add time.h include to Lcommandline_numbertheory.h (this should get upstreamed)
-
-=== lcalc-20100428-1.23.p3 (Mike Hansen, August 21, 2010) ===
- * Update to work on Cygwin.
- * #9775: lcalc should make a .dll file on Cygwin instead of .so file
-
-=== lcalc-20100428-1.23.p2 (John Cremona, August 13 2010 following Jeroen Demeyer, July 24, 2010) ===
- * Upgrade to PARI/GP 2.4.3 (#9343 and #9592).
- * Removed some code from spkg-install made redundant when upgrading to 1.23
- in March 2010.
-
-=== lcalc-20100428-1.23.p1 (Rishikesh, 2nd Aug 2010) ===
- * Detect OS X 10.4 and copy to libLfunction.dylib instead of libLfunction.so
-
-=== lcalc-20100428-1.23.p0 (David Kirkby, 27th May 2010) ===
- * See: #9043 - lcalc failing to build on OpenSolaris x64.
- * Force 64-bit build if SAGE64 is set to "yes" and not "yes"
- and "1" as before, since an early part of Sage ensures SAGE64
- can only be "yes" or "no", so it is pointless to check for "1" too.
- * Added a variable CXXFLAG64 to spkg-install, which defaults to
- -m64, but can be set as an environment variable to whatever flag
- is needed by the C++ compiler.
- * Export CXXFLAG64 if SAGE64 is set to "yes".
- * Added {$CXXFLAG64} to patches/Makefile.sage, so that the right flag
- is added for a 64-bit build at the link phase.
- * It should be noted the Makefile makes extensive use of $(FOOBAR),
- but such variables only work internally to the Makefile. If they need
- to be inported, then it needs to be ${FOOBAR}, and not $(FOOBAR).
- * Removed these 4 files from the source, since they serve no useful
- purpose (see note in Special Build Instructions).
- ./src/src/.Makefile.old.swp
- ./src/src/.Lcommandline.ggo.swp
- ./src/include/.Lvalue.h.swp
- ./src/include/.Lexplicit_formula.h.swp
-
-=== lcalc-20100428-1.23 (Rishikesh, 24th March 2010) ===
- * changed spkg-install to change location of header files (#4793)
- * changed compile flags so that lcalc compiles on OSX (#4793)
-
-=== lcalc-20100428-1.23 (Rishikesh, 9th March 2010) ===
- * Changed makefile to compile on solaris (#5396)
- * For lcalc wrapper, changed so that the library is copied(#5396)
- * Replace the hard coded path to pari makefile to the $SAGE_LOCAL(#5396)
-
-=== lcalc-20080205.p3 (David kirkby, 15th September, 2009) ===
- * A general tidy-up/improvement in many ways, including:
- * Force an exit on errors with 'set -e'
- * Check for SAGE_LOCAL in a better way
- * Build with debug flags as default, but allow them to be removed
- * Add flags to generate all warnings messages on both Sun and GNU compilers.
- This causes tons of warning messages from lcacl.
- * Check that the C, C++ and Fortran compilers are not a mix of Sun and GNU
- * Remove the flags which were sent directly to the assembler to
- suppress warnings. The -W flag, which works on the GNU assembler,
- is not portable and fails with Sun's assembler.
- * All tests performed in what I believe is the safest and most
- portable way, such as using || instead of -o in tests.
- * Changed the Makefile to use CXXFLAGS rather than CFLAGS, as the
- source is C++ not C, and the compiler used is the C++ compiler,
- which will ignore CFLAGS.
- * Added appropiate options to FCFLAGS. Not needed for 'lcalc', but I
- hope to use this as a template for more widespread use in Sage. It
- may however need more work, particularly in handling Fortran (There
- may be specific issues when the Fortran compiler is f90.)
- * Print variable names, to aid debugging.
- * Allow debug information to be removed from file, if
- SAGE_DEBUG is set to 'no', 'false' or '0'
- By default, debugging information will be supplied.
-
-=== lcalc-20080205.p2 (Michael Abshoff, July 15th, 2008) ===
- * remove "-static-libgcc" from CFLAGS (fixes #3647)
-
-=== lcalc-20080205.p1 (Michael Abshoff, May 18th, 2008) ===
- * add 64 bit OSX build support
-
-=== lcalc-20080205.p0 (Michael Abshoff, April 19th, 2008) ===
- * Apply Tim Abbott's Debian build fix (#2967)
-
-=== lcalc-20080205 (Michael Abshoff, April 13th, 2008) ===
- * update to lcalc 1.11 (2008-Feb-05)
- * Apply all three patches from patches directory
- * fix gcc 4.3 build issues
- * fix Solaris build
- * do not strip the lcalc binary
-
-=== lcalc-20070105 ===
- * modified Lcommandline_elliptic.cc to work with Cygwin
- by defining a certain macro. *** carry this change over when
- updating the package *** and of course backport it upstream.
-
-* New version from Mike R. on 2006-12-05.
-
-* I replaced the included Makefile with my own, since I'm only interested
- in building lcalc and not the library. Also, since I'm not doing
- development on lcalc, the dependencies aren't needed in order
- to minimize build time.
