- Update to 5.0.

- Add the following patches:
http://trac.sagemath.org/sage_trac/ticket/12400
http://trac.sagemath.org/sage_trac/ticket/12818
http://trac.sagemath.org/sage_trac/ticket/12828
http://trac.sagemath.org/sage_trac/ticket/12862
- Remove obsolete patches.
- Add options to build optional subpackages.
- Add option to use 387 FPU instead of SSE (amd64 only).
- Reduce size of what is installed in PREFIX.
- It now passes all tests (except minor floating point differences) under
amd64.  There are still unsolved failed tests with i386.

27 files changed, 605 insertions, 124 deletions

diff --git a/math/sage/Makefile b/math/sage/Makefile
index 5e951588927..de2cf56f885 100644
--- a/math/sage/Makefile
+++ b/math/sage/Makefile
@@ -6,11 +6,10 @@
 #
 
 PORTNAME=	sage
-PORTVERSION=	4.8
-PORTREVISION=	2
+PORTVERSION=	5.0
 CATEGORIES=	math
 MASTER_SITES=	http://modular.math.jmu.edu/src/ \
-		http://boxen.math.washington.edu/sage/src/ \
+		http://boxen.math.washington.edu/home/sagemath/sage-mirror/src/ \
 		http://mirrors.xmission.com/sage/src/ \
 		http://www.sagemath.org/src-old/
 EXTRACT_SUFX=	.tar
@@ -26,44 +25,148 @@ LIB_DEPENDS=	atlas:${PORTSDIR}/math/atlas \
 		jpeg:${PORTSDIR}/graphics/jpeg
 RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash
 
-PLIST_FILES=	bin/sage
+# 387 option: this only makes a difference for the amd64 architecture.  Causes
+# the internal floating point calculations to be performed with extended
+# precision.
+# Optional packages: see http://www.sagemath.org/packages/optional/
+OPTIONS=	\
+	387			"Use 387 instead of SSE FPU"	Off \
+	4TI2			4ti2				Off \
+	TOPCOM			TOPCOM				Off \
+	BIOPYTHON		biopython			Off \
+	CBC			cbc				Off \
+	CUNNINGHAM_TABLES	cunningham_tables		Off \
+	DB_CREMONA_ELLCURVE	db_cremona_ellcurve		Off \
+	DB_GAP			db_gap				Off \
+	DB_JONES_NUMFIELD	db_jones_numfield		Off \
+	DB_KOHEL		db_kohel			Off \
+	DB_ODLYZKO_ZETA		db_odlyzko_zeta			Off \
+	DB_SLOANE_OEIS		db_sloane_oeis			Off \
+	DB_STEIN_WATKINS_MINI	db_stein_watkins_mini		Off \
+	DB_SYMBOLIC_DATA	db_symbolic_data		Off \
+	DOT2TEX			dot2tex				Off \
+	EXTRA_DOCS		extra_docs			Off \
+	GAP_PACKAGES		gap_packages			Off \
+	GDBM			gdbm				Off \
+	GINV			ginv				Off \
+	GIT			git				Off \
+	GMPY			gmpy				Off \
+	GNUPLOTPY		gnuplotpy			Off \
+	GUPPY			guppy				Off \
+	JAVA3D			java3d				Off \
+	JSMATH_IMAGE_FONTS	jsmath_image_fonts		Off \
+	KASH3			kash3				Off \
+	KNOBOO			knoboo				Off \
+	LIE			lie				Off \
+	LRCALC			lrcalc				Off \
+	LRS			lrs				Off \
+	MPC			mpc				Off \
+	MPI4PY			mpi4py				Off \
+	NAUTY			nauty				Off \
+	NZMATH			nzmath				Off \
+	P_GROUP_COHOMOLOGY	p_group_cohomology		Off \
+	PYCRYPTOPLUS		pycryptoplus			Off \
+	PYOPENSSL		pyopenssl			Off \
+	PYX			pyx				Off \
+	QHULL			qhull				Off \
+	SAGE_MODE		sage-mode			Off \
+	TRAC			trac				Off
 
+PLIST_FILES=	bin/sage
 USE_FORTRAN=	yes
 USE_TK=		yes
 USE_GMAKE=	yes
 USE_ICONV=	yes
 MAKE_JOBS_SAFE=	yes
 LDFLAGS:=	-Wl,-rpath=${WRKSRC}/local/lib ${LDFLAGS}
-FFLAGS+=	-Wl,-rpath=${WRKSRC}/local/lib
-CFLAGS+=	-Wl,-rpath=${WRKSRC}/local/lib
-CXXFLAGS+=	-Wl,-rpath=${WRKSRC}/local/lib
+FFLAGS+=	-Wl,-rpath=${WRKSRC}/local/lib ${FPM_FLAG}
+CFLAGS+=	-Wl,-rpath=${WRKSRC}/local/lib ${FPM_FLAG}
+CXXFLAGS+=	-Wl,-rpath=${WRKSRC}/local/lib ${FPM_FLAG}
 # Note that the above addition to LDFLAGS, as a side effect, provides a
 # work-around for the make(1) idiosyncracy mentioned in PR 164361 (which
 # otherwise breaks the build of the maxima sub-package).
 
+.include <bsd.port.pre.mk>
+
+.if defined(WITH_4TI2) || defined(WITH_TOPCOM) || defined(WITH_BIOPYTHON) || \
+    defined(WITH_CBC) || defined(WITH_CUNNINGHAM_TABLES) || \
+    defined(WITH_DB_CREMONA_ELLCURVE) || defined(WITH_DB_GAP) || \
+    defined(WITH_DB_JONES_NUMFIELD) || defined(WITH_DB_KOHEL) || \
+    defined(WITH_DB_ODLYZKO_ZETA) || defined(WITH_DB_SLOANE_OEIS) || \
+    defined(WITH_DB_STEIN_WATKINS_MINI) || defined(WITH_DB_SYMBOLIC_DATA) || \
+    defined(WITH_DOT2TEX) || defined(WITH_EXTRA_DOCS) || \
+    defined(WITH_GAP_PACKAGES) || defined(WITH_GDBM) || defined(WITH_GINV) || \
+    defined(WITH_GIT) || defined(WITH_GMPY) || defined(WITH_GNUPLOTPY) || \
+    defined(WITH_GUPPY) || defined(WITH_JAVA3D) || \
+    defined(WITH_JSMATH_IMAGE_FONTS) || defined(WITH_KASH3) || \
+    defined(WITH_KNOBOO) || defined(WITH_LIE) || defined(WITH_LRCALC) || \
+    defined(WITH_LRS) || defined(WITH_MPC) || defined(WITH_MPI4PY) || \
+    defined(WITH_NAUTY) || defined(WITH_NZMATH) || \
+    defined(WITH_P_GROUP_COHOMOLOGY) || defined(WITH_PYCRYPTOPLUS) || \
+    defined(WITH_PYOPENSSL) || defined(WITH_PYX) || defined(WITH_QHULL) || \
+    defined(WITH_SAGE_MODE) || defined(WITH_TRAC)
+WITH_OPTIONAL_PKGS=	yes
+.endif
+
+.ifdef WITH_OPTIONAL_PKGS
+USE_PERL5_BUILD=	yes
+.endif
+
+# Optimization flags will be defined by the source
+CFLAGS:=	${CFLAGS:C/^-O.*$//}
+FFLAGS:=	${CFLAGS:C/^-O.*$//}
+
 MAKE_ENV+=	SAGE_PORT=yes \
 		SAGE_FORTRAN=${LOCALBASE}/bin/${FC} \
 		SAGE_FORTRAN_LIB=${LOCALBASE}/lib/gcc${GCC_DEFAULT_V}/libgfortran.so \
-		SAGE_ATLAS_LIB=${LOCALBASE}/lib
+		SAGE_ATLAS_LIB=${LOCALBASE}/lib \
+		DOT_SAGE=${WRKSRC}/tmp/.sage
 
