Fixes for parallel compilation, python, 64bit

(Portage version: 2.2.0_alpha6/cvs/Linux x86_64)

13 files changed, 680 insertions, 1311 deletions

diff --git a/sci-chemistry/azara/ChangeLog b/sci-chemistry/azara/ChangeLog
index f2a597c2aff5..67d19b793764 100644
--- a/sci-chemistry/azara/ChangeLog
+++ b/sci-chemistry/azara/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/azara
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/ChangeLog,v 1.6 2010/10/31 09:15:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/ChangeLog,v 1.7 2010/12/12 18:14:45 jlec Exp $
+
+*azara-2.8-r3 (12 Dec 2010)
+
+  12 Dec 2010; Justin Lecher <jlec@gentoo.org> +files/2.8-python.patch,
+  -files/2.7-impl-dec.patch, -azara-2.8-r1.ebuild, -azara-2.8-r2.ebuild,
+  -files/2.7-prll.patch, -files/2.8-impl-decng.patch, +azara-2.8-r3.ebuild,
+  +files/2.8-64bit.patch, -files/2.8-prllng.patch, files/2.8-impl-dec.patch,
+  -azara-2.7-r1.ebuild, files/2.8-prll.patch:
+  Fixes for parallel compilation, python, 64bit
 
 *azara-2.8-r2 (31 Oct 2010)
 