-
-
-* 2006-09-15: Fix to spkg-install suggested by Kate Minola:
-In lcalc-2006.03.05/spkg-install there is
-: CFLAGS="$CFLAGS -O2 -g -Wa,-W -fno-exceptions -Wno-deprecated"
-:
-: cd src
-:
-: echo "Building Rubinstein's lcalc program using $CXX..."
-:
-: make lcalc
-but since the environment variable CFLAGS is never exported, the subshell
-entered with 'make lcalc' does not pick up the new CFLAGS. You need to
-add
- export CFLAGS
-after the new definition of CLAGS.
-
-* Kate Minola:
- Added -static-libgcc
diff --git a/build/pkgs/lcalc/package-version.txt b/build/pkgs/lcalc/package-version.txt
index c63180d..a7292bf 100644
--- a/build/pkgs/lcalc/package-version.txt
+++ b/build/pkgs/lcalc/package-version.txt
@@ -1 +1 @@
-1.23.p11
+1.23.p12
diff --git a/build/pkgs/lcalc/patches/init_stack.patch b/build/pkgs/lcalc/patches/init_stack.patch
new file mode 100644
index 00000000..e9e0237
--- /dev/null
+++ b/build/pkgs/lcalc/patches/init_stack.patch
@@ -0,0 +1,31 @@
+diff -ru src/include/Lcommandline.h b/include/Lcommandline.h
+--- src/include/Lcommandline.h 2012-08-08 23:21:55.000000000 +0200
++++ b/include/Lcommandline.h 2014-01-06 14:04:55.981027532 +0100
+@@ -40,12 +40,7 @@
+ #include "Lcommandline_globals.h" //command line global variables
+ #ifdef INCLUDE_PARI
+ #include "pari.h" //for pari's elliptic curve functions
+-#undef init //pari has a '#define init pari_init' which
+- //causes trouble with the stream.h init.
+- //pari also causes trouble with things like abs.
+- //we place the pari include first since otherwise it
+- //messes up.
+-
++#include "paripriv.h" //for pari_init_stack()
+ #endif //ifdef INCLUDE_PARI
+
+
+diff -ru src/src/Lcommandline.cc b/src/Lcommandline.cc
+--- src/src/Lcommandline.cc 2012-08-08 23:21:56.000000000 +0200
++++ b/src/Lcommandline.cc 2014-01-06 14:02:19.463388366 +0100
+@@ -473,7 +473,9 @@
+
+ #ifdef INCLUDE_PARI
+ if(do_elliptic_curve){
+- allocatemoremem((int) N_terms*16+1000000); //XXXXXXXXX this should depend on whether we're double or long double or mpfr double
++ // Reallocate PARI stack
++ pari_init_stack((size_t)N_terms*16 + 1000000, top-bot); //XXXXXXXXX this should depend on whether we're double or long double or mpfr double
++
+ if (my_verbose>0) cout << "Will precompute " << N_terms << " elliptic L-function dirichlet coefficients..." << endl;
+ initialize_new_L(a1,a2,a3,a4,a6,N_terms);
+ }
diff --git a/build/pkgs/lcalc/patches/pari-2.4.4.patch b/build/pkgs/lcalc/patches/pari-2.4.4.patch
index 13ecf1b..cee0351 100644
--- a/build/pkgs/lcalc/patches/pari-2.4.4.patch
+++ b/build/pkgs/lcalc/patches/pari-2.4.4.patch
@@ -1,33 +1,3 @@
---- src/src/Lcommandline.cc 2010-01-31 16:16:45.000000000 +0100
-+++ src/src/Lcommandline.cc 2011-05-10 17:22:10.000000000 +0200
-@@ -31,6 +31,12 @@
- #include "Lcommandline.h"
- #include "cmdline.h"
-
-+/* No-operation error recovery routine for PARI. This is needed for
-+ * allocatemem(), which calls the error recovery routine (because
-+ * allocatemem() destroys the PARI stack).
-+ */
-+void pari_err_recover_nop(long errnum) {return;}
-+
- int main (int argc, char *argv[])
- {
-
-@@ -473,7 +479,13 @@
-
- #ifdef INCLUDE_PARI
- if(do_elliptic_curve){
-- allocatemoremem((int) N_terms*16+1000000); //XXXXXXXXX this should depend on whether we're double or long double or mpfr double
-+ /* allocatemem() calls the callback function cb_pari_err_recover(),
-+ * which we temporarily change to do nothing. */
-+ void (*saved_err_recover)(long) = cb_pari_err_recover;
-+ cb_pari_err_recover = pari_err_recover_nop;
-+ allocatemem(N_terms*16 + 1000000); //XXXXXXXXX this should depend on whether we're double or long double or mpfr double
-+ cb_pari_err_recover = saved_err_recover;
-+
- if (my_verbose>0) cout << "Will precompute " << N_terms << " elliptic L-function dirichlet coefficients..." << endl;
- initialize_new_L(a1,a2,a3,a4,a6,N_terms);
- }
--- src/src/Lcommandline_elliptic.cc 2010-01-31 16:16:45.000000000 +0100
+++ src/src/Lcommandline_elliptic.cc 2011-05-10 17:08:10.000000000 +0200
@@ -121,11 +121,11 @@
diff --git a/build/pkgs/ncurses/SPKG.txt b/build/pkgs/ncurses/SPKG.txt
index 2c62aa5..ee995e9 100644
--- a/build/pkgs/ncurses/SPKG.txt
+++ b/