Merge branch 'develop' of git://trac.sagemath.org/sage into t/24087/a…

…utomorphism_group_of_finite_abelian_groups_

Makefile

@@ -11,10 +11,14 @@ default: all
 
 build: all-build
 
+# The --stop flag below is just a random flag to induce graceful
+# breakage with non-GNU versions of make.
+# See https://trac.sagemath.org/ticket/24617
+
 # Defer unknown targets to build/make/Makefile
 %::
 	@if [ -x relocate-once.py ]; then ./relocate-once.py; fi
-	$(MAKE) build/make/Makefile
+	$(MAKE) build/make/Makefile --stop
 	+build/bin/sage-logger \
 		"cd build/make && ./install '$@'" logs/install.log
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.2.beta4, Release Date: 2018-01-27
+SageMath version 8.2.beta5, Release Date: 2018-02-09

build/pkgs/atlas/dependencies

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

build/pkgs/backports_functools_lru_cache/SPKG.txt

@@ -0,0 +1,5 @@
+= backports.functools_lru_cache =
+
+== Description ==
+
+A backport of functools.lru_cache from Python 3.3 as published at ActiveState.

build/pkgs/backports_functools_lru_cache/checksums.ini

@@ -0,0 +1,4 @@
+tarball=backports.functools_lru_cache-VERSION.tar.gz
+sha1=8a546e7887e961c2873c9b053f4e2cd2a96bd71d
+md5=b954e7d5e2ca0f0f66ad2ed12ba800e5
+cksum=2013684405

build/pkgs/backports_functools_lru_cache/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | setuptools_scm pip
+
+----------
+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/backports_functools_lru_cache/package-version.txt

@@ -0,0 +1 @@
+1.4

build/pkgs/backports_functools_lru_cache/spkg-install

@@ -0,0 +1,3 @@
+cd src
+
+sdh_pip_install .

build/pkgs/backports_functools_lru_cache/type

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

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=499badf9321c53c458652ca71580585463e574a3
-md5=e483eb587a1be5886b718e24f54a84a5
-cksum=3889320352
+sha1=ade416eb97804aa5dbc97afe9e55f63de0986270
+md5=a8b02b91f6650ecaf26ef7b2287a5e7f
+cksum=334528818

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-252
+253

build/pkgs/coxeter3/SPKG.txt

@@ -44,6 +44,6 @@ by spkg-install:
   its data and messages from the Sage installation tree
 - makefile.patch: handle compilation flags for Darwin and Cygwin
 - warning.patch: remove deprecation warnings
-- sage.cpp: add a function for Bruhat invervals which is simpler to
+- sage.cpp: add a function for Bruhat intervals which is simpler to
   code in C++ than Cython
 

