Merge remote-tracking branch 'origin/develop' into sage_depr

COPYING.txt

@@ -88,6 +88,8 @@ pari                        GPLv2+
 patch                       GPLv2+
 pexpect                     Python License
 pil                         Similar to MIT and modified BSD (see below)
+pkgconf                     ISC License (equivalent to Simplified BSD)
+pkgconfig                   MIT License
 polybori                    GPLv2+
 polytopes_db                None (database)
 ppl                         GPLv3+

VERSION.txt

@@ -1 +1 @@
-Sage version 6.2.beta2, released 2014-02-15
+Sage version 6.2.beta3, released 2014-03-03

build/deps

@@ -81,6 +81,8 @@ all-sage: \
      $(INST)/$(PARI) \
      $(INST)/$(PEXPECT) \
      $(INST)/$(PILLOW) \
+     $(INST)/$(PKGCONF) \
+     $(INST)/$(PKGCONFIG) \
      $(INST)/$(POLYBORI) \
      $(INST)/$(POLYTOPES_DB) \
      $(INST)/$(PPL) \
@@ -501,6 +503,12 @@ $(INST)/$(GCC): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(MPC) \
 $(INST)/$(PILLOW): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PILLOW) 2>&1" "tee -a $(SAGE_LOGS)/$(PILLOW).log"
 
+$(INST)/$(PKGCONF): 
+	+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
+
+$(INST)/$(PKGCONFIG): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(PKGCONFIG) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONFIG).log"
+
 $(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS)
 	+$(PIPE) "$(SAGE_SPKG) $(NUMPY) 2>&1" "tee -a $(SAGE_LOGS)/$(NUMPY).log"
 
@@ -521,6 +529,7 @@ $(INST)/$(CEPHES):
 # setuptools forgets to update easy-install.pth during parallel
 # builds, so we build the relevant packages serially.
 
+$(INST)/$(PILLOW): $(INST)/$(PKGCONFIG)
 $(INST)/$(SQLALCHEMY): $(INST)/$(PILLOW)
 $(INST)/$(PYGMENTS): $(INST)/$(SQLALCHEMY)
 $(INST)/$(JINJA2): $(INST)/$(PYGMENTS)

build/install

@@ -65,32 +65,6 @@ mkdir -p "$SAGE_SHARE"
 # Determine whether to install GCC (gcc, g++, gfortran).
 ###############################################################################
 
-# Give a deprecation message whenever SAGE_FORTRAN or SAGE_FORTRAN_LIB
-# is set to something. See Trac #13349.
-if [ -n "$SAGE_FORTRAN" ] || [ -n "$SAGE_FORTRAN_LIB" ]; then
-cat >&2 <<EOF
-WARNING: the environment variables SAGE_FORTRAN and SAGE_FORTRAN_LIB
-are deprecated since sage-5.3.
-
-The GNU Compiler Collection (GCC) is included in Sage and will be
-installed if you do not have a Fortran compiler. If you do have a
-Fortran compiler installed and you want to specify its path, you can
-use the standard environment variable FC (instead of SAGE_FORTRAN) to
-point to the Fortran compiler.
-
-As replacement to SAGE_FORTRAN_LIB, you can either add the directory
-containing the Fortran library to LIBRARY_PATH and/or LD_LIBRARY_PATH,
-or copy/symlink the Fortran library into \$SAGE_ROOT/local/lib. In most
-cases, none of this is needed as the compiler/linker should find the
-Fortran library by itself.
-
-Support for SAGE_FORTRAN and SAGE_FORTRAN_LIB might be removed from
-future versions of Sage. Moreover, these variables are not tested
-anymore and might not work as you expect.
-EOF
-sleep 5
-fi
-
 # Determine various compilers.  These variables should not be exported,
 # they are only used in this build/install script to determine whether to
 # install GCC.  The "real" $CC, $CXX,... variables for building Sage are
@@ -107,9 +81,7 @@ if [ -z "$CXX" ]; then
 fi
 
 if [ -z "$FC" ]; then
-    if [ -n "$SAGE_FORTRAN" ]; then
-        FC="$SAGE_FORTRAN"
-    elif command -v gfortran >/dev/null 2>/dev/null; then
+    if command -v gfortran >/dev/null 2>/dev/null; then
         FC=gfortran
     elif command -v g95 >/dev/null 2>/dev/null; then
         FC=g95
@@ -264,12 +236,11 @@ fi
 # Create the sage_fortran script.
 ###############################################################################
 