diff --git a/sci-chemistry/azara/azara-2.7-r1.ebuild b/sci-chemistry/azara/azara-2.7-r1.ebuild
deleted file mode 100644
index b7fe0de77139..000000000000
--- a/sci-chemistry/azara/azara-2.7-r1.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/azara-2.7-r1.ebuild,v 1.1 2010/08/06 10:50:04 jlec Exp $
-
-EAPI="3"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A suite of programmes to process and view NMR data"
-HOMEPAGE="http://www.bio.cam.ac.uk/azara/"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tar.gz"
-
-LICENSE="AZARA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="opengl X xpm"
-
-RDEPEND="
-	xpm? ( x11-libs/libXpm )
-	X? ( x11-libs/libX11 )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	echo "" > ENVIRONMENT
-
-#	epatch "${FILESDIR}"/help-makefile.patch
-	epatch "${FILESDIR}"/${PV}-prll.patch
-	epatch "${FILESDIR}"/${PV}-impl-dec.patch
-}
-
-src_compile() {
-	local mymake
-	local xpmuse
-	local makeflags
-
-	mymake="${mymake} help nongui"
-	use X && mymake="${mymake} gui"
-	use opengl && mymake="${mymake} gl"
-	use xpm && XPMUSE="XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm"
-
-	emake \
-		CC=$(tc-getCC) \
-		CFLAGS="${CFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		MATH_LIB="-lm" \
-		X11_INCLUDE_DIR="-I${EPREFIX}/usr/X11R6/include" \
-		MOTIF_INCLUDE_DIR="-I${EPREFIX}/usr/include" \
-		X11_LIB_DIR="-L${EPREFIX}/usr/$(get_libdir)" \
-		MOTIF_LIB_DIR="-L${EPREFIX}/usr/$(get_libdir)" \
-		${XPMUSE} \
-		X11_LIB="-lX11" \
-		MOTIF_LIB="-lXm -lXt" \
-		GL_INCLUDE_DIR="-I${EPREFIX}/usr/X11R6/include -I${EPREFIX}/usr/include" \
-		GL_LIB_DIR="-I${EPREFIX}/usr/$(get_libdir)" \
-		GL_LIB="-lglut -lGLU -lGL -lXmu -lX11 -lXext" \
-		ENDIAN_FLAG="-DLITTLE_ENDIAN_DATA" \
-		${mymake} || die
-}
-
-src_install() {
-	if ! use X; then
-		rm bin/plot* || die
-	fi
-	if ! use opengl; then
-		rm bin/viewer || die
-	fi
-	for bin in bin/*; do
-		newbin "${bin}" "${PN}-${bin}" || die "failed to install ${bin}"
-	done
-
-	dodoc CHANGES* README* || die
-	dohtml -r html/* || die
-}
-
-pkg_postinst() {
-	einfo "Due to collision we moved all binary to azara-*"
-}
diff --git a/sci-chemistry/azara/azara-2.8-r1.ebuild b/sci-chemistry/azara/azara-2.8-r1.ebuild
deleted file mode 100644
index 8139cfa6e9ed..000000000000
--- a/sci-chemistry/azara/azara-2.8-r1.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/azara-2.8-r1.ebuild,v 1.1 2010/08/06 10:50:04 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils python toolchain-funcs
-
-DESCRIPTION="A suite of programmes to process and view NMR data"
-HOMEPAGE="http://www.bio.cam.ac.uk/azara/"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz"
-
-LICENSE="AZARA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="X xpm"
-
-RDEPEND="
-	xpm? ( x11-libs/libXpm )
-	X? ( x11-libs/libX11 )"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_prepare() {
-	cat > ENVIRONMENT <<- EOF
-	CC=$(tc-getCC)
-	CFLAGS=${CFLAGS}
-	LFLAGS=${LDFLAGS}
-	MATH_LIB=-lm
-	X11_INCLUDE_DIR=-I${EPREFIX}/usr/X11R6/include
-	MOTIF_INCLUDE_DIR=-I${EPREFIX}/usr/include
-	X11_LIB_DIR=-L${EPREFIX}/usr/$(get_libdir)
-	MOTIF_LIB_DIR=-L${EPREFIX}/usr/$(get_libdir)
-	X11_LIB=-lX11
-	MOTIF_LIB=-lXm -lXt
-	PYTHON_INCLUDE_DIR=$(python_get_includedir)
-	SHARED_FLAGS = -shared
-	ENDIAN_FLAG=-DLITTLE_ENDIAN_DATA
-	EOF
-
-	use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT
-
-	epatch "${FILESDIR}"/${PV}-prll.patch
-	epatch "${FILESDIR}"/${PV}-impl-dec.patch
-}
-
-src_compile() {
-	local mymake
-	local makeflags
-
-	mymake="${mymake} help nongui DataRows"
-	use X && mymake="${mymake} gui"
-
-	emake ${mymake} || die
-}
-
-src_install() {
-	rm bin/pythonAzara || die
-	if ! use X; then
-		rm bin/plot* || die
-	fi
-	for bin in bin/*; do
-		newbin "${bin}" "${PN}-${bin}" || die "failed to install ${bin}"
-	done
-
-	dodoc CHANGES* README* || die
-	dohtml -r html/* || die
-}
-
-pkg_postinst() {
-	einfo "Due to collision we moved all binary to azara-*"
-}
diff --git a/sci-chemistry/azara/azara-2.8-r2.ebuild b/sci-chemistry/azara/azara-2.8-r2.ebuild
deleted file mode 100644
index dc9491d569bb..000000000000
--- a/sci-chemistry/azara/azara-2.8-r2.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/azara-2.8-r2.ebuild,v 1.1 2010/10/31 09:15:41 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils python toolchain-funcs
-
-DESCRIPTION="A suite of programmes to process and view NMR data"
-HOMEPAGE="http://www.bio.cam.ac.uk/azara/"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz"
-
-LICENSE="AZARA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="X xpm"
-
-RDEPEND="
-	xpm? ( x11-libs/libXpm )
-	X? ( x11-libs/libX11 )"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_prepare() {
-	cat > ENVIRONMENT <<- EOF
-	CC=$(tc-getCC)
-	CFLAGS=${CFLAGS}
-	LFLAGS=${LDFLAGS}
-	MATH_LIB=-lm
-	X11_INCLUDE_DIR=-I${EPREFIX}/usr/X11R6/include
-	MOTIF_INCLUDE_DIR=-I${EPREFIX}/usr/include -I../global
-	X11_LIB_DIR=-L${EPREFIX}/usr/$(get_libdir)
-	MOTIF_LIB_DIR=-L${EPREFIX}/usr/$(get_libdir)
-	X11_LIB=-lX11
-	MOTIF_LIB=-lXm -lXt
-	PYTHON_INCLUDE_DIR=$(python_get_includedir)
-	SHARED_FLAGS = -shared
-	ENDIAN_FLAG=-DLITTLE_ENDIAN_DATA
-	EOF
-
-	use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT
-
-	epatch "${FILESDIR}"/${PV}-prllng.patch
-	epatch "${FILESDIR}"/${PV}-impl-decng.patch
-}
-
-src_compile() {
-	local mymake
-	local makeflags
-
-	mymake="${mymake} help nongui DataRows"
-	use X && mymake="${mymake} gui"
-
-	emake -C global || die
-	emake ${mymake} || die
-}
-
-src_install() {
-	rm bin/pythonAzara || die
-	if ! use X; then
-		rm bin/plot* || die
-	fi
-
-	dodoc CHANGES* README* || die
-	dohtml -r html/* || die
-
-	cd bin
-	for bin in *; do
-		newbin ${bin} ${PN}-${bin} || die "failed to install ${bin}"
-	done
-}
-
-pkg_postinst() {
-	einfo "Due to collision we moved all binary to azara-*"
-}
diff --git a/sci-chemistry/azara/azara-2.8-r3.ebuild b/sci-chemistry/azara/azara-2.8-r3.ebuild
new file mode 100644
index 000000000000..82625a2822a8
--- /dev/null
+++ b/sci-chemistry/azara/azara-2.8-r3.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/azara-2.8-r3.ebuild,v 1.1 2010/12/12 18:14:45 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="python? 2"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="3.*"
+
+inherit eutils python toolchain-funcs
+
+DESCRIPTION="A suite of programmes to process and view NMR data"
+HOMEPAGE="http://www.bio.cam.ac.uk/azara/"
+SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz"
+
+LICENSE="AZARA"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="X python xpm"
+
+RDEPEND="
+	xpm? ( x11-libs/libXpm )
+	X? ( x11-libs/libX11 )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	cat > ENVIRONMENT <<- EOF
+	CC=$(tc-getCC)
+	CFLAGS = ${CFLAGS}
+	LFLAGS = ${LDFLAGS}
+	MATH_LIB = -lm
+	X11_INCLUDE_DIR = -I${EPREFIX}/usr/X11R6/include
+	MOTIF_INCLUDE_DIR = -I${EPREFIX}/usr/include -I../global
+	X11_LIB_DIR = -L${EPREFIX}/usr/$(get_libdir)
+	MOTIF_LIB_DIR = -L${EPREFIX}/usr/$(get_libdir)
+	X11_LIB = -lX11
+	MOTIF_LIB = -lXm -lXt
+	SHARED_FLAGS = -shared
+	ENDIAN_FLAG = -DBIG_ENDIAN_DATA -DWRITE_ENDIAN_PAR
+	PIC = -fPIC
+	EOF
+
+	use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT
+
+	epatch \
+		"${FILESDIR}"/${PV}-prll.patch \
+		"${FILESDIR}"/${PV}-impl-dec.patch \
+		"${FILESDIR}"/${PV}-python.patch \
+		"${FILESDIR}"/${PV}-64bit.patch
+}
+
+src_compile() {
+	local mymake
+	local makeflags
+
+	mymake="${mymake} help nongui"
+	use X && mymake="${mymake} gui"
+
+	emake ${mymake} || die
+
+	compilation() {
+		emake DataRows_clean || die
+		emake \
+			PYTHON_INCLUDE_DIR="-I${EPREFIX}/$(python_get_includedir)" \
+			PYTHON_LIB="$(python_get_library -l)" \
+			DataRows || die
+	}
+	use python && python_execute_function compilation
+}
+
+src_install() {
+	rm bin/pythonAzara || die
+	if ! use X; then
+		rm bin/plot* || die
+	fi
+
+	dodoc CHANGES* README* || die
+	dohtml -r html/* || die
+
+	installation() {
+		insinto "${EPREFIX}/$(python_get_sitedir)"
+		doins lib/DataRows.so || die
+	}
+	use python && python_execute_function installation
+
+	cd bin
+	dobin ${PN}|| die
+	rm ${PN}
+	for bin in *; do
+		newbin ${bin} ${bin}-${PN} || die "failed to install ${bin}"
+	done
+}
+
+pkg_postinst() {
+	einfo "Due to collision we moved all binary to *-${PN}"
+}
diff --git a/sci-chemistry/azara/files/2.7-impl-dec.patch b/sci-chemistry/azara/files/2.7-impl-dec.patch
deleted file mode 100644
index b491ec7691ec..000000000000
--- a/sci-chemistry/azara/files/2.7-impl-dec.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/global/macros.h b/global/macros.h
-index ddeaffa..2bcc433 100644
---- a/global/macros.h
-+++ b/global/macros.h
-@@ -6,6 +6,7 @@
- #include <math.h>
- #include <string.h>
- #include <stdlib.h>
-+#include <ctype.h>
- 
- #ifdef WIN32
- #include <ctype.h>
-diff --git a/plot2/script.c b/plot2/script.c
-index 2f55182..ef219cc 100644
---- a/plot2/script.c
-+++ b/plot2/script.c
-@@ -4,6 +4,7 @@
- #include "stack.h"
- #include "utility.h"
- 
-+
- #define  SCRIPT_COMMENT		'!'
- 
- #define  LOOP_KEY		"loop"
diff --git a/sci-chemistry/azara/files/2.7-prll.patch b/sci-chemistry/azara/files/2.7-prll.patch
deleted file mode 100644
index ced64d1760e1..000000000000
--- a/sci-chemistry/azara/files/2.7-prll.patch
+++ /dev/null
@@ -1,301 +0,0 @@
-diff --git a/help/makefile b/help/makefile
-index aa9274f..d349286 100644
---- a/help/makefile
-+++ b/help/makefile
-@@ -36,103 +36,103 @@ globals:
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
--hlp:
--	txt2hlp azara
--	txt2hlp combine
--	txt2hlp components
--	txt2hlp connect
--	txt2hlp contours
--	txt2hlp deflate
--	txt2hlp extract
--	txt2hlp peak_find
--	txt2hlp peak_fit
--	txt2hlp plot1
--	txt2hlp plot2
--	txt2hlp process
--	txt2hlp project
--	txt2hlp slides
--	txt2hlp reflate
--	txt2hlp unblock
--	txt2hlp viewer
--	txt2hlp plot2/baseline
--	txt2hlp plot2/data
--	txt2hlp plot2/extract
--	txt2hlp plot2/levels
--	txt2hlp plot2/object
--	txt2hlp plot2/output
--	txt2hlp plot2/peak
--	txt2hlp plot2/peaks
--	txt2hlp plot2/phase
--	txt2hlp plot2/property
--	txt2hlp plot2/region
--	txt2hlp plot2/rowcol
--	txt2hlp plot2/save
--	txt2hlp plot2/tracking
--	txt2hlp plot1/button
--	txt2hlp plot1/data
--	txt2hlp plot1/object
--	txt2hlp plot1/output
--	txt2hlp plot1/property
--	txt2hlp plot1/region
--	txt2hlp plot1/slider
--	txt2hlp plot1/text
--
--html:
--	txt2html azara
--	txt2html combine
--	txt2html components
--	txt2html connect
--	txt2html contours
--	txt2html deflate
--	txt2html extract
--	txt2html peak_find
--	txt2html peak_fit
--	txt2html plot1
--	txt2html plot2
--	txt2html process
--	txt2html project
--	txt2html slides
--	txt2html reflate
--	txt2html unblock
--	txt2html viewer
--	txt2html plot2/baseline
--	txt2html plot2/data
--	txt2html plot2/extract
--	txt2html plot2/levels
--	txt2html plot2/object
--	txt2html plot2/output
--	txt2html plot2/peak
--	txt2html plot2/peaks
--	txt2html plot2/phase
--	txt2html plot2/property
--	txt2html plot2/region
--	txt2html plot2/rowcol
--	txt2html plot2/save
--	txt2html plot2/tracking
--	txt2html plot1/button
--	txt2html plot1/data
--	txt2html plot1/object
--	txt2html plot1/output
--	txt2html plot1/property
--	txt2html plot1/region
--	txt2html plot1/slider
--	txt2html plot1/text
--	txt2html CHANGES
--	txt2html INSTALL
--	txt2html README-2.7
--	txt2html CHANGES-1.0-1
--	txt2html CHANGES-1.0-2
--	txt2html CHANGES-1.0-3
--	txt2html CHANGES-2.0-0
--	txt2html CHANGES-2.5-0
--	txt2html CHANGES-2.6-0
--	txt2html CHANGES-2.7-0
--	txt2html LICENSE
-+hlp: txt2hlp
-+	./txt2hlp azara
-+	./txt2hlp combine
-+	./txt2hlp components
-+	./txt2hlp connect
-+	./txt2hlp contours
-+	./txt2hlp deflate
-+	./txt2hlp extract
-+	./txt2hlp peak_find
-+	./txt2hlp peak_fit
-+	./txt2hlp plot1
-+	./txt2hlp plot2
-+	./txt2hlp process
-+	./txt2hlp project
-+	./txt2hlp slides
-+	./txt2hlp reflate
-+	./txt2hlp unblock
-+	./txt2hlp viewer
-+	./txt2hlp plot2/baseline
-+	./txt2hlp plot2/data
-+	./txt2hlp plot2/extract
-+	./txt2hlp plot2/levels
-+	./txt2hlp plot2/object
-+	./txt2hlp plot2/output
-+	./txt2hlp plot2/peak
-+	./txt2hlp plot2/peaks
-+	./txt2hlp plot2/phase
-+	./txt2hlp plot2/property
-+	./txt2hlp plot2/region
-+	./txt2hlp plot2/rowcol
-+	./txt2hlp plot2/save
-+	./txt2hlp plot2/tracking
-+	./txt2hlp plot1/button
-+	./txt2hlp plot1/data
-+	./txt2hlp plot1/object
-+	./txt2hlp plot1/output
-+	./txt2hlp plot1/property
-+	./txt2hlp plot1/region
-+	./txt2hlp plot1/slider
-+	./txt2hlp plot1/text
-+
-+html: txt2html
-+	./txt2html azara
-+	./txt2html combine
-+	./txt2html components
-+	./txt2html connect
-+	./txt2html contours
-+	./txt2html deflate
-+	./txt2html extract
-+	./txt2html peak_find
-+	./txt2html peak_fit
-+	./txt2html plot1
-+	./txt2html plot2
-+	./txt2html process
-+	./txt2html project
-+	./txt2html slides
-+	./txt2html reflate
-+	./txt2html unblock
-+	./txt2html viewer
-+	./txt2html plot2/baseline
-+	./txt2html plot2/data
