Merge branch 'develop' into public/refactor_integer_vectors-12453

* develop: (188 commits)
  Updated Sage version to 6.2.beta1
  Use posix locale for regex
  Let ncurses build again on Solaris.
  Tweaks for speed in sparse graph backend for #15715.
  Updated Sage version to 6.1.1
  trac #14508: better now?
  Trac 14508: bugfix in jordan_form
  Update README.txt re installation with OS X Mavericks
  Fix test for empty string in FLINT build system.
  Update to version 0.10.8.2
  Update sagenb to 0.10.8.1
  Replace two more "except StandardError:"
  Updated Sage version to 6.2.beta0
  Fix documentation syntax
  GSL FFT: indentation (& related) fixes in docstrings
  Minor documentation fixes.
  #Documentation for gsl/fft.pyx
  #10058: Segfault in backward and inverse FFT for 2**n elements
  Regression test for #7475
  Trac #8499: reviewer patch
  ...

Conflicts:
	src/sage/combinat/integer_vector.py

Makefile

@@ -16,7 +16,7 @@ logs:
 	mkdir -p $@
 
 build: logs configure
-	cd build && \
+	+cd build && \
 	"../$(PIPE)" \
 		"env SAGE_PARALLEL_SPKG_BUILD='$(SAGE_PARALLEL_SPKG_BUILD)' ./install all 2>&1" \
 		"tee -a ../logs/install.log"

README.txt

@@ -75,12 +75,23 @@ Installation Guide:
    "Precise"), you need the dpkg-dev package.
 
    OS X: Xcode. Make sure you have installed the most recent version
-   of Xcode. For pre-Lion versions of OS X, you can download Xcode
-   from http://developer.apple.com/downloads/. For OS X Lion, you can
-   install it using the App Store. With Xcode 4.3 or later, you need
-   to install the "Command Line Tools": from the File menu, choose
-   "Preferences", then the "Downloads" tab, and then "Install" the
-   Command Line Tools.
+   of Xcode. With recent versions of OS X (OS X Lion or later), you
+   can install Xcode for free from the App Store. For pre-Lion
+   versions of OS X, you can download Xcode from
+   http://developer.apple.com/downloads/.
+
+   With OS X, you also need to install the "command line tools". When
+   using OS X Mavericks, after installing Xcode, run this command from
+   a terminal window:
+
+      xcode-select --install
+
+   Then click "Install" in the pop-up window.
+
+   When using OS X Mountain Lion or earlier, you need to install the
+   command line tools from Xcode: run Xcode; then from the File
+   menu, choose "Preferences", then the "Downloads" tab, and then
+   "Install" the Command Line Tools.
 
    Other platforms: See detailed instructions below.
 

VERSION.txt

@@ -1 +1 @@
-Sage version 6.1.rc0, released 2014-01-25
+Sage version 6.2.beta1, released 2014-02-07

build/deps

@@ -265,9 +265,6 @@ $(INST)/$(LINBOX): $(INST)/$(MPIR) $(INST)/$(NTL) $(INST)/$(GIVARO) \
 $(INST)/$(IML): $(INST)/$(MPIR) $(INST)/$(GSL) $(INST)/$(ATLAS)
 	+$(PIPE) "$(SAGE_SPKG) $(IML) 2>&1" "tee -a $(SAGE_LOGS)/$(IML).log"
 
-$(INST)/$(ECLIB): $(INST)/$(MPIR) $(INST)/$(PARI) $(INST)/$(NTL)
-	+$(PIPE) "$(SAGE_SPKG) $(ECLIB) 2>&1" "tee -a $(SAGE_LOGS)/$(ECLIB).log"
-
 $(INST)/$(GENUS2REDUCTION): $(INST)/$(PARI)
 	+$(PIPE) "$(SAGE_SPKG) $(GENUS2REDUCTION) 2>&1" "tee -a $(SAGE_LOGS)/$(GENUS2REDUCTION).log"
 
@@ -395,6 +392,9 @@ $(INST)/$(FLINTQS): $(INST)/$(MPIR)
 $(INST)/$(FLINT): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(NTL)
 	+$(PIPE) "$(SAGE_SPKG) $(FLINT) 2>&1" "tee -a $(SAGE_LOGS)/$(FLINT).log"
 
+$(INST)/$(ECLIB): $(INST)/$(PARI) $(INST)/$(NTL) $(INST)/$(FLINT)
+	+$(PIPE) "$(SAGE_SPKG) $(ECLIB) 2>&1" "tee -a $(SAGE_LOGS)/$(ECLIB).log"
+
 $(INST)/$(M4RI): $(INST)/$(LIBPNG)
 	+$(PIPE) "$(SAGE_SPKG) $(M4RI) 2>&1" "tee -a $(SAGE_LOGS)/$(M4RI).log"
 
@@ -476,8 +476,6 @@ $(INST)/csage: $(INST)/$(SCONS) \
        $(INST)/$(MPIR) \
        $(INST)/$(NTL) \
        $(INST)/$(PARI) \
-       $(INST)/$(POLYBORI) \
-       $(INST)/$(PYNAC) \
        $(INST)/$(PYTHON)
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
 		cd $(SAGE_SRC) && source bin/sage-env && cd c_lib && \

build/install

@@ -310,9 +310,10 @@ fi
 # Create $SAGE_ROOT/build/Makefile starting from build/deps
 ###############################################################################
 
