Merge branch 'develop' into t/24630/inconsistency_in_conversion_from_…

…cif_and_complex

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.2.beta5, Release Date: 2018-02-09
+SageMath version 8.2.beta6, Release Date: 2018-02-18

build/pkgs/arb/checksums.ini

@@ -1,4 +1,4 @@
 tarball=arb-VERSION.tar.gz
-sha1=2f06bfb433cdaecde0e824c5e638094fd666a0d1
-md5=d63cdd1147104790826c93bc8651104f
-cksum=2745482665
+sha1=27476d0529e48a07d92da90bd0fb80dd18f443e3
+md5=733285d9705d10b8024e551ffa81952f
+cksum=2391183744

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.11.1.p0
+2.12.0.p0

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=ade416eb97804aa5dbc97afe9e55f63de0986270
-md5=a8b02b91f6650ecaf26ef7b2287a5e7f
-cksum=334528818
+sha1=5c564595c8dab9d93e86dcc43141b956086d9e16
+md5=9125aedb54d788ec1acb8f3112c5a04e
+cksum=251192083

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-253
+254

build/pkgs/cypari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cypari2-VERSION.tar.gz
-sha1=9e1848b5dc566133edad79437fd39e298e336642
-md5=f268f870d255bb98bd4e917f0d74a463
-cksum=3159551499
+sha1=d27b8a80470514471a59e38f3e7248c677c58abb
+md5=38149046fbdbecc390ce45e28fc10f8a
+cksum=296167081

build/pkgs/cypari/package-version.txt

@@ -1 +1 @@
-1.1.3
+1.1.4

build/pkgs/flint/package-version.txt

@@ -1 +1 @@
-2.5.2.p1
+2.5.2.p2

build/pkgs/flint/patches/linking_SunOS_FreeBSD.patch

@@ -0,0 +1,42 @@
+diff --git a/Makefile.in b/Makefile.in
+index 2d0475d..a8b2b44 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -118,6 +118,7 @@ $(FLINT_LIB): $(LOBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) |
+ 		$(LDCONFIG) -n "$(CURDIR)"; \
+ 	fi
+ 	ln -sf "$(FLINT_LIB)" "$(FLINT_LIBNAME)"; \
++	ln -sf "$(FLINT_LIB)" "$(FLINT_LIBNAME).$(FLINT_MAJOR)"; \
+
+ libflint.a: $(OBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) | build build/interfaces
+ 	$(AT)$(foreach ext, $(EXTENSIONS), $(foreach dir, $(filter-out %templates, $(patsubst $(ext)/%.h, %, $(wildcard $(ext)/*.h))), mkdir -p build/$(dir); BUILD_DIR=$(CURDIR)/build/$(dir); export BUILD_DIR; MOD_DIR=$(dir); export MOD_DIR; $(MAKE) -f $(CURDIR)/Makefile.subdirs -C $(ext)/$(dir) static || exit $$?;))
+diff --git a/configure b/configure
+index 424ab0a..959a650 100755
+--- a/configure
++++ b/configure
+@@ -450,7 +450,7 @@ fi
+
+ # sometimes LDCONFIG is not to be found in the path. Look at some common places.
+ case "$OS" in
+-   MINGW*|CYGWIN*|Darwin)
++   MINGW*|CYGWIN*|Darwin|FreeBSD)
+       LDCONFIG="true";;
+    *)
+       if [ -z "$LDCONFIG" ]; then
+@@ -551,6 +551,8 @@ if [ -z "$CFLAGS" ]; then
+       CFLAGS="-O2 -funroll-loops -g -D _WIN64 $POPCNT_FLAG $ABI_FLAG"
+    elif [ "$MACHINE" = "mips64" ]; then
+       CFLAGS="-O2 -funroll-loops -g $POPCNT_FLAG $ABI_FLAG"
++   elif [ "$KERNEL" = FreeBSD ]; then
++      CFLAGS="-std=c99 -pedantic -Wall -O2 -funroll-loops -g $POPCNT_FLAG $ABI_FLAG $OPENMP_FLAG"
+    else
+       CFLAGS="-ansi -pedantic -Wall -O2 -funroll-loops -g $POPCNT_FLAG $ABI_FLAG"
+    fi
+@@ -715,6 +717,7 @@ echo "FLINT_SHARED=$SHARED" >> Makefile
+ echo "FLINT_LIB=$FLINT_LIB" >> Makefile
+ echo "FLINT_LIBNAME=$FLINT_LIBNAME" >> Makefile
+ echo "FLINT_SOLIB=$FLINT_SOLIB" >> Makefile
++echo "FLINT_MAJOR=$FLINT_MAJOR" >> Makefile
+ echo "EXEEXT=$EXEEXT" >> Makefile
+ echo "PREFIX=$PREFIX" >> Makefile
+ echo "" >> Makefile