-+	./txt2html plot2/extract
-+	./txt2html plot2/levels
-+	./txt2html plot2/object
-+	./txt2html plot2/output
-+	./txt2html plot2/peak
-+	./txt2html plot2/peaks
-+	./txt2html plot2/phase
-+	./txt2html plot2/property
-+	./txt2html plot2/region
-+	./txt2html plot2/rowcol
-+	./txt2html plot2/save
-+	./txt2html plot2/tracking
-+	./txt2html plot1/button
-+	./txt2html plot1/data
-+	./txt2html plot1/object
-+	./txt2html plot1/output
-+	./txt2html plot1/property
-+	./txt2html plot1/region
-+	./txt2html plot1/slider
-+	./txt2html plot1/text
-+	./txt2html CHANGES
-+	./txt2html INSTALL
-+	./txt2html README-2.7
-+	./txt2html CHANGES-1.0-1
-+	./txt2html CHANGES-1.0-2
-+	./txt2html CHANGES-1.0-3
-+	./txt2html CHANGES-2.0-0
-+	./txt2html CHANGES-2.5-0
-+	./txt2html CHANGES-2.6-0
-+	./txt2html CHANGES-2.7-0
-+	./txt2html LICENSE
- 
- clean:
- 	rm *.o
- 
- realclean:
- 	rm *.o
--	rm txt2hlp
--	rm txt2html
-+	rm ./txt2hlp
-+	rm ./txt2html
-diff --git a/makefile b/makefile
-index 752f31d..e12f9c4 100644
---- a/makefile
-+++ b/makefile
-@@ -14,7 +14,7 @@ all: help nongui gui gl
- help: \
- 	help_program
- 
--nongui: \
-+nongui: help \
- 	process_program \
- 	peak_program \
- 	extract_program \
-@@ -30,66 +30,66 @@ nongui: \
- 	components_program \
- 	azara_program
- 
--gui: \
-+gui: help \
- 	plot2_program \
- 	plot1_program
- 
--gl: \
-+gl: help \
- 	viewer_program
- 
- process_program:
--	cd process; $(MAKE)
-+	$(MAKE) -C process
- 
- plot2_program:
--	cd plot2; $(MAKE)
-+	$(MAKE) -C plot2
- 
- plot1_program:
--	cd plot1; $(MAKE)
-+	$(MAKE) -C plot1
- 
- peak_program:
--	cd peak; $(MAKE)
-+	$(MAKE) -C peak
- 
- extract_program:
--	cd extract; $(MAKE)
-+	$(MAKE) -C extract
- 
- project_program:
--	cd project; $(MAKE)
-+	$(MAKE) -C project
- 
- unblock_program:
--	cd unblock; $(MAKE)
-+	$(MAKE) -C unblock
- 
- contours_program:
--	cd contours; $(MAKE)
-+	$(MAKE) -C contours
- 
- combine_program:
--	cd combine; $(MAKE)
-+	$(MAKE) -C combine
- 
- deflate_program:
--	cd deflate; $(MAKE)
-+	$(MAKE) -C deflate
- 
- reflate_program:
--	cd reflate; $(MAKE)
-+	$(MAKE) -C reflate
- 
- slides_program:
--	cd slides; $(MAKE)
-+	$(MAKE) -C slides
- 
- components_program:
--	cd components; $(MAKE)
-+	$(MAKE) -C components
- 
- utility_program:
--	cd utility; $(MAKE)
-+	$(MAKE) -C utility
- 
- connect_program:
--	cd connect; $(MAKE)
-+	$(MAKE) -C connect
- 
- viewer_program:
--	cd viewer; $(MAKE)
-+	$(MAKE) -C viewer
- 
- help_program:
- 	cd help; $(MAKE)
- 
- azara_program:
--	cd azara; $(MAKE)
-+	$(MAKE) -C azara
- 
- clean: \
- 	global_clean \
diff --git a/sci-chemistry/azara/files/2.8-64bit.patch b/sci-chemistry/azara/files/2.8-64bit.patch
new file mode 100644
index 000000000000..a2f804c41498
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-64bit.patch
@@ -0,0 +1,55 @@
+diff --git a/global/par.c b/global/par.c
+index ac87c88..1d171de 100644
+--- a/global/par.c
++++ b/global/par.c
+@@ -562,9 +562,9 @@ static Status get_varian_header(FILE *fp, String error_msg)
+     return  OK;
+ }
+ 
+-static long get_varian_long(int offset)
++static int get_varian_int(int offset)
+ {
+-    long x;
++    int x;
+ 
+     if (swapped)
+     {
+@@ -572,7 +572,7 @@ static long get_varian_long(int offset)
+ 	SWAP(varian_header[offset+1], varian_header[offset+2], char);
+     }
+ 
+-    x = *((long *) (varian_header + offset));
++    x = *((int *) (varian_header + offset));
+ 
+     return  x;
+ }
+@@ -591,7 +591,7 @@ static short get_varian_short(int offset)
+ 
+ static Status check_varian_header(String error_msg)
+ {
+-    long nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d;
++    int nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d;
+     short status;
+     FILE *fp;
+ 
+@@ -605,12 +605,14 @@ static Status check_varian_header(String error_msg)
+     FCLOSE(fp);
+ 
+     /* numbers in parentheses are offsets into header */
+-    nblocks = get_varian_long(0);   /* number of blocks in file */
+-    ntraces = get_varian_long(4);   /* number of traces per block */
+-    np = get_varian_long(8);	    /* number of elements per trace */
+-    ebytes = get_varian_long(12);   /* number of bytes per element */
+-    tbytes = get_varian_long(16);   /* number of bytes per trace */
+-    /*bbytes = get_varian_long(20);*/   /* number of bytes per block */
++    nblocks = get_varian_int(0);   /* number of blocks in file */
++    printf("nblocks = %ld\n", nblocks);
++    ntraces = get_varian_int(4);   /* number of traces per block */
++    printf("ntraces = %ld\n", ntraces);
++    np = get_varian_int(8);	    /* number of elements per trace */
++    ebytes = get_varian_int(12);   /* number of bytes per element */
++    tbytes = get_varian_int(16);   /* number of bytes per trace */
++    /*bbytes = get_varian_int(20);*/   /* number of bytes per block */
+ 	    /* short starting at 24 is software version */
+     status = get_varian_short(26);  /* status of whole file */
+ 	    /* long starting at 28 is number of block headers */
diff --git a/sci-chemistry/azara/files/2.8-impl-dec.patch b/sci-chemistry/azara/files/2.8-impl-dec.patch
index 644656a48e4a..62e8c7d6873b 100644
--- a/sci-chemistry/azara/files/2.8-impl-dec.patch
+++ b/sci-chemistry/azara/files/2.8-impl-dec.patch
@@ -1,3 +1,44 @@
+diff --git a/DataRows/data_rows.c b/DataRows/data_rows.c
+index 054fa1f..a07eedc 100644
+--- a/DataRows/data_rows.c
++++ b/DataRows/data_rows.c
+@@ -1,4 +1,5 @@
+ #include "data_rows.h"
++#include "utility.h"
+ 
+ #include "par.h"
+ 
+diff --git a/DataRows/py_data_rows.c b/DataRows/py_data_rows.c
+index fc8b3c8..985e6c3 100644
+--- a/DataRows/py_data_rows.c
++++ b/DataRows/py_data_rows.c
+@@ -1,4 +1,6 @@
+ #include "Python.h"             /* Python header files */
++#include "modsupport.h"
++#include "intobject.h"
+ 
+ #include "data_rows.h"
+ 
+diff --git a/connect/crosspeak.c b/connect/crosspeak.c
+index 0de57bf..7b016e1 100644
+--- a/connect/crosspeak.c
++++ b/connect/crosspeak.c
+@@ -1,4 +1,5 @@
+ #include "crosspeak.h"
++#include "utility.h"
+ 
+ #include "atom.h"
+ #include "table.h"
+diff --git a/connect/shift.c b/connect/shift.c
+index f54ba9f..a880001 100644
+--- a/connect/shift.c
++++ b/connect/shift.c
+@@ -1,4 +1,5 @@
+ #include "shift.h"
++#include "utility.h"
+ 
+ #include "atom.h"
+ #include "table.h"
 diff --git a/global/macros.h b/global/macros.h
 index 43fc43e..bb1d267 100644
 --- a/global/macros.h
@@ -10,3 +51,176 @@ index 43fc43e..bb1d267 100644
  