-NO_LATEST_LINK=	yes	# Conflicts with graphics/sage.
+LATEST_LINK=	sage-math	# Conflicts with graphics/sage.
 
 # The following is needed for the lapack subpackage.
 MAKE_ARGS+=	ARCH="${AR}"
 
+.if ${OSVERSION} < 701106
+BROKEN=		POSIX semaphores are required, and the support only works in FreeBSD 7-STABLE and later
+.endif
+
+.if defined(WITH_387) && ${ARCH} == amd64
+FPM_FLAG=	-mfpmath=387
+.else
+FPM_FLAG=
+.endif
+
+.if !defined(DISABLE_MAKE_JOBS)
+MAKE_ENV+=	MAKE="make -j${MAKE_JOBS_NUMBER}"
+.endif
+
 post-patch:
+# Create the wrappers for the compiler invokations.
 	@${MKDIR} ${WRKSRC}/local/bin
 	@${LN} -s -f ${LOCALBASE}/bin/gmake ${WRKSRC}/local/bin/make
 	@${LN} -s -f ${LOCALBASE}/bin/bash ${WRKSRC}/local/bin/sh
-	@${SED} -e 's#%%CC%%#${LOCALBASE}/bin/${CC}#' -e 's#%%CFLAGS%%#${CFLAGS}#' ${FILESDIR}/gcc.in > ${WRKSRC}/local/bin/cc
+	@${SED} -e 's#%%CC%%#${LOCALBASE}/bin/${CC}#' \
+		-e 's#%%LDFLAGS%%#${LDFLAGS} ${FPM_FLAG}#' \
+		${FILESDIR}/gcc.in > ${WRKSRC}/local/bin/cc
 	@${CHMOD} +x ${WRKSRC}/local/bin/cc
 	@${LN} -s -f cc ${WRKSRC}/local/bin/gcc
-	@${SED} -e 's#%%CC%%#${LOCALBASE}/bin/${CXX}#' -e 's#%%CFLAGS%%#${CXXFLAGS}#' ${FILESDIR}/gcc.in > ${WRKSRC}/local/bin/c++
+	@${SED} -e 's#%%CC%%#${LOCALBASE}/bin/${CXX}#' \
+		-e 's#%%LDFLAGS%%#${LDFLAGS} ${FPM_FLAG}#' \
+		${FILESDIR}/gcc.in > ${WRKSRC}/local/bin/c++
 	@${CHMOD} +x ${WRKSRC}/local/bin/c++
 	@${LN} -s -f c++ ${WRKSRC}/local/bin/g++
-	@${SED} -e 's#%%CC%%#${LOCALBASE}/bin/${FC}#' -e 's#%%CFLAGS%%#${FFLAGS}#' ${FILESDIR}/gcc.in > ${WRKSRC}/local/bin/gfortran
+	@${SED} -e 's#%%CC%%#${LOCALBASE}/bin/${FC}#' \
+		-e 's#%%LDFLAGS%%#${LDFLAGS} ${FPM_FLAG}#' \
+		${FILESDIR}/gcc.in > ${WRKSRC}/local/bin/gfortran
 	@${CHMOD} +x ${WRKSRC}/local/bin/gfortran
+
+# Apply the patches to the appropriate xz'ed tarballs contained in
+# ${WRKSRC}/spkg/standard.  The names of the patches are
+# spkg-${NAME_OF_TARBALL}_-_${NAME_OF_PATCH}.
+
 	@${MKDIR} ${WRKSRC}/tmp
+	@${RM} -rf ${WRKSRC}/tmp/*
 	@for p in ${FILESDIR}/spkg-patch-*; do \
 		q=$${p#*/spkg-patch-}; t=$${q%_-_*}; \
        		if ! [ -e ${WRKSRC}/spkg/standard/$$t.spkg ]; then \
@@ -80,36 +183,179 @@ post-patch:
 		if [ -e $$f-orig ]; then \
 			${MV} $$f-orig $$f; \
 		fi; \
-		${BZIP2_CMD} -dc $$f | ${TAR} -xf -; \
+		${TAR} -xf $$f; \
 		${ECHO_MSG} "Patching $$t:"; \
 		for p in ${FILESDIR}/spkg-patch-$${t}_-_*; do \
 			${ECHO_MSG} "	applying $${p#*_-_}" ; \
 			${PATCH} < $$p 2>/dev/null || exit 1; \
 		done; \
 		${MV} $$f $$f-orig; \
-		${TAR} -cf - $$t | ${BZIP2_CMD} -c > $$f; \
+		${TAR} -cyf $$f $$t; \
 		${RM} -rf $$t; \
 	done
 
-.include <bsd.port.pre.mk>
+# Here we check dependencies of the optional packages on ports, and on other
+# optional packages.  If you find any dependencies not listed here, please
+# contact the maintainer.
 