build/pkgs/giac/package-version.txt

@@ -1 +1 @@
-1.4.9.45.p1
+1.4.9.45.p2

build/pkgs/giac/patches/hashmap.patch

@@ -0,0 +1,13 @@
+diff --git a/giac-1.4.9.45-orig/src/src/index.h b/giac-1.4.9.45/src/src/index.h
+index e74be63..8ed12f9 100755
+--- a/src/index.h
++++ b/src/index.h
+@@ -42,7 +42,7 @@
+ #include <unordered_map>
+ #endif
+
+-#if defined UNORDERED_MAP  && !defined(__clang__) && !defined(VISUALC) // && !defined(__APPLE__)
++#if defined UNORDERED_MAP  && !defined(VISUALC) // && !defined(__APPLE__)
+ #include <tr1/unordered_map>
+ #define HASH_MAP_NAMESPACE std::tr1
+ #define hash_map unordered_map

build/pkgs/ipywidgets/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ipywidgets-VERSION.tar.gz
-sha1=3ec713b82cc415ebe63e2971cc7acae28e89d657
-md5=245c978e0ca64b9e686b716c71efb675
-cksum=3038350627
+sha1=8b32ce2f82665ab500b7f359bf93bbf803731cff
+md5=4538e533c99ac950d9bc39fdb8d07610
+cksum=475923855

build/pkgs/ipywidgets/package-version.txt

@@ -1 +1 @@
-6.0.0
+7.1.1

build/pkgs/mpfr/checksums.ini

@@ -1,4 +1,4 @@
 tarball=mpfr-VERSION.tar.bz2
-sha1=799245347044c8f0da9e513f86bb5e4c07974931
-md5=ef619f3bb68039e35c4a219e06be72d0
-cksum=3469661192
+sha1=fcbbafb37c683898e585b926608d540ed037609e
+md5=8c21d8ac7460493b2b9f3ef3cc610454
+cksum=3260550035

build/pkgs/mpfr/package-version.txt

@@ -1 +1 @@
-4.0.0
+4.0.1

build/pkgs/pandocfilters/SPKG.txt

@@ -20,5 +20,4 @@ Home page: https://github.com/jgm/pandocfilters
 == Special Update/Build Instructions ==
 
 Download the last release from
-https://github.com/jgm/pandocfilters/releases
-
+https://pypi.python.org/pypi/pandocfilters

build/pkgs/pandocfilters/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pandocfilters-VERSION.tar.gz
-sha1=fa54e5e61b896fe9bcffaf39035e1a7d282953ec
-md5=54301b11175a57120168d7695fe958e4
-cksum=1528146878
+sha1=46695990e2a2fedbab0d24b0f49fae8f1850d95a
+md5=dc391791ef54c7de1572d7b46b63361f
+cksum=2264149273

build/pkgs/pandocfilters/package-version.txt

@@ -1 +1 @@
-1.3.0
+1.4.2

build/pkgs/pandocfilters/spkg-install

@@ -1,15 +1 @@
-if [ "$SAGE_LOCAL" = "" ]; then
-   echo "SAGE_LOCAL undefined ... exiting";
-   echo "Maybe run 'sage -sh'?"
-   exit 1
-fi
-
-cd src
-
-sdh_pip_install .
-
-if [ $? -ne 0 ]; then
-    echo "Error installing pandocfilters ... exiting"
-    exit 1
-fi
-
+cd src && sdh_pip_install .