  #ifdef WIN32
  #include <ctype.h>
+diff --git a/global/parser.c b/global/parser.c
+index 007d926..0f19575 100644
+--- a/global/parser.c
++++ b/global/parser.c
+@@ -1,4 +1,5 @@
+ #include "parser.h"
++#include "utility.h"
+ 
+ #define  MAX_NARGS		20
+ 
+diff --git a/peak/fitter.c b/peak/fitter.c
+index ba6b175..b58f573 100644
+--- a/peak/fitter.c
++++ b/peak/fitter.c
+@@ -1,4 +1,5 @@
+ #include "fitter.h"
++#include "data.h"
+ 
+ #include "nonlinear_model.h"
+ 
+diff --git a/peak/peak_fit.c b/peak/peak_fit.c
+index 92c69a8..5b9791f 100644
+--- a/peak/peak_fit.c
++++ b/peak/peak_fit.c
+@@ -6,6 +6,7 @@
+ #include "output.h"
+ #include "ref.h"
+ #include "script_fit.h"
++#include "fitter.h"
+ 
+ #define  MEGAWORD		(1024 * 1024)
+ #define  DEFAULT_STORE		(2 * MEGAWORD)
+diff --git a/plot1/draw.c b/plot1/draw.c
+index 4fdce96..a2a2e8a 100644
+--- a/plot1/draw.c
++++ b/plot1/draw.c
+@@ -1,4 +1,5 @@
+ #include "draw.h"
++#include "ticks.h"
+ 
+ #include "color.h"
+ #include "data.h"
+diff --git a/plot1/object.c b/plot1/object.c
+index 973897c..e043a53 100644
+--- a/plot1/object.c
++++ b/plot1/object.c
+@@ -1,4 +1,5 @@
+ #include "object.h"
++#include "script.h"
+ 
+ #include "color.h"
+ #include "parser.h"
+diff --git a/plot1/output_popup.c b/plot1/output_popup.c
+index 0794584..e73976e 100644
+--- a/plot1/output_popup.c
++++ b/plot1/output_popup.c
+@@ -1,4 +1,5 @@
+ #include "output_popup.h"
++#include "script.h"
+ 
+ #include "output.hlp"
+ 
+diff --git a/plot1/plots.c b/plot1/plots.c
+index 3790f5b..7ac58df 100644
+--- a/plot1/plots.c
++++ b/plot1/plots.c
+@@ -1,4 +1,5 @@
+ #include "plots.h"
++#include "script.h"
+ 
+ #include "data.h"
+ #include "input.h"
+diff --git a/plot1/region_popup.c b/plot1/region_popup.c
+index 68b3930..f049d29 100644
+--- a/plot1/region_popup.c
++++ b/plot1/region_popup.c
+@@ -1,4 +1,5 @@
+ #include "region_popup.h"
++#include "data.h"
+ 
+ #include "region.hlp"
+ 
+diff --git a/plot2/data_popup.c b/plot2/data_popup.c
+index 851b1d4..1c9026e 100644
+--- a/plot2/data_popup.c
++++ b/plot2/data_popup.c
+@@ -1,4 +1,5 @@
+ #include "data_popup.h"
++#include "rowcol_popup.h"
+ 
+ #include "data.hlp"
+ 
+diff --git a/plot2/extract_popup.c b/plot2/extract_popup.c
+index 416aab0..a7fcbf3 100644
+--- a/plot2/extract_popup.c
++++ b/plot2/extract_popup.c
+@@ -1,4 +1,5 @@
+ #include "extract_popup.h"
++#include "script.h"
+ 
+ #include "extract.hlp"
+ 
+diff --git a/plot2/levels_popup.c b/plot2/levels_popup.c
+index 197cf2c..e1ac22c 100644
+--- a/plot2/levels_popup.c
++++ b/plot2/levels_popup.c
+@@ -1,4 +1,5 @@
+ #include "levels_popup.h"
++#include "levels_func.h"
+ 
+ #include "levels.hlp"
+ 
+diff --git a/plot2/plot2.c b/plot2/plot2.c
+index 9ca91c3..0c10d5a 100644
+--- a/plot2/plot2.c
++++ b/plot2/plot2.c
+@@ -1,4 +1,6 @@
+ #include "plot2.h"
++#include "object_popup.h"
++#include "prop_popup.h"
+ 
+ #include "baseline_popup.h"
+ #include "callback.h"
+diff --git a/plot2/rowcol_popup.c b/plot2/rowcol_popup.c
+index e9f4843..6c50426 100644
+--- a/plot2/rowcol_popup.c
++++ b/plot2/rowcol_popup.c
+@@ -1,4 +1,5 @@
+ #include "rowcol_popup.h"
++#include "ref_popup.h"
+ 
+ #include "rowcol.hlp"
+ 
+diff --git a/plot2/script.c b/plot2/script.c
+index 2f55182..d7d886f 100644
+--- a/plot2/script.c
++++ b/plot2/script.c
+@@ -1,4 +1,5 @@
+ #include "script.h"
++#include "macros.h"
+ 
+ #include "param.h"
+ #include "stack.h"
+diff --git a/plot2/slice_popup.c b/plot2/slice_popup.c
+index b601834..1b1e686 100644
+--- a/plot2/slice_popup.c
++++ b/plot2/slice_popup.c
+@@ -1,4 +1,5 @@
+ #include "slice_popup.h"
++#include "rowcol_func.h"
+ 
+ #include "baseline.h"
+ #include "baseline_popup.h"
+diff --git a/process/files.c b/process/files.c
+index e09127e..d95d681 100644
+--- a/process/files.c
++++ b/process/files.c
+@@ -1,4 +1,5 @@
+ #include "files.h"
++#include "macros.h"
+ 
+ #include <sys/types.h>
+ #include <sys/stat.h>
+diff --git a/project/project.c b/project/project.c
+index 92b70e3..a3e6d94 100644
+--- a/project/project.c
++++ b/project/project.c
+@@ -1,4 +1,5 @@
+ #include "project.h"
++#include "utility.h"
+ 
+ #include "block.h"
+ #include "par.h"
diff --git a/sci-chemistry/azara/files/2.8-impl-decng.patch b/sci-chemistry/azara/files/2.8-impl-decng.patch
deleted file mode 100644
index 053d90f3c3fe..000000000000
--- a/sci-chemistry/azara/files/2.8-impl-decng.patch
+++ /dev/null
@@ -1,205 +0,0 @@
-diff --git a/connect/crosspeak.c b/connect/crosspeak.c
-index 0de57bf..7b016e1 100644
---- a/connect/crosspeak.c
-+++ b/connect/crosspeak.c
-@@ -1,4 +1,5 @@
- #include "crosspeak.h"
-+#include "utility.h"
- 
- #include "atom.h"
- #include "table.h"
-diff --git a/connect/shift.c b/connect/shift.c
-index f54ba9f..a880001 100644
---- a/connect/shift.c
-+++ b/connect/shift.c
-@@ -1,4 +1,5 @@
- #include "shift.h"
-+#include "utility.h"
- 
- #include "atom.h"
- #include "table.h"
-diff --git a/global/macros.h b/global/macros.h
-index 43fc43e..bb1d267 100644
---- a/global/macros.h
-+++ b/global/macros.h
-@@ -8,6 +8,7 @@
- #include <math.h>
- #include <string.h>
- #include <stdlib.h>
-+#include <ctype.h>
- 
- #ifdef WIN32
- #include <ctype.h>
-diff --git a/global/parser.c b/global/parser.c
-index 007d926..0f19575 100644
---- a/global/parser.c
-+++ b/global/parser.c
-@@ -1,4 +1,5 @@
- #include "parser.h"
-+#include "utility.h"
- 
- #define  MAX_NARGS		20
- 
-diff --git a/peak/fitter.c b/peak/fitter.c
-index ba6b175..b58f573 100644
---- a/peak/fitter.c
-+++ b/peak/fitter.c
-@@ -1,4 +1,5 @@
- #include "fitter.h"
-+#include "data.h"
- 
- #include "nonlinear_model.h"
- 
-diff --git a/peak/peak_fit.c b/peak/peak_fit.c
-index 92c69a8..5b9791f 100644
---- a/peak/peak_fit.c
-+++ b/peak/peak_fit.c
-@@ -6,6 +6,7 @@
- #include "output.h"
- #include "ref.h"
- #include "script_fit.h"
-+#include "fitter.h"
- 
- #define  MEGAWORD		(1024 * 1024)
- #define  DEFAULT_STORE		(2 * MEGAWORD)
-diff --git a/plot1/draw.c b/plot1/draw.c
-index 4fdce96..a2a2e8a 100644
---- a/plot1/draw.c
-+++ b/plot1/draw.c
-@@ -1,4 +1,5 @@
- #include "draw.h"
-+#include "ticks.h"
- 
- #include "color.h"
- #include "data.h"
-diff --git a/plot1/object.c b/plot1/object.c
-index 973897c..e043a53 100644
---- a/plot1/object.c
-+++ b/plot1/object.c
-@@ -1,4 +1,5 @@
- #include "object.h"
-+#include "script.h"
- 
- #include "color.h"
- #include "parser.h"
-diff --git a/plot1/output_popup.c b/plot1/output_popup.c
-index 0794584..e73976e 100644
---- a/plot1/output_popup.c
-+++ b/plot1/output_popup.c
-@@ -1,4 +1,5 @@
- #include "output_popup.h"
-+#include "script.h"
- 
- #include "output.hlp"
- 
-diff --git a/plot1/plots.c b/plot1/plots.c
-index 3790f5b..7ac58df 100644
---- a/plot1/plots.c
-+++ b/plot1/plots.c
-@@ -1,4 +1,5 @@
- #include "plots.h"
-+#include "script.h"
- 
- #include "data.h"
- #include "input.h"
-diff --git a/plot1/region_popup.c b/plot1/region_popup.c
-index 68b3930..f049d29 100644
---- a/plot1/region_popup.c
-+++ b/plot1/region_popup.c
-@@ -1,4 +1,5 @@
- #include "region_popup.h"
-+#include "data.h"
- 
- #include "region.hlp"
- 