-# Don't use FC and SAGE_FORTRAN_LIB if we are installing GCC or have
+# Don't use FC if we are installing GCC or have
 # installed gfortran, as that can cause compatibility problems.
 # We want to use the Fortran compiler that we build as part of GCC.
 if [ "$need_to_install_gcc" = yes ] || [ -x "$SAGE_LOCAL/bin/gfortran" ]; then
     unset FC
-    unset SAGE_FORTRAN_LIB
 fi
 
 # Write sage_fortran script.
@@ -301,11 +272,6 @@ fi
 EOF
 chmod +x "$SAGE_LOCAL/bin/sage_fortran"
 
-# Make the fortran library symlink if requested
-if [ -f "$SAGE_FORTRAN_LIB" ]; then
-    ( cd "$SAGE_LOCAL/lib" && ln -sf "$SAGE_FORTRAN_LIB" . )
-fi
-
 ###############################################################################
 # Create $SAGE_ROOT/build/Makefile starting from build/deps
 ###############################################################################
@@ -413,6 +379,8 @@ PARI_SEADATA_SMALL=`newest_version pari_seadata_small`
 PATCH=`newest_version patch`
 PEXPECT=`newest_version pexpect`
 PILLOW=`newest_version pillow`
+PKGCONF=`newest_version pkgconf`
+PKGCONFIG=`newest_version pkgconfig`
 POLYBORI=`newest_version polybori`
 POLYTOPES_DB=`newest_version polytopes_db`
 PPL=`newest_version ppl`

build/pkgs/atlas/spkg-install

@@ -136,16 +136,16 @@ if 'SAGE_ATLAS_LIB' in os.environ:
         sym_gfortran = 'gfortran' in symbol_table
         sym_g95 = 'g95' in symbol_table
         if sym_gfortran and conf['fortran'] != 'gfortran':
-            print("Symbols in lib77blas indicate it was build with gfortran \n")
-            print("However SAGE is using a different fortran compiler \n")
-            print("If you wish to use this blas library, make sure SAGE_FORTRAN points \n")
-            print("to a fortran compiler compatible with this library. \n")
+            print("Symbols in lib77blas indicate it was built with gfortran.\n")
+            print("However, Sage is using a different fortran compiler.\n")
+            print("If you wish to use this blas library, make sure FC points\n")
+            print("to a fortran compiler compatible with this library.\n")
             sys.exit(2)
         if sym_g95 and conf['fortran'] != 'g95':
-            print("Symbols in lib77blas indicate it was build with g95 \n")
-            print("However SAGE is using a different fortran compiler \n")
-            print("If you wish to use this blas library, make sure SAGE_FORTRAN points \n")
-            print("to a fortran compiler compatible with this library. \n")
+            print("Symbols in lib77blas indicate it was built with g95 \n")
+            print("However, Sage is using a different fortran compiler.\n")
+            print("If you wish to use this blas library, make sure FC points\n")
+            print("to a fortran compiler compatible with this library.\n")
             sys.exit(2)
 
     SAGE_LOCAL_LIB = os.path.join(conf['SAGE_LOCAL'], 'lib')

build/pkgs/cliquer/SPKG.txt

@@ -6,7 +6,7 @@ weighted graph. It uses an exact branch-and-bound algorithm recently
 developed by Patr Ostergard.
 