-.if ${OSVERSION} < 701106
-IGNORE=		POSIX semaphores are required, and the support only works in FreeBSD 7-STABLE and later
+.ifdef WITH_4TI2
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|4ti2-
+.endif
+.ifdef WITH_TOPCOM
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|topcom-
+.endif
+.ifdef WITH_BIOPYTHON
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|biopython-
+.endif
+.ifdef WITH_CBC
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|cbc-
+.endif
+.ifdef WITH_CUNNINGHAM_TABLES
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|cunningham_tables-
+.endif
+.ifdef WITH_DB_CREMONA_ELLCURVE
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_cremona_ellcurve-
+.endif
+.ifdef WITH_DB_GAP
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_gap-
+.endif
+.ifdef WITH_DB_JONES_NUMFIELD
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_jones_numfield-
+.endif
+.ifdef WITH_DB_KOHEL
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_kohel-
+.endif
+.ifdef WITH_DB_ODLYZKO_ZETA
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_odlyzko_zeta-
+.endif
+.ifdef WITH_DB_SLOANE_OEIS
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_sloane_oeis-
 .endif
+.ifdef WITH_DB_STEIN_WATKINS_MINI
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_stein_watkins_mini
+.endif
+.ifdef WITH_DB_SYMBOLIC_DATA
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|database_symbolic_data-
+.endif
+.ifdef WITH_DOT2TEX
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|dot2tex-
+.endif
+.ifdef WITH_EXTRA_DOCS
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|extra_docs-
+.endif
+.ifdef WITH_GAP_PACKAGES
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|gap_packages-
+.endif
+.ifdef WITH_GDBM
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|gdbm-
+.endif
+.ifdef WITH_GINV
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|ginv-
+.endif
+.ifdef WITH_GIT
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|git-
+.endif
+.ifdef WITH_GMPY
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|gmpy-
+.endif
+.ifdef WITH_GNUPLOTPY
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|gnuplotpy-
+RUN_DEPENDS+=	gnuplot:${PORTSDIR}/math/gnuplot
+.endif
+.ifdef WITH_GUPPY
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|guppy-
+.endif
+.ifdef WITH_JAVA3D
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|java3d-
+USE_JAVA=	yes
+.endif
+.ifdef WITH_JSMATH_IMAGE_FONTS
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|jsmath_image_fonts-
+.endif
+.ifdef WITH_KASH3
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|kash3-
+.endif
+.ifdef WITH_KNOBOO
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|knoboo-
+.endif
+.ifdef WITH_LIE
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|lie-
+.endif
+.ifdef WITH_LRCALC
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|lrcalc-
+.endif
+.ifdef WITH_LRS
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|lrs-
+.endif
+.ifdef WITH_MPC
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|mpc-
+.endif
+.ifdef WITH_MPI4PY
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|mpi4py-
+LIB_DEPENDS+=	mpi:${PORTSDIR}/net/openmpi
+MAKE_ENV+=	PATH=$${PATH}:${LOCALBASE}/`${MAKE} -C ${PORTSDIR}/net/openmpi -V MPIDIR`/bin
+.endif
+.ifdef WITH_NAUTY
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|nauty-
+.endif
+.ifdef WITH_NZMATH
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|nzmath-
+.endif
+.ifdef WITH_P_GROUP_COHOMOLOGY
+.if !defined(WITH_DB_GAP)
+IGNORE=	DB_GAP must be set if P_GROUP_COHOMOLOGY is set
+.endif
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|p_group_cohomology-
+.endif
+.ifdef WITH_PYCRYPTOPLUS
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|pycryptoplus-
+.endif
+.ifdef WITH_PYOPENSSL
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|pyopenssl-
+.endif
+.ifdef WITH_PYX
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|pyx-
+.endif
+.ifdef WITH_QHULL
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|qhull-
+.endif
+.ifdef WITH_SAGE_MODE
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|sage_mode-
+.endif
+.ifdef WITH_TRAC
+OPT_PKG_LIST:=	${OPT_PKG_LIST}|trac-
+.endif
+OPT_PKG_LIST:=	${OPT_PKG_LIST:C/\|//}	# Remove the leading '|'
 
-.if !defined(DISABLE_MAKE_JOBS)
-MAKE_ENV+=	MAKE="make -j${MAKE_JOBS_NUMBER}"
+post-build:
+.ifdef WITH_OPTIONAL_PKGS
+	${SETENV} ${MAKE_ENV} ${WRKSRC}/sage -optional | \
+	${PERL} -lne 'print if $$p && /^\S+$$/; $$p=1 if /NOT INSTALLED:/' | \
+	${GREP} -E '^(${OPT_PKG_LIST})' | \
+	${XARGS} -n1 ${SETENV} ${MAKE_ENV} \
+	${WRKSRC}/sage -i
+#	${MAKE} -C ${.CURDIR} do-build # Not sure if this is necessary.
 .endif
+	${RM} -rf ${WRKSRC}/tmp/.sage
+	${CHMOD} -R a+rX ${WRKSRC}
 
 check regression-test test: build
-	@${ECHO_MSG} This test can also be performed after installation by typing \"sage --testall\".
+	@${ECHO_MSG} This test can also be performed after installation by typing \"sage -testall\".
 	@${ECHO_MSG}
-	cd ${WRKSRC}; local/bin/sage-starts; \
-	${LOCALBASE}/bin/bash -c ". local/bin/sage-env && sage-maketest"
+	cd ${WRKSRC} && ${SETENV} DOT_SAGE=${WRKSRC}/tmp/.sage ./sage -testall
+	${RM} -f ${WRKSRC}/python.core
 
 INSTALL_SAGE_DIR=	${PREFIX}/${PORTNAME}-${PORTVERSION}
 do-install:
-	cd ${WRKDIR} && ${FIND} -s ${WRKSRC} | ${SED} -e 's#${WRKDIR}/##' | \
+	cd ${WRKDIR} && ${FIND} -s ${WRKSRC} | \
+		${GREP} -v '^${WRKSRC}/spkg/standard/' | \
+		${GREP} -v '^${WRKSRC}/spkg/optional/' | \
+		${GREP} -v '^${WRKSRC}/spkg/logs/' | \
+		${GREP} -v '^${WRKSRC}/spkg/build/' | \
+		${GREP} -v '^${WRKSRC}/tmp' | \
+		${GREP} -v -E '^${WRKSRC}/[^\/]+\.log$$' | \
+		${GREP} -v '^${WRKSRC}/Makefile' | \
+		${SED} -e 's#${WRKDIR}/##' | \
 		${CPIO} -pmud -R ${BINOWN}:${BINGRP} ${PREFIX}
 	${ECHO_CMD} | ${SETENV} DOT_SAGE=${INSTALL_SAGE_DIR}/tmp/.sage ${INSTALL_SAGE_DIR}/sage
 	${RM} -rf ${INSTALL_SAGE_DIR}/tmp/.sage
diff --git a/math/sage/distinfo b/math/sage/distinfo
index 76d6d0d3b35..92875b031de 100644
--- a/math/sage/distinfo
+++ b/math/sage/distinfo
@@ -1,2 +1,2 @@
-SHA256 (sage-4.8.tar) = 7fcda2b5f86fb5669a871e4d69fcaca0a3c3624255e5836666c4180a175e7d6d
-SIZE (sage-4.8.tar) = 339159040
+SHA256 (sage-5.0.tar) = 883eab2a42df3751d2de777f6f5e9337c54c3fa286fe3d30997ef585f83d1f39
+SIZE (sage-5.0.tar) = 307988480
diff --git a/math/sage/files/gcc.in b/math/sage/files/gcc.in
index 49bd6e41946..5bc7c71bb3d 100644
--- a/math/sage/files/gcc.in
+++ b/math/sage/files/gcc.in
@@ -1,3 +1,14 @@
 #!/bin/sh
 