-diff --git a/plot2/data_popup.c b/plot2/data_popup.c
-index 851b1d4..1c9026e 100644
---- a/plot2/data_popup.c
-+++ b/plot2/data_popup.c
-@@ -1,4 +1,5 @@
- #include "data_popup.h"
-+#include "rowcol_popup.h"
- 
- #include "data.hlp"
- 
-diff --git a/plot2/extract_popup.c b/plot2/extract_popup.c
-index 416aab0..a7fcbf3 100644
---- a/plot2/extract_popup.c
-+++ b/plot2/extract_popup.c
-@@ -1,4 +1,5 @@
- #include "extract_popup.h"
-+#include "script.h"
- 
- #include "extract.hlp"
- 
-diff --git a/plot2/levels_popup.c b/plot2/levels_popup.c
-index 197cf2c..e1ac22c 100644
---- a/plot2/levels_popup.c
-+++ b/plot2/levels_popup.c
-@@ -1,4 +1,5 @@
- #include "levels_popup.h"
-+#include "levels_func.h"
- 
- #include "levels.hlp"
- 
-diff --git a/plot2/plot2.c b/plot2/plot2.c
-index 9ca91c3..0c10d5a 100644
---- a/plot2/plot2.c
-+++ b/plot2/plot2.c
-@@ -1,4 +1,6 @@
- #include "plot2.h"
-+#include "object_popup.h"
-+#include "prop_popup.h"
- 
- #include "baseline_popup.h"
- #include "callback.h"
-diff --git a/plot2/rowcol_popup.c b/plot2/rowcol_popup.c
-index e9f4843..6c50426 100644
---- a/plot2/rowcol_popup.c
-+++ b/plot2/rowcol_popup.c
-@@ -1,4 +1,5 @@
- #include "rowcol_popup.h"
-+#include "ref_popup.h"
- 
- #include "rowcol.hlp"
- 
-diff --git a/plot2/script.c b/plot2/script.c
-index 2f55182..d7d886f 100644
---- a/plot2/script.c
-+++ b/plot2/script.c
-@@ -1,4 +1,5 @@
- #include "script.h"
-+#include "macros.h"
- 
- #include "param.h"
- #include "stack.h"
-diff --git a/plot2/slice_popup.c b/plot2/slice_popup.c
-index b601834..1b1e686 100644
---- a/plot2/slice_popup.c
-+++ b/plot2/slice_popup.c
-@@ -1,4 +1,5 @@
- #include "slice_popup.h"
-+#include "rowcol_func.h"
- 
- #include "baseline.h"
- #include "baseline_popup.h"
-diff --git a/process/files.c b/process/files.c
-index e09127e..d95d681 100644
---- a/process/files.c
-+++ b/process/files.c
-@@ -1,4 +1,5 @@
- #include "files.h"
-+#include "macros.h"
- 
- #include <sys/types.h>
- #include <sys/stat.h>
-diff --git a/project/project.c b/project/project.c
-index 92b70e3..a3e6d94 100644
---- a/project/project.c
-+++ b/project/project.c
-@@ -1,4 +1,5 @@
- #include "project.h"
-+#include "utility.h"
- 
- #include "block.h"
- #include "par.h"
diff --git a/sci-chemistry/azara/files/2.8-prll.patch b/sci-chemistry/azara/files/2.8-prll.patch
index 20cce4534e4f..4720bb659445 100644
--- a/sci-chemistry/azara/files/2.8-prll.patch
+++ b/sci-chemistry/azara/files/2.8-prll.patch
@@ -1,94 +1,130 @@
 diff --git a/DataRows/makefile b/DataRows/makefile
-index 587e710..3d49953 100644
+index 587e710..4e0a312 100644
 --- a/DataRows/makefile
 +++ b/DataRows/makefile
-@@ -39,7 +39,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) python_objects
-+	$(MAKE) -C $(GLOBAL_DIR) python_objects
- 
- py_data_rows.o: py_data_rows.c
- 	$(CC) -c $(CFLAGS) $(PYTHON_INCLUDE_DIR) $<
+@@ -28,7 +28,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-DataRows.so: locals globals
++DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS)
 diff --git a/azara/makefile b/azara/makefile
-index 3ba0cd9..4de1857 100644
+index 3ba0cd9..f7b4ce5 100644
 --- a/azara/makefile
 +++ b/azara/makefile
-@@ -24,7 +24,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) azara_objects
-+	$(MAKE) -C $(GLOBAL_DIR) azara_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -12,7 +12,7 @@ LOCAL_OBJS = \
+ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/help.o
+ 
+-azara: locals globals
++azara: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/combine/makefile b/combine/makefile
-index a855236..11891f6 100644
+index a855236..7a83d8f 100644
 --- a/combine/makefile
 +++ b/combine/makefile
-@@ -32,7 +32,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) combine_objects
-+	$(MAKE) -C $(GLOBAL_DIR) combine_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -20,7 +20,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-combine: locals globals
++combine: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/connect/makefile b/connect/makefile
-index d75e7da..4769266 100644
+index d75e7da..d238507 100644
 --- a/connect/makefile
 +++ b/connect/makefile
-@@ -35,7 +35,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) connect_objects
-+	$(MAKE) -C $(GLOBAL_DIR) connect_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -23,7 +23,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-connect: locals globals
++connect: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/contours/makefile b/contours/makefile
-index 5b832b8..895fd74 100644
+index 5b832b8..49175dd 100644
 --- a/contours/makefile
 +++ b/contours/makefile
-@@ -31,7 +31,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) contours_objects
-+	$(MAKE) -C $(GLOBAL_DIR) contours_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -19,7 +19,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-contours: locals globals
++contours: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/deflate/makefile b/deflate/makefile
-index 4c4e02e..0b2cdc4 100644
+index 4c4e02e..42d5c30 100644
 --- a/deflate/makefile
 +++ b/deflate/makefile
-@@ -30,7 +30,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) deflate_objects
-+	$(MAKE) -C $(GLOBAL_DIR) deflate_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-deflate: locals globals
++deflate: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/extract/makefile b/extract/makefile
-index 3212cb9..b786746 100644
+index 3212cb9..fed874b 100644
 --- a/extract/makefile
 +++ b/extract/makefile
-@@ -30,7 +30,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) extract_objects
-+	$(MAKE) -C $(GLOBAL_DIR) extract_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-extract: locals globals
++extract: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
+diff --git a/global/makefile b/global/makefile
+index 364fa41..5272a31 100644
+--- a/global/makefile
++++ b/global/makefile
+@@ -42,6 +42,31 @@ LINPACK_OBJS = \
+ AZARA_OBJS = \
+ 	help.o
+ 
++all: \
++	azara_objects \
++	decay_objects \
++	simulate_objects \
++	viewer_objects \
++	components_objects \
++	shuffle_objects \
++	connect_objects \
++	slides_objects \
++	peak_find_objects \
++	peak_fit_objects \
++	plot1_objects \
++	reflate_objects \
++	deflate_objects \
++	combine_objects \
++	unblock_objects \
++	extract_objects \
++	project_objects \
++	contours_objects \
++	plot2_nog_objects \
++	plot2_objects \
++	process_objects \
++	python_objects \
++	integrate_objects
++
+ azara_objects: $(AZARA_OBJS)
+ 
+ DECAY_OBJS = \
 diff --git a/help/makefile b/help/makefile
 index 9e99a7c..59a86a3 100644
 --- a/help/makefile
@@ -112,7 +148,7 @@ index 9e99a7c..59a86a3 100644
  	$(TXT2HTML) combine
  	$(TXT2HTML) connect
 diff --git a/makefile b/makefile
-index 9965b07..3cee572 100644
+index 9965b07..f4383af 100644
 --- a/makefile
 +++ b/makefile
 @@ -14,7 +14,7 @@ all: help nongui DataRows gui
@@ -124,7 +160,7 @@ index 9965b07..3cee572 100644
  	process_program \
  	plot2_nog_program \
  	peak_program \
-@@ -29,63 +29,63 @@ nongui: \
+@@ -29,63 +29,66 @@ nongui: \
  	connect_program \
  	azara_program
  
