Merge branch 'develop' into 22572

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.2.beta5, Release Date: 2018-02-09
+SageMath version 8.2.beta7, Release Date: 2018-03-03

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=1e24a1ae606e4594d374ef5a6c44fdd803d28c3e
+md5=33cdee2c4d4a8cc293f083f503be8b20
+cksum=2711614580

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-253
+255

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/gcc/spkg-install

@@ -122,11 +122,10 @@ $MAKE BOOT_LDFLAGS="-Wl,-rpath,$SAGE_LOCAL/lib"
 $MAKE install
 
 
-# Force re-installation of gmp, mpir, mpfr and mpc with the GCC we just built.
-# Also mark gfortran as not installed.
+# Mark gfortran as not installed in case gfortran was installed earlier
 cd "$SAGE_SPKG_INST"
 rm -f gmp-* mpir-* mpfr-* mpc-* gfortran-*
 
-# Force re-configuration: the next time that "make" is run, we don't
-# want GCC to be built again, see Trac #19324
+# Force re-configuration: the next time that "make" is run, we need to
+# rebuild all packages (#24703) but we should not rebuild gcc (#19324)
 touch "$SAGE_ROOT/configure"

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/libatomic_ops/SPKG.txt

@@ -0,0 +1,22 @@
+= libatomic_ops =
+
+== Description ==
+
+A part of the Boehm-Demers-Weiser conservative garbage collector.
+
+== License ==
+
+* Permissive BSD + GPL 2.0+
+
+== Upstream Contact ==
+
+Webpage: http://www.hboehm.info/gc/
+Email List: bdwgc@lists.opendylan.org
+
+== Dependencies ==
+
+None.
+
+== Special Update/Build Instructions ==
+
+None.

build/pkgs/libatomic_ops/checksums.ini

@@ -0,0 +1,4 @@
+tarball=libatomic_ops-VERSION.tar.gz
+sha1=ebed1891250cc8e2c952b88fc07e1db2a213f7e2
+md5=395c0ceb46db60be209bbd3c0d6cd04d
+cksum=1257402450

build/pkgs/libatomic_ops/dependencies

@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/libatomic_ops/package-version.txt

@@ -0,0 +1 @@
+7.6.2

build/pkgs/libatomic_ops/spkg-check

@@ -0,0 +1,24 @@
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined ... exiting"
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+cd src
+
+if [ "$SAGE_DEBUG" = "yes" ]; then
+    export CFLAGS="-O0 -g $CFLAGS"
+else
+    export CFLAGS="-O2 -g $CFLAGS"
+fi
+
+if [ "$SAGE64" = "yes" ]; then
+    export CFLAGS="-m64 $CFLAGS"
+fi
+
+$MAKE check
+
+if [ $? -ne 0 ]; then
+   echo "Error testing libatomic_ops."
+   exit 1
+fi

build/pkgs/libatomic_ops/spkg-install

@@ -0,0 +1,21 @@
+cd src
+
+if [ "$SAGE_DEBUG" = "yes" ]; then
+    echo "Building a debug version of BoehmGC."
+    export CFLAGS="-O0 -g $CFLAGS"
+else
+    export CFLAGS="-O2 -g $CFLAGS"
+fi
+
+if [ "$SAGE64" = "yes" ]; then
+    echo "Building a 64-bit version of BoehmGC."
+    export CFLAGS="-m64 $CFLAGS"
+fi
+
+if [ "$UNAME" = "CYGWIN" ]; then
+    CONFIGURE_FLAGS="$CONFIGURE_FLAGS --enable-shared --disable-static"
+fi
+
+sdh_configure $CONFIGURE_FLAGS
+sdh_make
+sdh_make_install

build/pkgs/libatomic_ops/type

@@ -0,0 +1 @@
+standard

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