build/pkgs/fplll/package-version.txt

@@ -1 +1 @@
-5.2.0.p0
+5.2.0.p1

build/pkgs/fplll/patches/GCC-PR10200.patch

@@ -0,0 +1,74 @@
+commit f9ea48c350feb9054c7176c2adec9c8e4a06f503
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Mon Feb 5 11:24:14 2018 +0100
+
+    Work around https://gcc.gnu.org/bugzilla/show_bug.cgi?id=10200
+
+    This shows up in particular on Solaris systems with GCC-5.4.0
+
+diff --git a/fplll/sieve/sieve_gauss_2sieve.cpp b/fplll/sieve/sieve_gauss_2sieve.cpp
+index 83eb817..625c6f0 100644
+--- a/fplll/sieve/sieve_gauss_2sieve.cpp
++++ b/fplll/sieve/sieve_gauss_2sieve.cpp
+@@ -33,7 +33,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_2reduce(ListPo
+     for (lp_it = List.begin(); lp_it != List.end(); ++lp_it)
+     {
+       v = *lp_it;
+-      if (p->norm < v->norm)
++      if ((p->norm) < v->norm)
+         break;
+
+       /* if there is one reduction the vector should re-pass the list */
+diff --git a/fplll/sieve/sieve_gauss_3sieve.cpp b/fplll/sieve/sieve_gauss_3sieve.cpp
+index 3c3716c..3fdbca6 100644
+--- a/fplll/sieve/sieve_gauss_3sieve.cpp
++++ b/fplll/sieve/sieve_gauss_3sieve.cpp
+@@ -27,7 +27,7 @@ GaussSieve<ZT, F>::update_p_3reduce_2reduce(ListPoint<ZT> *p,
+     for (lp_it = List.begin(); lp_it != List.end(); ++lp_it)
+     {
+       v = *lp_it;
+-      if (p->norm < v->norm)
++      if ((p->norm) < v->norm)
+         break;
+       if (half_2reduce(p, v))
+       {
+@@ -166,7 +166,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_3reduce(ListPo
+         continue;
+       }
+       ++lp_it2;
+-      if (v1->norm < p->norm)
++      if ((v1->norm) < p->norm)
+       {
+         vnew2 = new_listpoint<ZT>(nc);
+         if (check_3reduce(v1, p, v2, vnew2) != 1)
+diff --git a/fplll/sieve/sieve_gauss_4sieve.cpp b/fplll/sieve/sieve_gauss_4sieve.cpp
+index 9eb586e..f2758a4 100644
+--- a/fplll/sieve/sieve_gauss_4sieve.cpp
++++ b/fplll/sieve/sieve_gauss_4sieve.cpp
+@@ -15,7 +15,7 @@ void GaussSieve<ZT, F>::update_p_4reduce_aux(ListPoint<ZT> *p,
+   for (lp_it = List.begin(); lp_it != List.end(); ++lp_it)
+   {
+     v = *lp_it;
+-    if (p->norm < v->norm)
++    if ((p->norm) < v->norm)
+       break;
+   }
+   lp_it_k = lp_it;
+@@ -119,7 +119,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_4reduce_3reduc
+         continue;
+       }
+       ++lp_it2;
+-      if (v1->norm < p->norm)
++      if ((v1->norm) < p->norm)
+       {
+         /*cout << "#   --- here 1 " << endl;
+         cout << v1->norm << endl;
+@@ -274,7 +274,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_4reduce(ListPo
+         }
+         ++lp_it3;
+         /* (v1, p, v2, v3) or (v1, v2, p, v3) */
+-        if (v1->norm < p->norm)
++        if ((v1->norm) < p->norm)
+         {
+           /* (v1, p, v2, v3) */
+           if (v2->norm > p->norm)

build/pkgs/fplll/patches/pow.patch

@@ -0,0 +1,27 @@
+commit 848a55ec1eaa425d6843303fcc0fac9eda397a83
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Mon Feb 5 11:22:54 2018 +0100
+
+    Fix pow() calls on Solaris
+
+diff --git a/fplll/nr/dpe.h b/fplll/nr/dpe.h
+index 1ad6562..c132378 100644
+--- a/fplll/nr/dpe.h
++++ b/fplll/nr/dpe.h
+@@ -708,14 +708,14 @@ DPE_INLINE void dpe_ugly_log(dpe_t x, const dpe_t y)
+ DPE_INLINE void dpe_ugly_exp(dpe_t x, const dpe_t y)
+ {
+   // printf ("## exp is %ld\n", DPE_EXP(y));
+-  dpe_set_d(x, exp(((double)DPE_MANT(y)) * pow(2, ((double)DPE_EXP(y)))));
++  dpe_set_d(x, exp(((double)DPE_MANT(y)) * pow(2.0, ((double)DPE_EXP(y)))));
+ }
+
+ /* More hacks */
+ /* x = y^k */
+ DPE_INLINE void dpe_pow_si(dpe_t x, const dpe_t y, const unsigned int k)
+ {
+-  DPE_MANT(x) = pow(DPE_MANT(y), k);
++  DPE_MANT(x) = pow(DPE_MANT(y), (double)k);
+   DPE_EXP(x)  = DPE_EXP(y) * k;
+   dpe_normalize(x);
+ }

build/pkgs/gcc/dependencies

@@ -1,4 +1,4 @@
-| $(MP_LIBRARY) mpfr mpc zlib xz
+$(MP_LIBRARY) mpfr mpc zlib | xz
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/gfortran/SPKG.txt

