Merge tag '6.4' into ticket/16640

Sage version 6.4

Conflicts:
	src/sage/plot/plot3d/base.pyx

README.txt

@@ -64,7 +64,7 @@ QUICK INSTRUCTIONS TO BUILD FROM SOURCE
 
 The following steps briefly outline the process of building Sage from
 source. More detailed instructions, including how to build faster on
-multicore machines are contained later in this README and in the
+multicore machines, are contained later in this README and in the
 Installation Guide:
 
     http://www.sagemath.org/doc/installation

VERSION.txt

@@ -1 +1 @@
-Sage version 6.4.rc0, released 2014-10-30
+Sage version 6.4, released 2014-11-14

build/install

@@ -129,30 +129,24 @@ else
                 # https://groups.google.com/forum/?fromgroups#!topic/sage-devel/KCeFqQ_w2FE
                 echo >&2 "Installing GCC because you have $CXX version $GCCVERSION, which is quite old."
                 need_to_install_gcc=yes;;
-            4.4*|4.5*)
+            4.4.*|4.5.*)
                 # GCC 4.4.x and GCC 4.5.x fail to compile PARI/GP on ia64:
                 # * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=46044
                 if [ x`uname -m` = xia64 ]; then
                     echo >&2 "Installing GCC because you have $CXX version $GCCVERSION on ia64."
                     echo >&2 "gcc <= 4.5 fails to compile PARI/GP on ia64."
                     need_to_install_gcc=yes
                 fi;;
-            4.6.[01])
-                # Also install GCC if we have version 4.6.0 or 4.6.1, which is
+            4.6.*)
+                # Also install GCC if we have version 4.6.* which is
                 # known to give trouble within Sage:
                 # * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48702
                 # * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48774
+                # * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=52061
+                # * https://groups.google.com/d/msg/sage-release/xgmJ3nAcUOY/jH8OZjftYRsJ
                 echo >&2 "Installing GCC because you have $CXX version $GCCVERSION."
-                echo >&2 "gcc-4.6.0 and gcc-4.6.1 have known bugs affecting Sage."
+                echo >&2 "gcc-4.6.* has known bugs affecting Sage."
                 need_to_install_gcc=yes;;
-            4.6*)
-                # GCC 4.6.x doesn't compile ECL on Cygwin:
-                # * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=52061
-                if uname | grep CYGWIN >/dev/null; then
-                    echo >&2 "Installing GCC because you have $CXX version $GCCVERSION on Cygwin."
-                    echo >&2 "gcc-4.6.x fails to compile ECL on Cygwin."
-                    need_to_install_gcc=yes
-                fi;;
             4.7.0)
                 # GCC 4.7.0 is very broken on ia64, see
                 # http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48496

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=f36dcb6fc8c54f740a1ac320d8431ab3c4dfb0cc
-md5=b0ca65bc85b94ba59aa45b7d2266bd1f
-cksum=1249053991
+sha1=3d31c6b8f81341adaf05d841fe7002529ba86d43
+md5=4e5a65be3826adbbaf4dc811ee124e08
+cksum=1057167572

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-51
+54

build/pkgs/gcc/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gcc-VERSION.tar.bz2
-sha1=3f303f403053f0ce79530dae832811ecef91197e
-md5=fddf71348546af523353bd43d34919c1
-cksum=1055529215
+sha1=79dbcb09f44232822460d80b033c962c0237c6d8
+md5=4df8ee253b7f3863ad0b86359cd39c43
+cksum=2698546200

build/pkgs/gcc/package-version.txt

@@ -1 +1 @@
-4.9.1.p0
+4.9.2

build/pkgs/gcc/spkg-install

@@ -81,6 +81,11 @@ if { uname -sr | grep 'Darwin 14\.' ;} &>/dev/null; then
     fi
 fi
 