-%%CC%% %%CFLAGS%% $*
+# This is a wrapper to redirect compiler invokations to the port of gcc that
+# contains fortran.  LDFLAGS needs to be added so that the linker knows where
+# to find the dynamic libraries.
+
+# If the compiler is invoked with the argument "-v", adding LDFLAGS to the
+# arguments results in an error which stops some packages being built.
+
+if [ "x$*" = "x-v" ]; then
+  exec %%CC%% "$@"
+else
+  exec %%CC%% %%LDFLAGS%% "$@"
+fi
diff --git a/math/sage/files/spkg-patch-flintqs-20070817.p6_-_patches_TonelliShanks.h.patch b/math/sage/files/spkg-patch-flintqs-20070817.p6_-_patches_TonelliShanks.h.patch
new file mode 100644
index 00000000000..5455cbda087
--- /dev/null
+++ b/math/sage/files/spkg-patch-flintqs-20070817.p6_-_patches_TonelliShanks.h.patch
@@ -0,0 +1,13 @@
+--- /dev/null	2012-04-08 00:45:00.000000000 +0000
++++ flintqs-20070817.p6/patches/TonelliShanks.h.patch	2012-04-08 00:45:31.000000000 +0000
+@@ -0,0 +1,10 @@
++--- src/TonelliShanks.h.orig	2007-05-05 22:52:39.000000000 +0000
+++++ src/TonelliShanks.h	2012-04-08 00:44:38.000000000 +0000
++@@ -19,6 +19,7 @@
++ 
++ ============================================================================*/
++ 
+++#include <stdint.h>
++ #include <stdlib.h>
++ 
++ // =====================================================================
diff --git a/math/sage/files/spkg-patch-flintqs-20070817.p6_-_spkg-install b/math/sage/files/spkg-patch-flintqs-20070817.p6_-_spkg-install
new file mode 100644
index 00000000000..91978d6f41a
--- /dev/null
+++ b/math/sage/files/spkg-patch-flintqs-20070817.p6_-_spkg-install
@@ -0,0 +1,10 @@
+--- flintqs-20070817.p6/spkg-install-orig	2012-04-08 00:46:21.000000000 +0000
++++ flintqs-20070817.p6/spkg-install	2012-04-08 00:55:33.000000000 +0000
+@@ -7,6 +7,7 @@
+ fi
+ 
+ cp patches/lanczos.h  src/
++patch -p0 < patches/TonelliShanks.h.patch
+ 
+ cd src
+ 
diff --git a/math/sage/files/spkg-patch-flintqs-20070817.p6_-_src_TonelliShanks.h b/math/sage/files/spkg-patch-flintqs-20070817.p6_-_src_TonelliShanks.h
deleted file mode 100644
index db8b6ed7e1c..00000000000
--- a/math/sage/files/spkg-patch-flintqs-20070817.p6_-_src_TonelliShanks.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- flintqs-20070817.p6/src/TonelliShanks.h-orig	2012-01-30 19:52:40.000000000 +0000
-+++ flintqs-20070817.p6/src/TonelliShanks.h	2012-01-30 19:53:04.000000000 +0000
-@@ -19,6 +19,7 @@
- 
- ============================================================================*/
- 
-+#include <stdint.h>
- #include <stdlib.h>
- 
- // =====================================================================
diff --git a/math/sage/files/spkg-patch-gfan-0.4plus.p1_-_patches_Makefile b/math/sage/files/spkg-patch-gfan-0.4plus.p1_-_patches_Makefile
deleted file mode 100644
index 1c35d7f0722..00000000000
--- a/math/sage/files/spkg-patch-gfan-0.4plus.p1_-_patches_Makefile
+++ /dev/null
@@ -1,11 +0,0 @@
---- gfan-0.4plus.p1/patches/Makefile-orig	2012-02-01 18:41:42.000000000 +0000
-+++ gfan-0.4plus.p1/patches/Makefile	2012-02-01 18:42:10.000000000 +0000
-@@ -270,7 +270,7 @@
- default: $(OBJECTS) $(ADDITIONALOBJECTS) $(EXECS)
- 
- $(MAIN): $(OBJECTS)
--	$(CXX) $(CXXFLAG64) $(OBJECTS) $(ADDITIONALLINKOPTIONS) $(GPROFFLAG) -o $(MAIN)
-+	$(CXX) ${LDFLAGS} $(CXXFLAG64) $(OBJECTS) $(ADDITIONALLINKOPTIONS) $(GPROFFLAG) -o $(MAIN)
- 
- release:
- 	rm -f -r $(RELEASEDIR)/*
diff --git a/math/sage/files/spkg-patch-linbox-1.1.6.p6_-_spkg-install b/math/sage/files/spkg-patch-linbox-1.1.6.p6_-_spkg-install
deleted file mode 100644
index 16ebc8e53d7..00000000000
--- a/math/sage/files/spkg-patch-linbox-1.1.6.p6_-_spkg-install
+++ /dev/null
@@ -1,12 +0,0 @@
---- linbox-1.1.6.p6/spkg-install-orig	2012-01-23 04:02:57.000000000 +0000
-+++ linbox-1.1.6.p6/spkg-install	2012-01-23 04:03:12.000000000 +0000
-@@ -8,9 +8,6 @@
- 
- CUR=`pwd`
- 
--echo "Copying commentator patch"
--cp patches/commentator.C src/linbox/util/                                                                                
--
- if [ $? -ne 0 ]; then
-     echo "Error copying commentator OSX 10.4 fix"
-     exit 1
diff --git a/math/sage/files/spkg-patch-linbox-1.1.6.p6_-_src_linbox_util_commentator.h b/math/sage/files/spkg-patch-linbox-1.1.6.p6_-_src_linbox_util_commentator.h
deleted file mode 100644
index 02aa3255667..00000000000
--- a/math/sage/files/spkg-patch-linbox-1.1.6.p6_-_src_linbox_util_commentator.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- linbox-1.1.6.p6/src/linbox/util/commentator.h-orig	2012-01-23 03:20:53.000000000 +0000
-+++ linbox-1.1.6.p6/src/linbox/util/commentator.h	2012-01-23 03:21:22.000000000 +0000
-@@ -76,7 +76,7 @@
- #define LVL_BLABLA =  10,
- #define LVL_NEVER  =  (2*PRINT_EVERYTHING)
- 
--#ifndef DISABLE_COMMENTATOR
-+#ifndef XXDISABLE_COMMENTATOR
- namespace LinBox 
- {
- 	// Forward declaration
diff --git a/math/sage/files/spkg-patch-polybori-0.8.1.p1_-_custom.py b/math/sage/files/spkg-patch-polybori-0.8.1.p1_-_custom.py
new file mode 100644
index 00000000000..54d8c061769
--- /dev/null
+++ b/math/sage/files/spkg-patch-polybori-0.8.1.p1_-_custom.py
@@ -0,0 +1,11 @@
+--- polybori-0.8.1.p1/custom.py-orig	2012-04-10 03:58:28.000000000 +0000
++++ polybori-0.8.1.p1/custom.py	2012-04-10 04:01:48.000000000 +0000
+@@ -60,6 +60,8 @@
+ HAVE_TEX4HT=False
+ HAVE_PYTHON_EXTENSION=False
+ EXTERNAL_PYTHON_EXTENSION=True
++BOOST_TEST=False
++BOOST_PYTHON=False
+ 
+ # (CC and CXX should have been set by sage-env, but never mind...:)
+ try:
