Merge branch 'develop' into t/16023/ticket/16023

* develop: (546 commits)
  Updated Sage version to 6.3.beta6
  Trac 12947: handle numerical noise correctly
  in doc of input-parameter: is_zero=None (= instead of ==)
  one Type, one ``...```, one PEP8
  removed trac reference, since this does not give additional information; operators-->operands
  rewrote def multioperand_add to lambda-function
  make def logical_and, def logical_or inline (lambda) functions
  Trac 13331: fix doctests on 32 bits
  Include labels if not lattice polytope is not fully-dimensional.
  Enhance is_Markov_chain to handle symbolic probabilities
  Force upgrade of Singular and fix doctests on 64 bits.
  Let Singular build with clang.
  Fixed repetition of error for super additive
  Reorder arguments description.
  Fixed docstring formatting.
  Trac 12880: reviewer patch
  Trac 11474: fix doctest that depended on the extended Cremona database
  trac #16186: transducers.add for arbitrary length input vectors
  New common transducers "all" and "or"
  New common transducer Wait
  ...

Conflicts:
	src/sage/functions/bessel.py

.gitignore

@@ -37,6 +37,9 @@
 .idea
 .iml
 
+# XCode
+xcuserdata/
+
 # Eclipse
 *.pydevproject
 .project

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.beta4, released 2014-06-19
+Sage version 6.3.beta6, released 2014-07-19

build/deps

@@ -336,7 +336,7 @@ $(INST)/$(SAGETEX): $(INST)/$(PYTHON) \
 $(INST)/$(SETUPTOOLS): $(INST)/$(PYTHON)
 	+$(PIPE) "$(SAGE_SPKG) $(SETUPTOOLS) 2>&1" "tee -a $(SAGE_LOGS)/$(SETUPTOOLS).log"
 
-$(INST)/$(SINGULAR): $(INST)/$(MPIR) $(INST)/$(NTL) \
+$(INST)/$(SINGULAR): $(INST)/$(MPIR) $(INST)/$(NTL) $(INST)/$(FLINT) \
 		     $(INST)/$(READLINE) $(INST)/$(MPFR)
 	+$(PIPE) "$(SAGE_SPKG) $(SINGULAR) 2>&1" "tee -a $(SAGE_LOGS)/$(SINGULAR).log"
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=100d46c2358df82a93feb63bc339620f413caa1b
-md5=d10af4cfec628f992109225444e68ba3
-cksum=553182482
+sha1=3265062e02ba06ebe5897596eea08fb04cb3c554
+md5=f3a75a886044f86dab6565b399141bde
+cksum=666076577

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-34
+36

build/pkgs/libgap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=libgap-VERSION.tar.gz
-sha1=4ae83174267adbe615be9cab0d1f4a3c53bddb5e
-md5=e69513efa609ac1fa095db981b6c7c2b
-cksum=2720542483
+sha1=6880c1c36a59051a1e94f4866848a37f4d79cb7c
+md5=f797ca3b8d3232cb24b5fe3be704a08a
+cksum=1046627126

build/pkgs/libgap/package-version.txt

@@ -1 +1 @@
-4.7.5
+4.7.5.1

build/pkgs/lrcalc/SPKG.txt

@@ -29,42 +29,3 @@ Anders S. Buch (asbuch@math.rutgers.edu)
    spkg-src and the patch patches/build.diff. So, whenever you update
    the sources, you should use/modify the spkg-src script.
 
-== Changelog ==
-
-=== lrcalc-1.1.6.p0 (Jeroen Demeyer, 8 May 2013)  ===
- * Trac #14487: fix various build and packaging issues, add spkg-src
-   and patches/build.diff (to be applied at packaging time).
-
-=== lrcalc-1.1.6 (Jean-Pierre Flori, December 2012 - February 2013)  ===
-
- * Trac #13839:
-  * Updated to lrcalc-sage-1.1.6: let lrcalc build a shared library on Cygwin.
-  * Stop tracking the src directory which is now tracked upstream.
-
-=== lrcalc-1.1.6beta1 (Nicolas M. Thiéry, June 2012)  ===
-
- * Updated to lrcalc-1.1.6beta1:
-   * Fixed segmentation fault on Open Solaris (name conflict with hash_insert)
-   * Added quantum and fusion calculations in the README and testsuite
- * Don't install the lrcalc binaries, only the libraries and headers
-
-=== lrcalc-1.1.6beta.p0 (Nicolas M. Thiéry, June 2012)  ===
-
- * Fixed make -> $MAKE
-
-=== lrcalc-1.1.6beta (Nicolas M. Thiéry, January 2012)  ===
-
- * Upgrade to lrcalc 1.1.6beta which combines:
-   * lrcalc-1.1.5.tar.gz
-   * schmult-1.1.5.tar.gz
-   * an autotools build system
-
- * First release as optional spkg (see #10333)
-
-=== lrcalc-1.1.5b (Nicolas M. Thiéry, May 2011) ===
-
- * An alpha prerelease of 1.1.6beta
-
-=== lrcalc-1.1.4 (Mike Hansen, May 2010) ===
-
- * Initial version