+# On OSX: isl/cloog libraries are almost certainly from Homebrew and won't work
+if [ "$UNAME" = "Darwin" ]; then
+    GCC_CONFIGURE="--without-isl --without-cloog $GCC_CONFIGURE"
+fi
+
 # Let GCC 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"

build/pkgs/openssl/checksums.ini

@@ -1,4 +1,4 @@
 tarball=openssl-VERSION.tar.gz
-sha1=b2239599c8bf8f7fc48590a55205c26abe560bf8
-md5=8d6d684a9430d5cc98a62a5d8fbda8cf
-cksum=3773835410
+sha1=cff86857507624f0ad42d922bb6f77c4f1c2b819
+md5=f7175c9cd3c39bb1907ac8bba9df8ed3
+cksum=490651201

build/pkgs/openssl/package-version.txt

@@ -1 +1 @@
-1.0.1h
+1.0.1j

build/pkgs/pkgconf/SPKG.txt

@@ -24,3 +24,6 @@ https://github.com/pkgconf/pkgconf
 == Special Update/Build Instructions ==
 
 * install.patch: Use install script from AC_PROG_INSTALL
+
+Pkgconf is used in bzip2, so we must not use the bzip2-compressed
+tarball.

build/pkgs/pkgconf/checksums.ini

@@ -1,4 +1,4 @@
-tarball=pkgconf-VERSION.tar.bz2
-sha1=2d353227f5dfbcaa2c0f48f045f828dac2abcff0
-md5=88f34448e9c5c20b23c328824043a239
-cksum=997423134
+tarball=pkgconf-VERSION.tar.gz
+sha1=9943ba508c3293cd3afb5187f633104f8305af42
+md5=56837bbee89a542ffe7012b4a52caf5b
+cksum=320066684

build/pkgs/pkgconf/package-version.txt

@@ -1 +1 @@
-0.9.4
+0.9.7

build/pkgs/ppl/SPKG.txt

@@ -42,7 +42,7 @@ Enea Zaffanella (University of Parma)
 
 == Special Update/Build Instructions ==
 
-Patches:
-
+=== Patches ===
 * ptrdiff_t-ppl-1.1.patch: Fixes to compile with gcc 4.9; C++ name
   lookup issue.
+* weak.patch: disable use of weak symbols on Cygwin64.

build/pkgs/ppl/patches/weak.patch

@@ -0,0 +1,24 @@
+diff -druN ppl-1.1.orig/src/assert.hh ppl-1.1/src/assert.hh
+--- ppl-1.1.orig/src/assert.hh	2013-10-28 13:38:33.000000000 +0100
++++ ppl-1.1/src/assert.hh	2014-04-08 11:40:48.924491100 +0200
+@@ -98,7 +98,7 @@
+
+ namespace Parma_Polyhedra_Library {
+
+-#if PPL_CXX_SUPPORTS_ATTRIBUTE_WEAK
++#if PPL_CXX_SUPPORTS_ATTRIBUTE_WEAK && ! (defined(__CYGWIN__) && defined(__x86_64__))
+ #define PPL_WEAK_NORETURN __attribute__((weak, noreturn))
+ #else
+ #define PPL_WEAK_NORETURN __attribute__((noreturn))
+diff -druN ppl-1.1.orig/src/ppl.hh.dist ppl-1.1/src/ppl.hh.dist
+--- ppl-1.1.orig/src/ppl.hh.dist	2013-10-28 13:47:20.000000000 +0100
++++ ppl-1.1/src/ppl.hh.dist	2014-04-08 11:01:13.361991100 +0200
+@@ -1739,7 +1739,7 @@
+
+ namespace Parma_Polyhedra_Library {
+
+-#if PPL_CXX_SUPPORTS_ATTRIBUTE_WEAK
++#if PPL_CXX_SUPPORTS_ATTRIBUTE_WEAK && ! (defined(__CYGWIN__) && defined(__x86_64__))
+ #define PPL_WEAK_NORETURN __attribute__((weak, noreturn))
+ #else
+ #define PPL_WEAK_NORETURN __attribute__((noreturn))