-exec 3>Makefile
+# Trac #15624: use file descriptor 5 since make uses 3 and 4
+exec 5>Makefile
 
-cat >&3 <<EOF
+cat >&5 <<EOF
 #==============================================================================
 # This file has been automatically generated by
 #   $SAGE_ROOT/build/install
@@ -323,16 +324,16 @@ EOF
 
 # Use bash as shell for the Makefile (bash obviously exists, since
 # this build/install script runs under bash).
-echo >&3 "SHELL = `command -v bash`"
-echo >&3
+echo >&5 "SHELL = `command -v bash`"
+echo >&5
 
 # If the user (or the Makefile) has set SAGE_PARALLEL_SPKG_BUILD=no,
 # then turn off parallel building: disable just building multiple
 # packages at the same time.   Individual packages can still be built
 # in parallel by specifying '-j' in $MAKE.
 if [ "${SAGE_PARALLEL_SPKG_BUILD:-yes}" = no ]; then
-    echo ".NOTPARALLEL:" >&3
-    echo "" >&3
+    echo ".NOTPARALLEL:" >&5
+    echo "" >&5
 fi
 
 # Usage: newest_version $pkg
@@ -349,7 +350,7 @@ newest_version() {
     fi
 }
 
-cat >&3 <<EOF
+cat >&5 <<EOF
 # Standard packages
 ATLAS=`newest_version atlas`
 BOEHM_GC=`newest_version boehm_gc`
@@ -445,40 +446,40 @@ INST=`echo "$SAGE_SPKG_INST" | sed 's/ /\\\\ /g'`
 EOF
 
 # $(TOOLCHAIN) variable containing prerequisites for the build
-echo >&3 -n 'TOOLCHAIN ='
+echo >&5 -n 'TOOLCHAIN ='
 if [ "$SAGE_INSTALL_CCACHE" = yes ]; then
-    echo >&3 -n ' $(INST)/ccache'
+    echo >&5 -n ' $(INST)/ccache'
 fi
 if [ "$need_to_install_gcc" = yes ]; then
-    echo >&3 -n ' $(INST)/$(GCC)'
+    echo >&5 -n ' $(INST)/$(GCC)'
     # Use this option for the prereq configure script, such that it
     # will skip all compiler checks.
     export PREREQ_OPTIONS="--disable-compiler-checks $PREREQ_OPTIONS"
 fi
-echo >&3
+echo >&5
 
-echo >&3 'SCRIPT_SOURCES = \'
+echo >&5 'SCRIPT_SOURCES = \'
 for file in "$SAGE_SRC/bin/"*; do
-    echo >&3 "                 \$(SAGE_SRC)${file#$SAGE_SRC} \\"
+    echo >&5 "                 \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
-echo >&3
-echo >&3 'SCRIPTS = \'
+echo >&5
+echo >&5 'SCRIPTS = \'
 for file in "$SAGE_SRC/bin/"*; do
-    echo >&3 "                 \$(SAGE_LOCAL)${file#$SAGE_SRC} \\"
+    echo >&5 "                 \$(SAGE_LOCAL)${file#$SAGE_SRC} \\"
 done
-echo >&3
-echo >&3 'EXTCODE_SOURCES = \'
+echo >&5
+echo >&5 'EXTCODE_SOURCES = \'
 for file in `find "$SAGE_SRC"/ext -type f`; do
-    echo >&3 "                  \$(SAGE_SRC)${file#$SAGE_SRC} \\"
+    echo >&5 "                  \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
-echo >&3
-echo >&3 'EXTCODE = \'
+echo >&5
+echo >&5 'EXTCODE = \'
 for file in `find "$SAGE_SRC"/ext -type f`; do
-    echo >&3 "                  \$(SAGE_EXTCODE)${file#$SAGE_SRC/ext} \\"
+    echo >&5 "                  \$(SAGE_EXTCODE)${file#$SAGE_SRC/ext} \\"
 done
-echo >&3
+echo >&5
 
-cat >&3 <<EOF
+cat >&5 <<EOF
 # don't just use \`install\` since we don't want to change permissions
 \$(SAGE_LOCAL)/bin/%: \$(SAGE_SRC)/bin/%
 	cp \$< \$@
@@ -492,7 +493,7 @@ cat >&3 <<EOF
 EOF
 
 # Copy build/deps
-cat >&3 <<EOF
+cat >&5 <<EOF
 
 #==============================================================================
 # What follows now is a copy of
@@ -501,10 +502,10 @@ cat >&3 <<EOF
 
 EOF
 
-cat "$SAGE_ROOT/build/deps" >&3
+cat "$SAGE_ROOT/build/deps" >&5
 
 # Close the Makefile
-exec 3>&-
+exec 5>&-
 
 ###############################################################################
 # Skip the rest if nothing to do (i.e., to [re]build).