diff --git a/math/sage/files/spkg-patch-polybori-0.8.1.p1_-_patches_Cudd.cudd.cudd.h b/math/sage/files/spkg-patch-polybori-0.8.1.p1_-_patches_Cudd.cudd.cudd.h
new file mode 100644
index 00000000000..97ebd6a393e
--- /dev/null
+++ b/math/sage/files/spkg-patch-polybori-0.8.1.p1_-_patches_Cudd.cudd.cudd.h
@@ -0,0 +1,18 @@
+--- polybori-0.8.1.p1/patches/Cudd.cudd.cudd.h.patch.orig	2012-04-13 01:19:43.000000000 +0000
++++ polybori-0.8.1.p1/patches/Cudd.cudd.cudd.h.patch	2012-04-13 01:22:34.000000000 +0000
+@@ -0,0 +1,15 @@
++--- polybori-0.8.1/Cudd/cudd/cudd.h.orig	2012-03-15 22:47:56.000000000 +0000
+++++ polybori-0.8.1/Cudd/cudd/cudd.h	2012-04-13 01:21:09.000000000 +0000
++@@ -87,6 +87,12 @@
++ #endif
++ 
++ #ifdef __cplusplus
+++#include <cstdio>
+++#else
+++#include <stdio.h>
+++#endif
+++
+++#ifdef __cplusplus
++ extern "C" {
++ #endif
++ 
diff --git a/math/sage/files/spkg-patch-pycrypto-2.1.0_-_patches_src.libtom.tomcrypt_pk.h b/math/sage/files/spkg-patch-pycrypto-2.1.0_-_patches_src.libtom.tomcrypt_pk.h
new file mode 100644
index 00000000000..908f078cb7c
--- /dev/null
+++ b/math/sage/files/spkg-patch-pycrypto-2.1.0_-_patches_src.libtom.tomcrypt_pk.h
@@ -0,0 +1,14 @@
+--- /dev/null	2012-04-08 01:30:00.000000000 +0000
++++ pycrypto-2.1.0/patches_src.libtom.tomcrypt_pk.h	2012-04-08 01:30:26.000000000 +0000
+@@ -0,0 +1,11 @@
++--- src/src/libtom/tomcrypt_pk.h-orig	2012-01-21 19:43:56.000000000 +0000
+++++ src/src/libtom/tomcrypt_pk.h	2012-01-21 19:45:01.000000000 +0000
++@@ -496,7 +496,7 @@
++ int der_printable_value_decode(int v);
++ 
++ /* UTF-8 */
++-#if (defined(SIZE_MAX) || __STDC_VERSION__ >= 199901L || defined(WCHAR_MAX) || defined(_WCHAR_T) || defined(_WCHAR_T_DEFINED)) && !defined(LTC_NO_WCHAR)
+++#if (defined(SIZE_MAX) || __STDC_VERSION__ >= 199901L || defined(WCHAR_MAX) || defined(_WCHAR_T) || defined(_WCHAR_T_DEFINED) || defined(_GCC_WCHAR_T)) && !defined(LTC_NO_WCHAR)
++ #include <wchar.h>
++ #else
++ typedef ulong32 wchar_t;
diff --git a/math/sage/files/spkg-patch-pycrypto-2.1.0_-_spkg-install b/math/sage/files/spkg-patch-pycrypto-2.1.0_-_spkg-install
new file mode 100644
index 00000000000..902149044e2
--- /dev/null
+++ b/math/sage/files/spkg-patch-pycrypto-2.1.0_-_spkg-install
@@ -0,0 +1,11 @@
+--- pycrypto-2.1.0/spkg-install-orig	2012-04-08 01:30:47.000000000 +0000
++++ pycrypto-2.1.0/spkg-install	2012-04-08 01:31:41.000000000 +0000
+@@ -12,6 +12,8 @@
+     LDFLAGS="-m64 "; export LDFLAGS
+ fi
+ 
++patch -p0 < patches_src.libtom.tomcrypt_pk.h
++
+ CFLAGS="-I$SAGE_LOCAL/include -L$SAGE_LOCAL/lib $CFLAGS"
+ export CFLAGS
+ 
diff --git a/math/sage/files/spkg-patch-pycrypto-2.1.0_-_src_libtom_tomcrypt_pk.h b/math/sage/files/spkg-patch-pycrypto-2.1.0_-_src_libtom_tomcrypt_pk.h
deleted file mode 100644
index e4916df23ee..00000000000
--- a/math/sage/files/spkg-patch-pycrypto-2.1.0_-_src_libtom_tomcrypt_pk.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- pycrypto-2.1.0/src/src/libtom/tomcrypt_pk.h-orig	2012-01-21 19:43:56.000000000 +0000
-+++ pycrypto-2.1.0/src/src/libtom/tomcrypt_pk.h	2012-01-21 19:45:01.000000000 +0000
-@@ -496,7 +496,7 @@
- int der_printable_value_decode(int v);
- 
- /* UTF-8 */
--#if (defined(SIZE_MAX) || __STDC_VERSION__ >= 199901L || defined(WCHAR_MAX) || defined(_WCHAR_T) || defined(_WCHAR_T_DEFINED)) && !defined(LTC_NO_WCHAR)
-+#if (defined(SIZE_MAX) || __STDC_VERSION__ >= 199901L || defined(WCHAR_MAX) || defined(_WCHAR_T) || defined(_WCHAR_T_DEFINED) || defined(_GCC_WCHAR_T)) && !defined(LTC_NO_WCHAR)
- #include <wchar.h>
- #else
- typedef ulong32 wchar_t;
diff --git a/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Doc_library_fcntl.rst b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Doc_library_fcntl.rst
new file mode 100644
index 00000000000..550fd75eefc
--- /dev/null
+++ b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Doc_library_fcntl.rst
@@ -0,0 +1,11 @@
+--- python-2.7.2.p4/src/Doc/library/fcntl.rst.orig	2011-06-11 15:46:23.000000000 +0000
++++ python-2.7.2.p4/src/Doc/library/fcntl.rst	2012-04-22 00:31:48.000000000 +0000
+@@ -50,8 +50,6 @@
+    operations are typically defined in the library module :mod:`termios` and the
+    argument handling is even more complicated.
+ 
+-   The op parameter is limited to values that can fit in 32-bits.
+-
+    The parameter *arg* can be one of an integer, absent (treated identically to the
+    integer ``0``), an object supporting the read-only buffer interface (most likely
+    a plain Python string) or an object supporting the read-write buffer interface.
diff --git a/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Modules__ctypes_libffi_configure b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Modules__ctypes_libffi_configure
new file mode 100644
index 00000000000..e320f86715e
--- /dev/null
+++ b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Modules__ctypes_libffi_configure
@@ -0,0 +1,21 @@
+--- python-2.7.2.p4/src/Modules/_ctypes/libffi/configure.orig	2011-06-11 15:46:26.000000000 +0000
++++ python-2.7.2.p4/src/Modules/_ctypes/libffi/configure	2012-04-22 00:23:14.000000000 +0000
+@@ -6289,7 +6289,7 @@
+   rm -rf conftest*
+   ;;
+ 
+-x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
++amd64-*-freebsd*|x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+   # Find out which ABI we are using.
+   echo 'int i;' > conftest.$ac_ext
+@@ -11275,6 +11275,9 @@
+   powerpc-*-freebsd*)
+ 	TARGET=POWERPC_FREEBSD; TARGETDIR=powerpc
+ 	;;
++  powerpc64-*-freebsd*)
++	TARGET=POWERPC; TARGETDIR=powerpc
++	;;
+   powerpc*-*-rtems*)