@@ -0,0 +1,25 @@
+= gfortran =
+
+== Description ==
+
+The GNU Compiler Collection, including the C, C++ and Fortran compiler.
+This particular package is meant to only make gfortran available.
+
+== License ==
+
+GPL version 2 or version 3
+
+== Upstream Contact ==
+
+http://gcc.gnu.org/
+
+== Dependencies ==
+
+ * zlib
+ * MPIR
+ * MPFR
+ * MPC
+
+== Special Update/Build Instructions ==
+
+None.

build/pkgs/gfortran/checksums.ini

@@ -0,0 +1 @@
+../gcc/checksums.ini

build/pkgs/gfortran/dependencies

@@ -0,0 +1 @@
+../gcc/dependencies

build/pkgs/gfortran/package-version.txt

@@ -0,0 +1 @@
+../gcc/package-version.txt

build/pkgs/gfortran/spkg-install

@@ -0,0 +1,77 @@
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+# This spkg shouldn't be installed if gcc is already installed
+if [ -a "$SAGE_LOCAL"/bin/gcc ]; then
+    echo >&2 "Error: gcc is already installed"
+    exit 1
+fi
+
+# Exit on error
+set -e
+
+# Build in a separate directory, not in src/ (a.k.a. a VPATH build).
+# This is the recommended way to build GCC.
+mkdir gcc-build
+cd gcc-build
+
+
+# On OSX:
+if [ "$UNAME" = "Darwin" ]; then
+    # isl/cloog libraries are almost certainly from Homebrew and won't work
+    GCC_CONFIGURE="--without-isl --without-cloog $GCC_CONFIGURE"
+
+    # Use 'bootstrap-debug' build configuration to force stripping of object
+    # files prior to comparison during bootstrap (broken by Xcode 6.3).
+    # See #18156
+    GCC_CONFIGURE="--with-build-config=bootstrap-debug $GCC_CONFIGURE"
+fi
+
+# Let Gfortran build on Raspberry Pi using hard floats.
+if [ `uname -m` = "armv6l" ]; then
+    GCC_CONFIGURE="--with-arch=armv6 --with-fpu=vfp --with-float=hard $GCC_CONFIGURE"
+fi
+
+# Let Gfortran build on more recent ARM boards using hard floats.
+if [ `uname -m` = "armv7l" ]; then
+    GCC_CONFIGURE="--with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard $GCC_CONFIGURE"
+fi
+
+if [ "$SAGE_CHECK" = yes ]; then
+    # Enable internal checks in GCC.  These checks do not affect the
+    # binaries produced by GCC, but they do increase the compile time
+    # of everything compiled with GCC.
+    GCC_CONFIGURE="$GCC_CONFIGURE --enable-checking=yes"
+fi
+
+# Use the assembler/linker specified by $AS/$LD if they differ from the
+# default.
+if [ -n "$AS" -a "$AS" != "as" ]; then
+    CONFIGURE_AS="--with-as=$AS"
+fi
+if [ -n "$LD" -a "$LD" != "ld" ]; then
+    CONFIGURE_LD="--with-ld=$LD"
+fi
+
+../src/configure \
+    --prefix="$SAGE_LOCAL" \
+    --with-local-prefix="$SAGE_LOCAL" \
+    --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" --with-mpc="$SAGE_LOCAL" \
+    --with-system-zlib \
+    --disable-multilib \
+    --disable-nls \
+    --enable-languages=fortran \
+    --disable-bootstrap \
+    --disable-libitm \
+    $GCC_CONFIGURE "$CONFIGURE_AS" "$CONFIGURE_LD"
+
+$MAKE BOOT_LDFLAGS="-Wl,-rpath,$SAGE_LOCAL/lib"
+
+$MAKE install
+
+# The spkg still installs a minimal C compiler that needs to be removed
+# so it doesn't conflict with the configured C compiler.
+rm -f "$SAGE_LOCAL"/bin/gcc "$SAGE_LOCAL"/bin/cpp