build/pkgs/ppl/package-version.txt

@@ -1 +1 @@
-1.2
+1.2.p1

build/pkgs/ppl/patches/clang5-support.patch

@@ -0,0 +1,37 @@
+From: Roberto Bagnara <bagnara@cs.unipr.it>
+Date: Sun, 11 Feb 2018 08:11:09 +0000 (+0100)
+Subject: Added missing "template" and "typename" keywords.
+X-Git-Url: http://www.cs.unipr.it/git/gitweb.cgi?p=ppl%2Fppl.git;a=commitdiff_plain;h=c39f6a07b51f89e365b05ba4147aa2aa448febd7;hp=3a5e1e20a94cffb830182f22132b153d6691b7c5
+
+Added missing "template" and "typename" keywords.
+(Thanks to Dmitrii Pasechnik.)
+---
+
+diff --git a/src/Determinate_inlines.hh b/src/Determinate_inlines.hh
+index 2749953..5b47275 100644
+--- a/src/Determinate_inlines.hh
++++ b/src/Determinate_inlines.hh
+@@ -289,8 +289,8 @@ operator()(Determinate& x, const Determinate& y) const {
+
+ template <typename PSET>
+ template <typename Binary_Operator_Assign>
+-inline
+-Determinate<PSET>::Binary_Operator_Assign_Lifter<Binary_Operator_Assign>
++inline typename
++Determinate<PSET>::template Binary_Operator_Assign_Lifter<Binary_Operator_Assign>
+ Determinate<PSET>::lift_op_assign(Binary_Operator_Assign op_assign) {
+   return Binary_Operator_Assign_Lifter<Binary_Operator_Assign>(op_assign);
+ }
+diff --git a/src/OR_Matrix_inlines.hh b/src/OR_Matrix_inlines.hh
+index b20b697..8124b7f 100644
+--- a/src/OR_Matrix_inlines.hh
++++ b/src/OR_Matrix_inlines.hh
+@@ -97,7 +97,7 @@ OR_Matrix<T>::Pseudo_Row<U>::Pseudo_Row(const Pseudo_Row<V>& y)
+
+ template <typename T>
+ template <typename U>
+-inline OR_Matrix<T>::Pseudo_Row<U>&
++inline typename OR_Matrix<T>::template Pseudo_Row<U>&
+ OR_Matrix<T>::Pseudo_Row<U>::operator=(const Pseudo_Row& y) {
+   first = y.first;
+ #if PPL_OR_MATRIX_EXTRA_DEBUG

build/pkgs/pynac/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pynac-VERSION.tar.bz2
-sha1=ec322d219a9c02b95a29789ca221b28c6cca7a14
-md5=10f21726733209ae6f641b5736c4c9fb
-cksum=2341458065
+sha1=6884e38508746afc3bb35ed544a2b6605b7d1c13
+md5=ce413448e8adbda7239a59f326128341
+cksum=1898847628