+ 	TARGET=POWERPC; TARGETDIR=powerpc
+ 	;;
diff --git a/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Modules_fcntlmodule.c b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Modules_fcntlmodule.c
new file mode 100644
index 00000000000..bebebb08996
--- /dev/null
+++ b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Modules_fcntlmodule.c
@@ -0,0 +1,53 @@
+--- python-2.7.2.p4/src/Modules/fcntlmodule.c.orig	2011-06-11 15:46:27.000000000 +0000
++++ python-2.7.2.p4/src/Modules/fcntlmodule.c	2012-04-22 00:23:34.000000000 +0000
+@@ -97,20 +97,15 @@
+ {
+ #define IOCTL_BUFSZ 1024
+     int fd;
+-    /* In PyArg_ParseTuple below, we use the unsigned non-checked 'I'
++    /* In PyArg_ParseTuple below, we use the unsigned non-checked 'k'
+        format for the 'code' parameter because Python turns 0x8000000
+        into either a large positive number (PyLong or PyInt on 64-bit
+        platforms) or a negative number on others (32-bit PyInt)
+        whereas the system expects it to be a 32bit bit field value
+        regardless of it being passed as an int or unsigned long on
+-       various platforms.  See the termios.TIOCSWINSZ constant across
+-       platforms for an example of thise.
+-
+-       If any of the 64bit platforms ever decide to use more than 32bits
+-       in their unsigned long ioctl codes this will break and need
+-       special casing based on the platform being built on.
++       various platforms.
+      */
+-    unsigned int code;
++    unsigned long code;
+     int arg;
+     int ret;
+     char *str;
+@@ -118,7 +113,7 @@
+     int mutate_arg = 1;
+     char buf[IOCTL_BUFSZ+1];  /* argument plus NUL byte */
+ 
+-    if (PyArg_ParseTuple(args, "O&Iw#|i:ioctl",
++    if (PyArg_ParseTuple(args, "O&kw#|i:ioctl",
+                          conv_descriptor, &fd, &code,
+                          &str, &len, &mutate_arg)) {
+         char *arg;
+@@ -169,7 +164,7 @@
+     }
+ 
+     PyErr_Clear();
+-    if (PyArg_ParseTuple(args, "O&Is#:ioctl",
++    if (PyArg_ParseTuple(args, "O&ks#:ioctl",
+                          conv_descriptor, &fd, &code, &str, &len)) {
+         if (len > IOCTL_BUFSZ) {
+             PyErr_SetString(PyExc_ValueError,
+@@ -191,7 +186,7 @@
+     PyErr_Clear();
+     arg = 0;
+     if (!PyArg_ParseTuple(args,
+-         "O&I|i;ioctl requires a file or file descriptor,"
++         "O&k|i;ioctl requires a file or file descriptor,"
+          " an integer and optionally an integer or buffer argument",
+                           conv_descriptor, &fd, &code, &arg)) {
+       return NULL;
diff --git a/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Python_thread_pthread.h b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Python_thread_pthread.h
new file mode 100644
index 00000000000..68ccb349c2c
--- /dev/null
+++ b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_Python_thread_pthread.h
@@ -0,0 +1,55 @@
+--- python-2.7.2.p4/src/Python/thread_pthread.h.orig	2011-06-11 15:46:28.000000000 +0000
++++ python-2.7.2.p4/src/Python/thread_pthread.h	2012-04-22 00:23:46.000000000 +0000
+@@ -38,13 +38,18 @@
+ #endif
+ #endif
+ 
++#ifdef __FreeBSD__
++#include <osreldate.h>
++#endif
++
+ /* The POSIX spec says that implementations supporting the sem_*
+    family of functions must indicate this by defining
+    _POSIX_SEMAPHORES. */
+ #ifdef _POSIX_SEMAPHORES
+ /* On FreeBSD 4.x, _POSIX_SEMAPHORES is defined empty, so
+    we need to add 0 to make it work there as well. */
+-#if (_POSIX_SEMAPHORES+0) == -1
++#if defined(__FreeBSD__) && __FreeBSD_version < 701104 && \
++    (_POSIX_SEMAPHORES+0) == -1
+ #define HAVE_BROKEN_POSIX_SEMAPHORES
+ #else
+ #include <semaphore.h>
+@@ -56,7 +61,6 @@
+    in default setting.  So the process scope is preferred to get
+    enough number of threads to work. */
+ #ifdef __FreeBSD__
+-#include <osreldate.h>
+ #if __FreeBSD_version >= 500000 && __FreeBSD_version < 504101
+ #undef PTHREAD_SYSTEM_SCHED_SUPPORTED
+ #endif
+@@ -161,6 +165,7 @@
+ {
+     pthread_t th;
+     int status;
++    sigset_t set, oset;
+ #if defined(THREAD_STACK_SIZE) || defined(PTHREAD_SYSTEM_SCHED_SUPPORTED)
+     pthread_attr_t attrs;
+ #endif
+@@ -189,6 +194,8 @@
+ #if defined(PTHREAD_SYSTEM_SCHED_SUPPORTED)
+     pthread_attr_setscope(&attrs, PTHREAD_SCOPE_SYSTEM);
+ #endif
++    sigfillset(&set);
++    SET_THREAD_SIGMASK(SIG_BLOCK, &set, &oset);
+ 
+     status = pthread_create(&th,
+ #if defined(THREAD_STACK_SIZE) || defined(PTHREAD_SYSTEM_SCHED_SUPPORTED)
+@@ -200,6 +207,7 @@
+                              (void *)arg
+                              );
+ 
++    SET_THREAD_SIGMASK(SIG_SETMASK, &oset, NULL);
+ #if defined(THREAD_STACK_SIZE) || defined(PTHREAD_SYSTEM_SCHED_SUPPORTED)
+     pthread_attr_destroy(&attrs);
+ #endif
diff --git a/math/sage/files/spkg-patch-python-2.6.4.p13_-_src_setup.py b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_setup.py
index 815551cdcb1..395e96dd924 100644
--- a/math/sage/files/spkg-patch-python-2.6.4.p13_-_src_setup.py
+++ b/math/sage/files/spkg-patch-python-2.7.2.p4_-_src_setup.py
@@ -1,29 +1,29 @@
---- python-2.6.4.p13/src/setup.py-orig	2012-01-21 21:42:43.000000000 +0000
-+++ python-2.6.4.p13/src/setup.py	2012-01-21 21:45:11.000000000 +0000
-@@ -1273,16 +1273,24 @@
-                 )
+--- python-2.7.2.p4/src/setup.py-orig	2012-04-22 00:04:08.000000000 +0000
++++ python-2.7.2.p4/src/setup.py	2012-04-22 00:10:25.000000000 +0000
+@@ -1432,10 +1432,24 @@
+             macros = dict()
              libraries = []
  