@@ -137,176 +173,215 @@ index 9965b07..3cee572 100644
 +DataRows: help \
  	DataRows
  
- process_program:
+-process_program:
 -	cd process; $(MAKE)
-+	$(MAKE) -C process
++global:
++	$(MAKE) -C global
  
- plot2_program:
+-plot2_program:
 -	cd plot2; $(MAKE) plot2
-+	$(MAKE) -C plot2
++process_program: global
++	$(MAKE) -C process
  
- plot2_nog_program:
+-plot2_nog_program:
 -	cd plot2; $(MAKE) plot2_nog
-+	$(MAKE) -C plot2 plot2_nog
++plot2_program: global
++	$(MAKE) -C plot2
  
- plot1_program:
+-plot1_program:
 -	cd plot1; $(MAKE)
-+	$(MAKE) -C plot1
++plot2_nog_program: global
++	$(MAKE) -C plot2 plot2_nog
  
- peak_program:
+-peak_program:
 -	cd peak; $(MAKE)
-+	$(MAKE) -C peak
++plot1_program: global
++	$(MAKE) -C plot1
  
- extract_program:
+-extract_program:
 -	cd extract; $(MAKE)
-+	$(MAKE) -C extract
++peak_program:  global process_program
++	$(MAKE) -C peak
  
- project_program:
+-project_program:
 -	cd project; $(MAKE)
-+	$(MAKE) -C project
++extract_program: global
++	$(MAKE) -C extract
  
- unblock_program:
+-unblock_program:
 -	cd unblock; $(MAKE)
-+	$(MAKE) -C unblock
++project_program: global
++	$(MAKE) -C project
  
- contours_program:
+-contours_program:
 -	cd contours; $(MAKE)
-+	$(MAKE) -C contours
++unblock_program: global
++	$(MAKE) -C unblock
  
- combine_program:
+-combine_program:
 -	cd combine; $(MAKE)
-+	$(MAKE) -C combine
++contours_program: global
++	$(MAKE) -C contours
  
- deflate_program:
+-deflate_program:
 -	cd deflate; $(MAKE)
-+	$(MAKE) -C deflate
++combine_program: global
++	$(MAKE) -C combine
  
- reflate_program:
+-reflate_program:
 -	cd reflate; $(MAKE)
-+	$(MAKE) -C reflate
++deflate_program: global
++	$(MAKE) -C deflate
  
- utility_program:
+-utility_program:
 -	cd utility; $(MAKE)
-+	$(MAKE) -C utility
++reflate_program: global
++	$(MAKE) -C reflate
  
- connect_program:
+-connect_program:
 -	cd connect; $(MAKE)
-+	$(MAKE) -C connect
++utility_program: global
++	$(MAKE) -C utility
  
- help_program:
- 	cd help; $(MAKE)
+-help_program:
+-	cd help; $(MAKE)
++connect_program: global
++	$(MAKE) -C connect
  
- azara_program:
+-azara_program:
 -	cd azara; $(MAKE)
-+	$(MAKE) -C azara
++help_program: global
++	$(MAKE) -C help
  
- DataRows:
+-DataRows:
 -	cd DataRows; $(MAKE)
++azara_program: global
++	$(MAKE) -C azara
++
++DataRows: global
 +	$(MAKE) -C DataRows
  
  clean: \
  	global_clean \
+@@ -227,3 +230,5 @@ azara_realclean:
+ DataRows_realclean:
+ 	cd DataRows; $(MAKE) realclean
+ 
++
++.PHONY: global process_program
 diff --git a/peak/makefile b/peak/makefile
-index f3c13b7..77b3bac 100644
+index f3c13b7..4211221 100644
 --- a/peak/makefile
 +++ b/peak/makefile
-@@ -116,7 +116,7 @@ local_find:
- 	$(MAKE) local_find_objects
- 
- global_find:
--	cd $(GLOBAL_DIR); $(MAKE) peak_find_objects
-+	$(MAKE) -C $(GLOBAL_DIR) peak_find_objects
- 
- local_fit_objects: $(LOCAL_FIT_OBJS)
- 
-@@ -124,10 +124,10 @@ local_fit:
- 	$(MAKE) local_fit_objects
- 
- global_fit:
--	cd $(GLOBAL_DIR); $(MAKE) peak_fit_objects
-+	$(MAKE) -C $(GLOBAL_DIR) peak_fit_objects
- 
- commands:
--	cd $(COMMAND_DIR); $(MAKE) peak
-+	$(MAKE) -C $(COMMAND_DIR) peak
- 
- 
- .c.o:;	$(CC) -c $(CFLAGS) $<
+@@ -97,13 +97,13 @@ COMMAND_OBJS = \
+ 
+ all: peak_find peak_fit
+ 
+-peak_find: local_find global_find
++peak_find: $(LOCAL_FIND_OBJS) $(GLOBAL_FIND_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_FIND_OBJS) \
+ 		$(GLOBAL_FIND_OBJS) \
+ 		$(LIB) $(MATH_LIB)
+ 
+-peak_fit: local_fit global_fit commands
++peak_fit: $(LOCAL_FIT_OBJS) $(GLOBAL_FIT_OBJS) $(COMMAND_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_FIT_OBJS) \
+ 		$(GLOBAL_FIT_OBJS) \
 diff --git a/plot1/makefile b/plot1/makefile
-index d1dce2d..73ed1ac 100644
+index d1dce2d..e729443 100644
 --- a/plot1/makefile
 +++ b/plot1/makefile
-@@ -108,7 +108,7 @@ locals:
- 	$(MAKE) local_objects
- 
+@@ -95,7 +95,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/utility.o \
+ 	$(GLOBAL_DIR)/window.o
+ 
+-plot1: locals globals
++plot1: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
+@@ -110,7 +110,7 @@ locals:
  globals:
--	cd $(GLOBAL_DIR); $(MAKE) plot1_objects
-+	$(MAKE) -C $(GLOBAL_DIR) plot1_objects
+ 	cd $(GLOBAL_DIR); $(MAKE) plot1_objects
  