build/pkgs/lrcalc/checksums.ini

@@ -1,4 +1,4 @@
-tarball=lrcalc-VERSION.tar.bz2
-sha1=b36a8bdfab9f8ca0cfc7f922b4f4b0064d364464
-md5=e41f12d2f1f04e868c5d651951f9b0ff
-cksum=3021882451
+tarball=lrcalc-VERSION.tar.gz
+sha1=8149a4c676f4b21ce9dc23145b272a061a04240a
+md5=a1d85113d9c915b41ba38fcf1741e637
+cksum=4041239855

build/pkgs/lrcalc/package-version.txt

@@ -1 +1 @@
-1.1.6.p0
+1.1.7

build/pkgs/lrcalc/patches/lrcalc-1.1.7-jump.patch

@@ -0,0 +1,138 @@
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/coprod.c lrcalc-sage-1.1.7/lrcoef/coprod.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/coprod.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/coprod.c	2014-06-29 09:51:37.000000000 +1200
+@@ -11,7 +11,7 @@
+ #include <vectarg.h>
+
+ #include "symfcn.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/lrcalc.c lrcalc-sage-1.1.7/lrcoef/lrcalc.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/lrcalc.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/lrcalc.c	2014-06-29 09:52:25.000000000 +1200
+@@ -12,7 +12,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ #define MULT_USAGE \
+ "lrcalc mult [-mz] [-r rows] [-q rows,cols] [-f rows,level] part1 - part2\n"
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/lrcoef.c lrcalc-sage-1.1.7/lrcoef/lrcoef.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/lrcoef.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/lrcoef.c	2014-06-29 09:52:50.000000000 +1200
+@@ -14,7 +14,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/lrskew.c lrcalc-sage-1.1.7/lrcoef/lrskew.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/lrskew.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/lrskew.c	2014-06-29 09:53:16.000000000 +1200
+@@ -11,7 +11,7 @@
+ #include <vectarg.h>
+
+ #include "symfcn.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/mult.c lrcalc-sage-1.1.7/lrcoef/mult.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/mult.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/mult.c	2014-06-29 09:53:45.000000000 +1200
+@@ -12,7 +12,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/sat.c lrcalc-sage-1.1.7/lrcoef/sat.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/sat.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/sat.c	2014-06-29 09:54:08.000000000 +1200
+@@ -10,7 +10,7 @@
+ #include <vector.h>
+
+ #include "symfcn.h"
+-
++#include "lrcalc_jump.h"
+
+ #define NUM_PRIMES	50
+
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/skew.c lrcalc-sage-1.1.7/lrcoef/skew.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/skew.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/skew.c	2014-06-29 09:54:40.000000000 +1200
+@@ -13,7 +13,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/alloc.c lrcalc-sage-1.1.7/mathlib/alloc.c
+--- lrcalc-sage-1.1.7-orig/mathlib/alloc.c	2013-06-09 16:12:17.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/alloc.c	2014-06-29 09:55:08.000000000 +1200
+@@ -8,6 +8,7 @@
+ #include <string.h>
+
+ #include "alloc.h"
++#include "lrcalc_jump.h"
+
+ #if 0
+ #define DEBUG_MEMORY_PRINT
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/alloc.h lrcalc-sage-1.1.7/mathlib/alloc.h
+--- lrcalc-sage-1.1.7-orig/mathlib/alloc.h	2013-06-09 16:12:17.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/alloc.h	2014-06-29 09:50:13.000000000 +1200
+@@ -2,13 +2,6 @@
+ #define _ALLOC_H
+
+ #include <stdlib.h>
+-#include <setjmp.h>
+-
+-/*  Programs using the lrcalc library should set lrcalc_panic_frame
+- *  with setjmp(lrcalc_panic_frame).  The lrcalc library will call
+- *  longjmp(lrcalc_panic_frame, 1) if an "out of memory" event occurs.
+- */
+-jmp_buf lrcalc_panic_frame;
+
+ void *amalloc(size_t size);
+ void *acalloc(size_t num, size_t size);
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/lrcalc_jump.h lrcalc-sage-1.1.7/mathlib/lrcalc_jump.h
+--- lrcalc-sage-1.1.7-orig/mathlib/lrcalc_jump.h	1970-01-01 12:00:00.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/lrcalc_jump.h	2014-06-29 09:49:42.000000000 +1200
+@@ -0,0 +1,11 @@
++#ifndef _JUMP_H
++
++#include <setjmp.h>
++
++/*  Programs using the lrcalc library should set lrcalc_panic_frame
++ *  with setjmp(lrcalc_panic_frame).  The lrcalc library will call
++ *  longjmp(lrcalc_panic_frame, 1) if an "out of memory" event occurs.
++ */
++jmp_buf lrcalc_panic_frame;
++
++#endif
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/salloc.c lrcalc-sage-1.1.7/mathlib/salloc.c
+--- lrcalc-sage-1.1.7-orig/mathlib/salloc.c	2013-06-09 16:12:17.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/salloc.c	2014-06-29 09:55:34.000000000 +1200
+@@ -13,6 +13,7 @@
+ #include <string.h>
+
+ #include "alloc.h"
++#include "lrcalc_jump.h"
+
+ typedef struct mlink {
+   struct mlink *next;