 -        elif platform in ('freebsd4', 'freebsd5', 'freebsd6', 'freebsd7', 'freebsd8'):
 +        elif platform in ('freebsd4', 'freebsd5', 'freebsd6'):
              # FreeBSD's P1003.1b semaphore support is very experimental
              # and has many known problems. (as of June 2008)
--            macros = dict(                  # FreeBSD
+-            macros = dict()
 +            macros = dict(                  # FreeBSD 4-6
-                 HAVE_SEM_OPEN=0,
-                 HAVE_SEM_TIMEDWAIT=0,
-                 HAVE_FD_TRANSFER=1,
-                 )
-             libraries = []
- 
++                HAVE_SEM_OPEN=0,
++                HAVE_SEM_TIMEDWAIT=0,
++                HAVE_FD_TRANSFER=1,
++                )
++            libraries = []
++
 +        elif platform in ('freebsd7', 'freebsd8', 'freebsd9', 'freebsd10'):
++            # FreeBSD's P1003.1b semaphore support is very experimental
++            # and has many known problems. (as of June 2008)
 +            macros = dict(                  # FreeBSD 7+
 +                HAVE_SEM_OPEN=1,
 +                HAVE_SEM_TIMEDWAIT=1,
 +                HAVE_FD_TRANSFER=1,
-+               )
-+            libraries = []
-+
++                )
+             libraries = []
+ 
          elif platform.startswith('openbsd'):
-             macros = dict(                  # OpenBSD
-                 HAVE_SEM_OPEN=0,            # Not implemented
diff --git a/math/sage/files/spkg-patch-sage-5.0_-_sage_combinat_partitions_c.cc b/math/sage/files/spkg-patch-sage-5.0_-_sage_combinat_partitions_c.cc
new file mode 100644
index 00000000000..8fa517504fd
--- /dev/null
+++ b/math/sage/files/spkg-patch-sage-5.0_-_sage_combinat_partitions_c.cc
@@ -0,0 +1,11 @@
+--- sage-5.0.beta13/sage/combinat/partitions_c.cc-orig	2012-04-20 01:01:41.000000000 +0000
++++ sage-5.0/sage/combinat/partitions_c.cc	2012-04-20 01:02:47.000000000 +0000
+@@ -152,7 +152,7 @@
+ const unsigned int double_precision = DBL_MANT_DIG;                         // The assumed precision of a double.
+ 
+ 
+-#if defined(__sparc) || defined(__CYGWIN__)
++#if defined(__sparc) || defined(__CYGWIN__) || defined(__FreeBSD__)
+ // On sparc solaris long double is bad/broken/different, etc.  E.g.,
+ // LDBL_MANT_DIG is 113 rather than 106, which causes all kinds of trouble.
+ // So we only use double_precision.
diff --git a/math/sage/files/spkg-patch-sage-5.0_-_sage_misc_getusage.py b/math/sage/files/spkg-patch-sage-5.0_-_sage_misc_getusage.py
new file mode 100644
index 00000000000..a44ca946f56
--- /dev/null
+++ b/math/sage/files/spkg-patch-sage-5.0_-_sage_misc_getusage.py
@@ -0,0 +1,40 @@
+--- sage-5.0.beta13/sage/misc/getusage.py-orig	2012-04-11 00:14:47.000000000 +0000
++++ sage-5.0/sage/misc/getusage.py	2012-04-11 00:47:03.000000000 +0000
+@@ -20,6 +20,8 @@
+     """
+     Return the 'top' or 'prstat' line that contains this running Sage
+     process.
++    For FreeBSD, return the line containing this running Sage process from
++    'ps -axwww -o pid,user,vsz,rss,state,pri,nice,time,cpu,comm'.
+ 
+     OUTPUT:
+ 
+@@ -53,6 +55,8 @@
+         cmd = 'top -l 1 |grep "^ *%s "' % pid
+     elif U == 'sunos':
+         cmd = '/usr/bin/prstat -n 100000 1 1  | grep "^ *%s "' % pid
++    elif U == 'freebsd':
++        cmd = 'ps -axwww -o pid,user,vsz,rss,state,pri,nice,time,cpu,comm | grep "^ *%s "' % pid
+     else:
+         raise NotImplementedError("top not implemented on platform %s" % U)
+     
+@@ -83,6 +87,9 @@
+       usage, ``prstat`` will output the data in KB, MB or GB. In each
+       case, the value returned by this function will always be in MB.
+ 
++    - ``FreeBSD`` - Returns float number (in megabytes) that matches
++      RSS column of ``ps -auxwww``
++
+     - ``other`` - not implemented for any other operating systems
+ 
+     EXAMPLES::
+@@ -129,6 +136,9 @@
+             m = float(memory_in_KB_MB_or_GB.strip("M"))
+         elif memory_in_KB_MB_or_GB.endswith("G"):
+             m = float(memory_in_KB_MB_or_GB.strip("G")) * 1024
++    elif U == 'freebsd':
++        memory_in_KB = top().split()[3]
++        m = float(memory_in_KB) / 1024
+     else:
+         raise NotImplementedError("memory usage not implemented on platform %s" % U)
+     
diff --git a/math/sage/files/spkg-patch-singular-3-1-3-3.p3_-_src_omalloc_configure b/math/sage/files/spkg-patch-singular-3-1-3-3.p3_-_src_omalloc_configure
deleted file mode 100644