build/pkgs/gfortran/type

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

build/pkgs/giac/SPKG.txt

@@ -16,8 +16,11 @@
 
 == Licence ==
 
-GPLv3+ except the french html documentation which is freely redistributable
-       for non commercial only purposes. This doc has been removed in the spkg)
+GPLv3+
+
+Note: except the french html documentation which is freely
+redistributable for non commercial only purposes. This doc has been
+removed in the Sage package, see spkg-src
 
 == Upstream Contact ==
 
@@ -30,12 +33,8 @@ GPLv3+ except the french html documentation which is freely redistributable
   * gettext, readline
   * giac will benefit of ntl, pari, mpfr, gsl, lapack but they should be already installed by sage.
   * giac can also benefit of mpfi for arithmetic on intervals.
-  * The Documentation is  pre-built, hevea or latex or ... are not needed to install the package.
+  * The Documentation is pre-built, hevea or latex or ... are not needed to install the package.
 
 == Special Update/Build Instructions ==
 
-  * The script_subdirectory of the pexpect giac interface is create in spkg-install.
-  * Some gcc 4.7.2 gives a seg fault when compiling giac, but earlier or later version
-    should be fine.
-    http://gcc.gnu.org/bugzilla/show_bug.cgi?id=54986
-  * pari support has been enabled in spkg-install. To allow this, giac have been patched to not always init pari. (See the comments in patches/README.txt for details)
+  * Use spkg-src to update this package

build/pkgs/giac/package-version.txt

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

build/pkgs/giac/patches/alloca.patch

@@ -0,0 +1,38 @@
+Always use ALLOCA macro instead of alloca()
+
+diff -ru a/src/gen.cc b/src/gen.cc
+--- a/src/gen.cc	2018-01-10 14:16:00.000000000 +0100
++++ b/src/gen.cc	2018-02-01 19:36:02.128020823 +0100
+@@ -11153,7 +11153,7 @@
+
+   /* I/O: Input routines */
+
+-  gen chartab2gen(char * & s,GIAC_CONTEXT){
++  gen chartab2gen(char * s,GIAC_CONTEXT){
+     gen res;
+     // subtype=0;
+     // initialize as a null _INT_
+@@ -11200,11 +11200,7 @@
+     if (l>0 && s[l-1]=='.'){
+       // make a copy of s, call chartab2gen recursivly, 
+       // because some implementations of strtod do not like a . at the end
+-#ifdef FREERTOS
+       ALLOCA(char, scopy, l+2); 
+-#else
+-      char * scopy=(char *)alloca(l+2);
+-#endif
+       strcpy(scopy,s);
+       scopy[l]='0';
+       scopy[l+1]=0;
+diff -ru a/src/gen.h b/src/gen.h
+--- a/src/gen.h	2017-12-19 21:15:00.000000000 +0100
++++ b/src/gen.h	2018-02-01 19:35:56.090020807 +0100
+@@ -930,7 +930,7 @@
+   void gen_sort_f(iterateur it,iterateur itend,bool (*f)(const gen &a,const gen &b));
+   void gen_sort_f_context(iterateur it,iterateur itend,bool (*f)(const gen &a,const gen &b,GIAC_CONTEXT),GIAC_CONTEXT);
+   gen makemap(); // make a new map
+-  gen chartab2gen(char * & s,GIAC_CONTEXT);
++  gen chartab2gen(char * s,GIAC_CONTEXT);
+
+
+   bool is_zero(const gen & a,GIAC_CONTEXT0);