build/pkgs/lrcalc/spkg-install

@@ -8,6 +8,15 @@ fi
 
 cd src
 
+for patch in ../patches/*.patch; do
+    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
+    patch -p1 <"$patch"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error applying '$patch'"
+        exit 1
+    fi
+done
+
 ./configure --prefix="$SAGE_LOCAL"
 if [ $? -ne 0 ]; then
    echo "Error configuring lrcalc."

build/pkgs/openssl/SPKG.txt

@@ -22,27 +22,5 @@ library in a variety of computer languages are available.
 
 === Patches ===
 
- * src/Configure: Sage's gcc doesn't recognize the '-arch' option,
-   while Apple's gcc does, so we remove this flag.
  * src/config: patched to fix a problem on Solaris.
 
-== Changelog ==
-
-=== openssl-1.0.1c.p0 (John Palmieri, 17 June 2012) ===
- * Trac #13126: Update source to 1.0.1c
- * Created hg repository
- * Cleaned up spkg-install
- * Created spkg-check
- * Patch to build on OS X Lion
- * Patch to build on Solaris
-
-=== openssl-1.0.1a (Mariah Lenox, 23 April 2012) ===
- * upgraded source
-
-=== openssl-1.0.0.p0 (William Stein, June 3, 2010) ===
- * Fix issue with openssl libraries getting installed to lib64,
-   as recommended by Mariah (the referee).
-
-=== openssl-1.0.0 (William Stein, April 27, 2010) ===
- * Initial version in modernized format
-

build/pkgs/openssl/checksums.ini

@@ -1,4 +1,4 @@
 tarball=openssl-VERSION.tar.gz
-sha1=3f1b1223c9e8189bfe4e186d86449775bd903460
-md5=66bf6f10f060d561929de96f9dfe5b8c
-cksum=4124470397
+sha1=b2239599c8bf8f7fc48590a55205c26abe560bf8
+md5=8d6d684a9430d5cc98a62a5d8fbda8cf
+cksum=3773835410

build/pkgs/openssl/package-version.txt

@@ -1 +1 @@
-1.0.1e
+1.0.1h

build/pkgs/python/checksums.ini

@@ -1,4 +1,4 @@
 tarball=python-VERSION.tar.gz
-sha1=1db01d7f325d8ceaf986976800106018b82ae45a
-md5=cf842800b67841d64e7fb3cd8acb5663
-cksum=559226099
+sha1=511960dd78451a06c9df76509635aeec05b2051a
+md5=d4bca0159acb0b44a781292b5231936f
+cksum=3938213866

build/pkgs/python/package-version.txt

@@ -1 +1 @@
-2.7.7
+2.7.8

build/pkgs/r/SPKG.txt

@@ -46,4 +46,4 @@ much code written for S runs unaltered under R.
    libintl library.
  * large_address_aware.patch: don't pass --large-address-aware to ld on
    Cygwin64.
-
+ * 3.1 : Upstream now handles some of these issues. Some examples changed.

build/pkgs/r/checksums.ini

@@ -1,4 +1,4 @@
-tarball=r-VERSION.tar.bz2
-sha1=0ba9c6e5ceda749cccf5bd9cf5b535ff163deefe
-md5=9247263d8a7d1e2e6794ba41f265eda4
-cksum=1117391428
+tarball=r-3.1.0.tar.gz
+sha1=a9d13932c739cc12667c6a17fabd9361624a1708
+md5=a1ee52446bee81820409661e6d114ab1
+cksum=3701745191

build/pkgs/r/package-version.txt

@@ -1 +1 @@
-3.0.2.p1
+3.1.0.p0

build/pkgs/r/patches/configure.patch

@@ -1,7 +1,7 @@
 diff -ru src/configure src.configure/configure
 --- src/configure	2011-10-24 00:05:54.000000000 +0200
 +++ src.configure/configure	2012-03-30 16:31:51.409247321 +0200
-@@ -22492,7 +22492,7 @@
+@@ -22876,7 +22492,7 @@
  if ac_fn_f77_try_compile "$LINENO"; then :
    ac_cv_prog_f77_v=
  # Try some options frequently used verbose output
@@ -10,7 +10,7 @@ diff -ru src/configure src.configure/configure
    cat > conftest.$ac_ext <<_ACEOF
        program main
 
-@@ -22808,7 +22808,7 @@
+@@ -23232,7 +22808,7 @@
  if ac_fn_c_try_compile "$LINENO"; then :
    r_cv_prog_c_v=
  # Try some options frequently used verbose output