index 3d574426ca5..00000000000
--- a/math/sage/files/spkg-patch-singular-3-1-3-3.p3_-_src_omalloc_configure
+++ /dev/null
@@ -1,12 +0,0 @@
---- singular-3-1-3-3.p3/src/omalloc/configure-orig	2012-01-21 19:51:08.000000000 +0000
-+++ singular-3-1-3-3.p3/src/omalloc/configure	2012-01-21 19:51:32.000000000 +0000
-@@ -1293,9 +1293,6 @@
-   echo "$ac_t""no" 1>&6
- fi
- 
--if test "$ac_cv_prog_AR" != ar; then
--  { echo "configure: error: *** ar program not found" 1>&2; exit 1; }
--fi
- for ac_prog in perl
- do
- # Extract the first word of "$ac_prog", so it can be a program name with args.
diff --git a/math/sage/files/spkg-patch-singular-3-1-3-3.p6_-_patches_omalloc.configure.patch b/math/sage/files/spkg-patch-singular-3-1-3-3.p6_-_patches_omalloc.configure.patch
new file mode 100644
index 00000000000..381934fd794
--- /dev/null
+++ b/math/sage/files/spkg-patch-singular-3-1-3-3.p6_-_patches_omalloc.configure.patch
@@ -0,0 +1,16 @@
+--- /dev/null	2012-04-08 00:25:00.000000000 +0000
++++ singular-3-1-3-3.p6/patches/omalloc.configure.patch	2012-04-08 00:25:39.000000000 +0000
+@@ -0,0 +1,13 @@
++diff -ur src/omalloc/configure patches/omalloc/configure
++--- src/omalloc/configure	2011-05-12 08:32:11.000000000 +0000
+++++ patches/omalloc/configure	2012-04-08 00:22:37.000000000 +0000
++@@ -1293,9 +1293,6 @@
++   echo "$ac_t""no" 1>&6
++ fi
++ 
++-if test "$ac_cv_prog_AR" != ar; then
++-  { echo "configure: error: *** ar program not found" 1>&2; exit 1; }
++-fi
++ for ac_prog in perl
++ do
++ # Extract the first word of "$ac_prog", so it can be a program name with args.
diff --git a/math/sage/files/spkg-patch-singular-3-1-3-3.p6_-_spkg-install b/math/sage/files/spkg-patch-singular-3-1-3-3.p6_-_spkg-install
new file mode 100644
index 00000000000..f64c6337ed6
--- /dev/null
+++ b/math/sage/files/spkg-patch-singular-3-1-3-3.p6_-_spkg-install
@@ -0,0 +1,11 @@
+--- singular-3-1-3-3.p6/spkg-install-orig	2012-04-08 01:57:01.000000000 +0000
++++ singular-3-1-3-3.p6/spkg-install	2012-04-08 01:58:19.000000000 +0000
+@@ -108,7 +108,7 @@
+ 
+     patches="assert.h.diff sing_win.cc.diff Minor.h.patch os_x_ppc.patch \
+ 	Singular.configure.patch make_parallel.patch Singular.Makefile.in.shared.patch \
+-	factory.GNUmakefile.in.patch"
++	factory.GNUmakefile.in.patch omalloc.configure.patch"
+ 
+     if [ "$UNAME" = "CYGWIN" ]; then
+         patches="$patches IntegerProgramming-Makefile.in.diff"
diff --git a/math/sage/files/spkg-patch-sympow-1.018.1.p11_-_src_disk.c b/math/sage/files/spkg-patch-sympow-1.018.1.p11_-_src_disk.c
new file mode 100644
index 00000000000..6efde556339
--- /dev/null
+++ b/math/sage/files/spkg-patch-sympow-1.018.1.p11_-_src_disk.c
@@ -0,0 +1,11 @@
+--- sympow-1.018.1.p11/src/disk.c-orig	2012-04-19 02:33:51.000000000 +0000
++++ sympow-1.018.1.p11/src/disk.c	2012-04-19 02:34:22.000000000 +0000
+@@ -39,7 +39,7 @@
+  else if (((sp&3)==0) && CM_CASE) {if (2*ep==sp) S[3]='l'; else S[3]='h';}
+  else {if (2*ep==sp) S[3]='L'; else S[3]='H';}
+  if (HECKE && dv) {TACKS[which]=malloc(dv*sizeof(QD)); TACKON[which]=dv;}
+- else if (dv<=sp/2) TACKON[which]=0;
++ else if (dv<=sp/2) {TACKS[which]=NULL; TACKON[which]=0;}
+  else {TACKS[which]=malloc((dv-sp/2)*sizeof(QD)); TACKON[which]=dv-sp/2;}
+  S[4]=0; F=fopen("datafiles/param_data","r"); strcpy(U,S);
+  if (ANAL_RANK) {if (dv>0) U[0]='A'; else U[0]='m';}
diff --git a/math/sage/files/spkg-patch-sympow-1.018.1.p9_-_src_fpu.c b/math/sage/files/spkg-patch-sympow-1.018.1.p9_-_src_fpu.c
deleted file mode 100644
index 50223f54363..00000000000
--- a/math/sage/files/spkg-patch-sympow-1.018.1.p9_-_src_fpu.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- sympow-1.018.1.p9/src/fpu.c-orig	2012-02-01 01:01:04.000000000 +0000
-+++ sympow-1.018.1.p9/src/fpu.c	2012-02-01 01:01:18.000000000 +0000
-@@ -1,8 +1,4 @@
- 
- void fpu_53bits()
- {
--#ifdef x86
--#include <fpu_control.h>
--fpu_control_t fpu_control=0x027f; _FPU_SETCW(fpu_control);
--#endif
- }
diff --git a/math/sage/pkg-descr b/math/sage/pkg-descr
index fefc0f5361d..b7fea2d7b67 100644
--- a/math/sage/pkg-descr
+++ b/math/sage/pkg-descr
@@ -5,8 +5,4 @@ Python-based interface.
 Mission: Creating a viable free open source alternative to Magma, Maple,
 Mathematica and Matlab.
 
-This port is a work in progress.  It creates a sage that is mostly functional,
-but it does fail a few tests.  Suggestions for improvement to the maintainer
-are welcome.
-
 WWW: http://www.sagemath.org/