build/pkgs/sagenb/checksums.ini

@@ -1,4 +1,4 @@
 tarball=sagenb-VERSION.tar
-sha1=a6e39573251fcdbb02f7a851041d49b7fb286395
-md5=75665520800ebc0addadb67e274bf9eb
-cksum=404833031
+sha1=5f731ed387351cd1d1d130769ca309764cd2ecd9
+md5=eb4fd89c8c907171a098fa6f06891bd8
+cksum=3318210891

build/pkgs/sagenb/package-version.txt

@@ -1 +1 @@
-0.11.0
+0.11.1

build/pkgs/setuptools/package-version.txt

@@ -1 +1 @@
-3.6
+3.6.p0

build/pkgs/setuptools/patches/easy_install_lock.patch

@@ -1,58 +1,31 @@
-diff -ur setuptools-2.0.1-orig/setuptools/command/easy_install.py setuptools-2.0.1/setuptools/command/easy_install.py
---- setuptools-2.0.1-orig/setuptools/command/easy_install.py	2013-12-13 17:31:51.000000000 +0100
-+++ setuptools-2.0.1/setuptools/command/easy_install.py	2014-02-28 20:03:44.805017754 +0100
-@@ -26,6 +26,7 @@
- import warnings
- import site
- import struct
-+import fcntl
- from glob import glob
- from distutils import log, dir_util
-
-@@ -1432,12 +1433,14 @@
-         for path in yield_lines(self.paths):
+diff -ru src/setuptools/command/easy_install.py b/setuptools/command/easy_install.py
+--- src/setuptools/command/easy_install.py	2014-10-31 14:42:35.779973945 +0100
++++ b/setuptools/command/easy_install.py	2014-10-31 15:07:53.067034724 +0100
+@@ -1446,6 +1446,11 @@
              list(map(self.add, find_distributions(path, True)))
 
--    def _load(self):
--        self.paths = []
-+    def _load(self, lock=True, paths=[]):
-+        self.paths = list(paths)
+     def _load(self):
++        # Lock self.filename until save() is called
++        import fcntl
++        self.lock = open(self.filename, 'a')
++        fcntl.flock(self.lock, fcntl.LOCK_EX)
++
+         self.paths = []
          saw_import = False
          seen = dict.fromkeys(self.sitedirs)
-         if os.path.isfile(self.filename):
-             f = open(self.filename,'rt')
-+            if lock:
-+                fcntl.flock(f, fcntl.LOCK_SH)
-             for line in f:
-                 if line.startswith('import'):
-                     saw_import = True
-@@ -1465,10 +1468,12 @@
-
+@@ -1479,6 +1484,7 @@
      def save(self):
          """Write changed .pth file back to disk"""
--        if not self.dirty:
--            return
-+        lock = open(self.filename, 'a')
-+        fcntl.flock(lock, fcntl.LOCK_EX)
-+        self._load(lock=False, paths=self.paths)
-
--        data = '\n'.join(map(self.make_relative,self.paths))
-+        relative_paths = set(map(self.make_relative,self.paths))
-+        data = '\n'.join(relative_paths)
-         if data:
-             log.debug("Saving %s", self.filename)
-             data = (
-@@ -1486,11 +1491,12 @@
-             f.write(data)
-             f.close()
+         if not self.dirty:
++            self.lock.close()
+             return
 
--        elif os.path.exists(self.filename):
-+        else:
-             log.debug("Deleting empty %s", self.filename)
+         data = '\n'.join(map(self.make_relative,self.paths))
+@@ -1504,6 +1510,7 @@
              os.unlink(self.filename)
 
          self.dirty = False
-+        lock.close()
++        self.lock.close()
 
      def add(self, dist):
          """Add `dist` to the distribution map"""

build/pkgs/setuptools/spkg-install

@@ -18,6 +18,7 @@ cd src
 # Apply patches.  See SPKG.txt for information about what each patch
 # does.
 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'"