- .c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $<
+-.c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $<
++.c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) -I../plot2 $<
  
+ clean:
+ 	rm -f *.o
 diff --git a/plot2/makefile b/plot2/makefile
-index a6b7b4a..f1cd86c 100644
+index a6b7b4a..98e286e 100644
 --- a/plot2/makefile
 +++ b/plot2/makefile
-@@ -149,7 +149,7 @@ local_plot2:
- 	$(MAKE) local_plot2_objects
- 
- global_plot2:
--	cd $(GLOBAL_DIR); $(MAKE) plot2_objects
-+	$(MAKE) -C $(GLOBAL_DIR) plot2_objects
- 
- local_plot2_nog_objects: $(LOCAL_PLOT2_NOG_OBJS)
- 
+@@ -129,7 +129,7 @@ GLOBAL_PLOT2_NOG_OBJS = \
+ 
+ all: plot2 plot2_nog
+ 
+-plot2: local_plot2 global_plot2
++plot2: $(LOCAL_PLOT2_OBJS) $(GLOBAL_PLOT2_OBJS) 
+ 	$(CC) -o $@ $(CFLAGS) $(LFLAGS) \
+ 		$(LOCAL_PLOT2_OBJS) \
+ 		$(GLOBAL_PLOT2_OBJS) \
+@@ -137,7 +137,7 @@ plot2: local_plot2 global_plot2
+ 		$(LIB) $(MATH_LIB) \
+ 		$(MOTIF_LIB) $(X11_LIB) $(XPM_LIB)
+ 
+-plot2_nog: local_plot2_nog global_plot2_nog
++plot2_nog: $(LOCAL_PLOT2_NOG_OBJS) $(GLOBAL_PLOT2_NOG_OBJS)
+ 	$(CC) -o $@ $(CFLAGS) $(LFLAGS) \
+ 		$(LOCAL_PLOT2_NOG_OBJS) \
+ 		$(GLOBAL_PLOT2_NOG_OBJS) \
 diff --git a/process/makefile b/process/makefile
-index 22ceeed..33e811b 100644
+index 22ceeed..72d587b 100644
 --- a/process/makefile
 +++ b/process/makefile
-@@ -86,7 +86,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) process_objects
-+	$(MAKE) -C $(GLOBAL_DIR) process_objects
- 
- peak:
- 	$(MAKE) peak_objects
+@@ -72,7 +72,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/utility.o \
+ 	$(LINPACK_OBJS)
+ 
+-process: locals globals
++process: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/project/makefile b/project/makefile
-index 78143fc..6d7745c 100644
+index 78143fc..ed0f296 100644
 --- a/project/makefile
 +++ b/project/makefile
-@@ -30,7 +30,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) project_objects
-+	$(MAKE) -C $(GLOBAL_DIR) project_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-project: locals globals
++project: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/reflate/makefile b/reflate/makefile
-index 079a3fc..cdf8d8d 100644
+index 079a3fc..01ec311 100644
 --- a/reflate/makefile
 +++ b/reflate/makefile
-@@ -30,7 +30,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) reflate_objects
-+	$(MAKE) -C $(GLOBAL_DIR) reflate_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-reflate: locals globals
++reflate: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
 diff --git a/unblock/makefile b/unblock/makefile
-index 510dc9e..e006685 100644
+index 510dc9e..d9a0f2b 100644
 --- a/unblock/makefile
 +++ b/unblock/makefile
-@@ -30,7 +30,7 @@ locals:
- 	$(MAKE) local_objects
- 
- globals:
--	cd $(GLOBAL_DIR); $(MAKE) unblock_objects
-+	$(MAKE) -C $(GLOBAL_DIR) unblock_objects
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
+@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
+ 	$(GLOBAL_DIR)/ref.o \
+ 	$(GLOBAL_DIR)/utility.o
+ 
+-unblock: locals globals
++unblock: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) -o $@ $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+ 		$(GLOBAL_OBJS) \
diff --git a/sci-chemistry/azara/files/2.8-prllng.patch b/sci-chemistry/azara/files/2.8-prllng.patch
deleted file mode 100644
index 1912d00da4c8..000000000000
--- a/sci-chemistry/azara/files/2.8-prllng.patch
+++ /dev/null
@@ -1,361 +0,0 @@
-diff --git a/DataRows/makefile b/DataRows/makefile
-index 587e710..4e0a312 100644
---- a/DataRows/makefile
-+++ b/DataRows/makefile
-@@ -28,7 +28,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--DataRows.so: locals globals
-+DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS)
-diff --git a/azara/makefile b/azara/makefile
-index 3ba0cd9..f7b4ce5 100644
---- a/azara/makefile
-+++ b/azara/makefile
-@@ -12,7 +12,7 @@ LOCAL_OBJS = \
- GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/help.o
- 
--azara: locals globals
-+azara: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/combine/makefile b/combine/makefile
-index a855236..7a83d8f 100644
---- a/combine/makefile
-+++ b/combine/makefile
-@@ -20,7 +20,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--combine: locals globals
-+combine: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/connect/makefile b/connect/makefile
-index d75e7da..d238507 100644
---- a/connect/makefile
-+++ b/connect/makefile
-@@ -23,7 +23,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--connect: locals globals
-+connect: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/contours/makefile b/contours/makefile
-index 5b832b8..49175dd 100644
---- a/contours/makefile
-+++ b/contours/makefile
-@@ -19,7 +19,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--contours: locals globals
-+contours: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/deflate/makefile b/deflate/makefile
-index 4c4e02e..42d5c30 100644
---- a/deflate/makefile
-+++ b/deflate/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--deflate: locals globals
-+deflate: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/extract/makefile b/extract/makefile
-index 3212cb9..fed874b 100644
---- a/extract/makefile
-+++ b/extract/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--extract: locals globals
-+extract: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/global/makefile b/global/makefile
-index 364fa41..5272a31 100644
---- a/global/makefile
-+++ b/global/makefile
-@@ -42,6 +42,31 @@ LINPACK_OBJS = \
- AZARA_OBJS = \
- 	help.o
- 
-+all: \
-+	azara_objects \
-+	decay_objects \
-+	simulate_objects \
-+	viewer_objects \
-+	components_objects \
-+	shuffle_objects \
-+	connect_objects \
-+	slides_objects \
-+	peak_find_objects \
-+	peak_fit_objects \
-+	plot1_objects \
-+	reflate_objects \
-+	deflate_objects \
-+	combine_objects \
-+	unblock_objects \
-+	extract_objects \
-+	project_objects \
-+	contours_objects \
-+	plot2_nog_objects \
-+	plot2_objects \
-+	process_objects \
-+	python_objects \
-+	integrate_objects
-+
- azara_objects: $(AZARA_OBJS)
- 
- DECAY_OBJS = \
-diff --git a/help/makefile b/help/makefile
-index 9e99a7c..59a86a3 100644
---- a/help/makefile
-+++ b/help/makefile
-@@ -39,7 +39,7 @@ globals:
- 
- .c.o:;  $(CC) -c $(CFLAGS) $<
- 
--hlp:
-+hlp: txt2hlp
- 	$(TXT2HLP) azara
- 	$(TXT2HLP) combine
- 	$(TXT2HLP) connect
-@@ -78,7 +78,7 @@ hlp:
- 	$(TXT2HLP) plot1/text
- 	$(TXT2HLP) DataRows
- 
--html:
-+html: txt2html
- 	$(TXT2HTML) azara
- 	$(TXT2HTML) combine
- 	$(TXT2HTML) connect
-diff --git a/makefile b/makefile
-index 9965b07..6f3bdd0 100644
---- a/makefile
-+++ b/makefile
-@@ -14,7 +14,7 @@ all: help nongui DataRows gui
- help: \
- 	help_program
- 
--nongui: \
-+nongui: help \
- 	process_program \
- 	plot2_nog_program \
- 	peak_program \
-@@ -29,63 +29,63 @@ nongui: \
- 	connect_program \
- 	azara_program
- 
--gui: \
-+gui: help \
- 	plot2_program \
- 	plot1_program
- 
--DataRows: \
-+DataRows: help \
- 	DataRows
- 
- process_program:
--	cd process; $(MAKE)
-+	$(MAKE) -C process
- 
- plot2_program:
--	cd plot2; $(MAKE) plot2
-+	$(MAKE) -C plot2
- 
- plot2_nog_program:
--	cd plot2; $(MAKE) plot2_nog
-+	$(MAKE) -C plot2 plot2_nog
- 
- plot1_program:
--	cd plot1; $(MAKE)
-+	$(MAKE) -C plot1
- 
- peak_program:
--	cd peak; $(MAKE)
-+	$(MAKE) -C peak
- 
- extract_program:
--	cd extract; $(MAKE)
-+	$(MAKE) -C extract
- 
- project_program:
--	cd project; $(MAKE)
-+	$(MAKE) -C project
- 
- unblock_program:
--	cd unblock; $(MAKE)
-+	$(MAKE) -C unblock
- 
- contours_program:
--	cd contours; $(MAKE)
-+	$(MAKE) -C contours
- 
- combine_program:
--	cd combine; $(MAKE)
-+	$(MAKE) -C combine
- 
- deflate_program:
--	cd deflate; $(MAKE)
-+	$(MAKE) -C deflate
- 
- reflate_program:
--	cd reflate; $(MAKE)
-+	$(MAKE) -C reflate
- 
- utility_program:
--	cd utility; $(MAKE)
-+	$(MAKE) -C utility
- 
- connect_program:
--	cd connect; $(MAKE)
-+	$(MAKE) -C connect
- 
- help_program:
--	cd help; $(MAKE)
-+	$(MAKE) -C help
- 
- azara_program:
--	cd azara; $(MAKE)
-+	$(MAKE) -C azara
- 
- DataRows:
--	cd DataRows; $(MAKE)
-+	$(MAKE) -C DataRows
- 
- clean: \
- 	global_clean \
-diff --git a/peak/makefile b/peak/makefile
-index f3c13b7..4211221 100644
---- a/peak/makefile
-+++ b/peak/makefile
-@@ -97,13 +97,13 @@ COMMAND_OBJS = \
- 
- all: peak_find peak_fit
- 
--peak_find: local_find global_find
-+peak_find: $(LOCAL_FIND_OBJS) $(GLOBAL_FIND_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_FIND_OBJS) \
- 		$(GLOBAL_FIND_OBJS) \
- 		$(LIB) $(MATH_LIB)
- 
--peak_fit: local_fit global_fit commands
-+peak_fit: $(LOCAL_FIT_OBJS) $(GLOBAL_FIT_OBJS) $(COMMAND_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_FIT_OBJS) \
- 		$(GLOBAL_FIT_OBJS) \
-diff --git a/plot1/makefile b/plot1/makefile
-index d1dce2d..e729443 100644
---- a/plot1/makefile
-+++ b/plot1/makefile
-@@ -95,7 +95,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/utility.o \
- 	$(GLOBAL_DIR)/window.o
- 
--plot1: locals globals
-+plot1: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-@@ -110,7 +110,7 @@ locals:
- globals:
- 	cd $(GLOBAL_DIR); $(MAKE) plot1_objects
- 
--.c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $<
-+.c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) -I../plot2 $<
- 
- clean:
- 	rm -f *.o
-diff --git a/plot2/makefile b/plot2/makefile
-index a6b7b4a..98e286e 100644
---- a/plot2/makefile
-+++ b/plot2/makefile
-@@ -129,7 +129,7 @@ GLOBAL_PLOT2_NOG_OBJS = \
- 
- all: plot2 plot2_nog
- 
--plot2: local_plot2 global_plot2
-+plot2: $(LOCAL_PLOT2_OBJS) $(GLOBAL_PLOT2_OBJS) 
- 	$(CC) -o $@ $(CFLAGS) $(LFLAGS) \
- 		$(LOCAL_PLOT2_OBJS) \
- 		$(GLOBAL_PLOT2_OBJS) \
-@@ -137,7 +137,7 @@ plot2: local_plot2 global_plot2
- 		$(LIB) $(MATH_LIB) \
- 		$(MOTIF_LIB) $(X11_LIB) $(XPM_LIB)
- 
--plot2_nog: local_plot2_nog global_plot2_nog
-+plot2_nog: $(LOCAL_PLOT2_NOG_OBJS) $(GLOBAL_PLOT2_NOG_OBJS)
- 	$(CC) -o $@ $(CFLAGS) $(LFLAGS) \
- 		$(LOCAL_PLOT2_NOG_OBJS) \
- 		$(GLOBAL_PLOT2_NOG_OBJS) \
-diff --git a/process/makefile b/process/makefile
-index 22ceeed..72d587b 100644
---- a/process/makefile
-+++ b/process/makefile
-@@ -72,7 +72,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/utility.o \
- 	$(LINPACK_OBJS)
- 
--process: locals globals
-+process: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/project/makefile b/project/makefile
-index 78143fc..ed0f296 100644
---- a/project/makefile
-+++ b/project/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--project: locals globals
-+project: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/reflate/makefile b/reflate/makefile
-index 079a3fc..01ec311 100644
---- a/reflate/makefile
-+++ b/reflate/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--reflate: locals globals
-+reflate: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
-diff --git a/unblock/makefile b/unblock/makefile
-index 510dc9e..d9a0f2b 100644
---- a/unblock/makefile
-+++ b/unblock/makefile
-@@ -18,7 +18,7 @@ GLOBAL_OBJS = \
- 	$(GLOBAL_DIR)/ref.o \
- 	$(GLOBAL_DIR)/utility.o
- 
--unblock: locals globals
-+unblock: $(LOCAL_OBJS) $(GLOBAL_OBJS)
- 	$(CC) -o $@ $(LFLAGS) \
- 		$(LOCAL_OBJS) \
- 		$(GLOBAL_OBJS) \
diff --git a/sci-chemistry/azara/files/2.8-python.patch b/sci-chemistry/azara/files/2.8-python.patch
new file mode 100644
index 000000000000..9834c77a77dc
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-python.patch
@@ -0,0 +1,44 @@
+diff --git a/DataRows/makefile b/DataRows/makefile
+index 4e0a312..ce261ab 100644
+--- a/DataRows/makefile
++++ b/DataRows/makefile
+@@ -22,16 +22,17 @@ LOCAL_OBJS = \
+ 	data_rows.o
+ 
+ GLOBAL_OBJS = \
+-	$(GLOBAL_DIR)/block_io.o \
+-	$(GLOBAL_DIR)/par.o \
+-	$(GLOBAL_DIR)/parse.o \
+-	$(GLOBAL_DIR)/ref.o \
+-	$(GLOBAL_DIR)/utility.o
++	block_io.o \
++	par.o \
++	parse.o \
++	ref.o \
++	utility.o
+ 
+ DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS)
+ 	$(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \
+ 		$(LOCAL_OBJS) \
+-		$(GLOBAL_OBJS)
++		$(GLOBAL_OBJS) \
++		$(PYTHON_LIB)
+ 
+ local_objects: $(LOCAL_OBJS)
+ 
+@@ -42,9 +43,13 @@ globals:
+ 	cd $(GLOBAL_DIR); $(MAKE) python_objects
+ 
+ py_data_rows.o: py_data_rows.c
+-	$(CC) -c $(CFLAGS) $(PYTHON_INCLUDE_DIR) $<
++	$(CC) -c $(CFLAGS) $(PIC) $(PYTHON_INCLUDE_DIR) $<
+ 
+-.c.o:;	$(CC) -c $(CFLAGS) $<
++data_rows.o: data_rows.c
++	$(CC) -c $(CFLAGS) $(PIC) $<
++
++%.o: $(GLOBAL_DIR)/%.c
++	$(CC) -c $(CFLAGS) $(PIC) $<
+ 
+ clean:
+ 	rm -f *.o