 == License ==
-Cliquer is licensed under the GNU General Public License v2 ( June 1991 )
+GNU General Public License v2
 
 == SPKG Maintainers ==
 Nathann Cohen ([email protected])
@@ -18,92 +18,8 @@ http://users.tkk.fi/pat/cliquer.html
 == Dependencies ==
  * None
 
-== TODO ==
- * A MAJOR cleanup of this package is required, see #9870, #14349
-
 == Patches ==
- * Makefile.patch: Patch the Makefile for Sage. This custom Makefile
-   contains Sage specific compilation and linking flags. More
-   importantly, we're building cliquer as a dynamic shared library,
-   instead of a stand alone program.
- * cl_c.patch, cl_h.patch: Hook into cliquer to access internal
-   functions. Could probably be done better (see TODO)
-
-== Changelog ==
-
-=== cliquer-1.21.p1 (Volker Braun, Felix Salfelder, 15 July 2013) ===
- * Trac #14892: Track all patches, remove unnecessary graph.c.patch
-
-=== cliquer-1.21.p0 (Nathann Cohen, 4 May 2012) ===
- * Solved memory leaks reported on #12905
- * Incidentally updated Cliquer to version 1.21
- * Incidentally removed Sage's code that was formerly directly
-   inserted in the original files. This code is now inserted during
-   installation from patches located in the patches/ folder. A bit
-   cleaner. A long way to go. But God this code really is messy and
-   full of global variables.
-
-=== cliquer-1.2.p11 (John Palmieri, 23 March 2012) ===
- * #12311: Remove explicit path to testcc.sh in spkg-install.
-
-=== cliquer-1.2.p10 (Karl-Dieter Crisman, 28 June 2011) ===
- * #11547: Make sure that libcliquer.so is copied as both
-   .dll and .so files on Cygwin
-
-=== cliquer-1.2.p9 (Jeroen Demeyer, 4 May 2011) ===
- * #11227: Apply workaround also for versions 4.6.1 of gcc, not only
-   version 4.6.0.  This is to support pre-release versions of
-   gcc 4.6.1, the bug should be fixed in the final gcc 4.6.1.
-
-=== cliquer-1.2.p8 (Jeroen Demeyer, 25 April 2011) ===
- * #11227: When compiling with gcc 4.6.0, add compiler flag -fno-ivopts
-   to work around a gcc bug.
- * Use `patch` for patching the Makefile and put patches/Makefile.patch
-   under hg control.
- * Some minor cleanup of spkg-install and Makefile.
-
-=== cliquer-1.2.p7 David Kirkby, Leif Leonhardy  (14 September 2010) ===
- * #9871 Change flags passed to the linker on Solaris to avoid problems with the
-   link-editor believing the shared library contains text relocations. This
-   problem can be seen on 32-bit builds of Solaris and OpenSolaris using
-   /usr/bin/elfdump, but the problems are much more serious on 64-bit
-   builds of Solaris - in some cases stopping code from building.
- * Added the linker flag -ztext on Solaris too, as -ztest forces a fatal
-   error if any  relocations   against   non-writable,  allocatable  sections
-   remain. This will make it easier to catch any similar bugs in future.
-
-=== cliquer-1.2.p6 Nathann Cohen, David Kirkby (31 August 2010) ===
- * #9766: Additions to SPKG.txt
-      - URL of the original website to the SPKG.txt file
-      - "Special Update/Build Instructions" section
-      - "Dependencies" section
- * Added an entry to SPKG showing when this package was first put into
-   Sage. The first mercurial log is dated 17th July 2009.
- * Added a note on to the cliquer-1.2.p0 entry in SPKG.txt that 'scons'
-   was no longer used.
-
-=== cliquer-1.2.p5 Mike Hansen (15 February 2010) ===
- * Fixed Trac #8279 to make the cliquer spkg work on Cygwin with the Sage library.
-
-=== cliquer-1.2.p4 Mike Hansen, William Stein (12 February 2010) ===
- * Fixed Trac #7308 to make the cliquer spkg work on Cygwin.
-
-=== cliquer-1.2.p3 (Peter Jeremy, 2010-01-25) ===
- * #7824: add FreeBSD support
-
-=== cliquer-1.2.p2 (?, ?) ===
- * changelog lost to history
-
-=== cliquer-1.2.p1 Karl-Dieter Crisman, Georg S. Weber (7th October 2009) ===
- * fix trac #7115: Re-add support for building cliquer on Mac OS X 10.4
-
-=== cliquer-1.2.p0 Minh Van Nguyen (16th September 2009) ===
- * Support for building cliquer 1.2 in 64-bit mode on Mac OS X 10.5.x
-   and 64-bit openSUSE 11.1.
- * Add custom compilation and linking flags on top of the Makefile of
-   cliquer 1.2.
- * Removed dependancy of cliquer on 'scons'
-
-=== cliquer-1.2 Nathann Cohen (17th July 2009) ===
- * First release put into Sage.
-
+ * Makefile.patch: Patch the Makefile for Sage. Remove hardcoded
+   compiler and linker flags, allow flags to be set from spkg-install.
+   More importantly, we're building cliquer as a dynamic shared library,
+   instead of a stand-alone program.