build/pkgs/pynac/package-version.txt

@@ -1 +1 @@
-0.7.15
+0.7.16.p0

build/pkgs/pynac/patches/memleak.patch

@@ -0,0 +1,68 @@
+diff --git a/ginac/numeric.cpp b/ginac/numeric.cpp
+index c92dffa..0e1352c 100644
+--- a/ginac/numeric.cpp
++++ b/ginac/numeric.cpp
+@@ -1969,7 +1969,6 @@ numeric & operator+=(numeric & lh, const numeric & rh)
+                         }
+                         lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                         Py_DECREF(p);
+-                        Py_INCREF(lh.v._pyobject);
+                         return lh;
+                         }
+                 default:
+@@ -2049,7 +2048,6 @@ numeric & operator-=(numeric & lh, const numeric & rh)
+                         }
+                         lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                         Py_DECREF(p);
+-                        Py_INCREF(lh.v._pyobject);
+                         return lh;
+                         }
+                 default:
+@@ -2131,7 +2129,6 @@ numeric & operator*=(numeric & lh, const numeric & rh)
+                         }
+                         lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                         Py_DECREF(p);
+-                        Py_INCREF(lh.v._pyobject);
+                         return lh;
+                         }
+                 default:
+@@ -2265,7 +2262,6 @@ numeric & operator/=(numeric & lh, const numeric & rh)
+                                         }
+                                         lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                                         Py_DECREF(p);
+-                                        Py_INCREF(lh.v._pyobject);
+                                         return lh;
+                                 } else if (PyLong_Check(rh.v._pyobject)) {
+                                         PyObject* d = py_funcs.py_integer_from_python_obj(rh.v._pyobject);
+@@ -2277,7 +2273,6 @@ numeric & operator/=(numeric & lh, const numeric & rh)
+                                         lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                                         Py_DECREF(d);
+                                         Py_DECREF(p);
+-                                        Py_INCREF(lh.v._pyobject);
+                                         return lh;
+                                 }
+                         } else if (PyLong_Check(p)) {
+@@ -2290,7 +2285,6 @@ numeric & operator/=(numeric & lh, const numeric & rh)
+                                 lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                                 Py_DECREF(n);
+                                 Py_DECREF(p);
+-                                Py_INCREF(lh.v._pyobject);
+                                 return lh;
+                         }
+                         }
+@@ -2306,7 +2300,6 @@ numeric & operator/=(numeric & lh, const numeric & rh)
+                                 lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                                 Py_DECREF(n);
+                                 Py_DECREF(p);
+-                                Py_INCREF(lh.v._pyobject);
+                                 return lh;
+                         }
+                         }
+@@ -2318,7 +2311,6 @@ numeric & operator/=(numeric & lh, const numeric & rh)
+                         }
+                         lh.hash = (long)PyObject_Hash(lh.v._pyobject);
+                         Py_DECREF(p);
+-                        Py_INCREF(lh.v._pyobject);
+                         return lh;
+                         }
+                 default:

build/pkgs/sqlite/checksums.ini

@@ -1,4 +1,4 @@
-tarball=sqlite-VERSION.tar.gz
-sha1=7bcff1c158ed9e2c0e159c1b4b6c36d4d65dff8c
-md5=450a95a7bde697c9fe4de9ae2fffdcca
-cksum=2662976810
+tarball=sqlite-autoconf-VERSION.tar.gz
+sha1=2fb24ec12001926d5209d2da90d252b9825366ac
+md5=96b5648d542e8afa6ab7ffb8db8ddc3d
+cksum=1556846983

build/pkgs/sqlite/package-version.txt

@@ -1 +1 @@
-autoconf-3170000.p0
+3220000

build/pkgs/subprocess32/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | pip
+$(PYTHON) | pip python3
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/subprocess32/fix_config.py

@@ -0,0 +1,48 @@
+# Fix build of subprocess32
+#
+# subprocess32 is a backport from Python 3 to Python 2. But only the C
+# sources were backported, not the configure script. This way, macros
+# like HAVE_DIRFD which come from the Python 3 configure script are
+# always undefined. This causes breakage on certain platforms.
+# See upstream bug
+# https://github.com/google/python-subprocess32/issues/40
+#
+# In Sage, we fix this by using the actual pyconfig.h file from our
+# Python 3 installation.
+#
+# This Python script should be run with the Python version where
+# subprocess32 will eventually be installed.
+
+
+import os
+from sysconfig import get_path
+from subprocess import check_output
+
+
+# Path to the Python 3 includes
+cmd = "from sysconfig import get_path; print(get_path('include'), end='')"
+py3incdir = check_output(["python3", "-c", cmd])
+
+# Path to the includes of the Python installation where subprocess32
+# will be installed
+incdir = get_path("include")
+
+
+# Create a fake "Python.h" file which includes "pyconfig.h" from
+# Python 3 and then includes the real Python.h header
+header = '''
+/* Include pyconfig.h from Python 3 */
+#include "{}/pyconfig.h"
+
+/* Make sure that the Python 2 version of pyconfig.h can also be included */
+#undef Py_PYCONFIG_H
+
+/* Include the real Python.h file */
+#include "{}/Python.h"
+'''.format(py3incdir, incdir)
+
+
+print("NOTE: Using Python 3 configuration to build subprocess32 for Python 2")
+
+with open("Python.h", "w") as f:
+    f.write(header)

build/pkgs/subprocess32/package-version.txt

@@ -1 +1 @@
-3.2.7
+3.2.7.p0