build/pkgs/cliquer/package-version.txt

@@ -1 +1 @@
-1.21.p1
+1.21.p2

build/pkgs/cliquer/patches/Makefile.patch

@@ -1,27 +1,32 @@
-diff -ur src/Makefile src.patched/Makefile
---- src/Makefile	2010-02-16 05:26:57.000000000 +0100
-+++ src.patched/Makefile	2011-04-26 09:46:41.000000000 +0200
-@@ -1,14 +1,17 @@
-
- ##### Configurable options:
-
-+# Don't need to set any of these compiler variables. They have already been
-+# set when running SAGE_ROOT/local/bin/sage-env as part of installing a
-+# package.
- ## Compiler:
+diff -ru src/Makefile b/Makefile
+--- src/Makefile	2010-01-22 08:53:21.000000000 +0100
++++ b/Makefile	2014-01-16 14:55:51.977047191 +0100
+@@ -1,24 +1,3 @@
+-
+-##### Configurable options:
+-
+-## Compiler:
 -CC=gcc
-+#CC=gcc
- #CC=cc
-
- ## Compiler flags:
-
- # GCC:  (also -march=pentium etc, for machine-dependent optimizing)
+-#CC=cc
+-
+-## Compiler flags:
+-
+-# GCC:  (also -march=pentium etc, for machine-dependent optimizing)
 -CFLAGS=-Wall -O3 -fomit-frame-pointer -funroll-loops
-+#CFLAGS=-Wall -O3 -fomit-frame-pointer -funroll-loops
-
- # GCC w/ debugging:
- #CFLAGS=-Wall -g -DINLINE=
-@@ -29,14 +32,14 @@
+-
+-# GCC w/ debugging:
+-#CFLAGS=-Wall -g -DINLINE=
+-
+-# Compaq C / Digital C:
+-#CFLAGS=-arch=host -fast
+-
+-# SunOS:
+-#CFLAGS=-fast
+-
+ ## Program options:
+
+ # Enable long options for cl (eg. "cl --help"), comment out to disable.
+@@ -29,14 +8,14 @@
  ##### End of configurable options
 
 

build/pkgs/cliquer/spkg-check

@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+
+if [ "$SAGE_LOCAL" = "" ]; then
+    echo "SAGE_LOCAL undefined ... exiting";
+    echo "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+OPTIMIZATION_FLAGS="-O3 -funroll-loops -fomit-frame-pointer"
+# Work around a bug in gcc 4.6.0: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48774
+if [ "`testcc.sh $CC`" = GCC ] ; then
+    if $CC -dumpversion 2>/dev/null |grep >/dev/null '^4\.6\.[01]' ; then
+        echo "Warning: Working around bug in gcc 4.6.0"
+        OPTIMIZATION_FLAGS="$OPTIMIZATION_FLAGS -fno-ivopts"
+    fi
+fi
+
+CFLAGS="$CFLAGS `testcflags.sh -g $OPTIMIZATION_FLAGS -fPIC -KPIC -Wall`"
+CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
+LDFLAGS="$LDFLAGS -L$SAGE_LOCAL/lib"
+
+# Compile for 64-bit if SAGE64 is set to 'yes'.
+# On 64-bit hardware, we don't need to set this variable to true. A
+# 64-bit cliquer library would be built on such platform.
+if [ "$SAGE64" = yes ]; then
+    CFLAGS="$CFLAGS -m64 "
+    LDFLAGS="$LDFLAGS -m64 "
+fi
+
+# Export everything
+export CFLAGS
+export CPPFLAGS
+export LDFLAGS
+
+cd src && $MAKE test