Version bump and prll make fixes

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

8 files changed, 606 insertions, 57 deletions

diff --git a/sci-chemistry/azara/ChangeLog b/sci-chemistry/azara/ChangeLog
index 57b62adc10bd..58f8c903574e 100644
--- a/sci-chemistry/azara/ChangeLog
+++ b/sci-chemistry/azara/ChangeLog
@@ -1,6 +1,14 @@
 # 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 1.3 2010/04/11 18:24:13 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/ChangeLog,v 1.4 2010/08/04 14:52:26 jlec Exp $
+
+*azara-2.8 (04 Aug 2010)
+
+  04 Aug 2010; Justin Lecher <jlec@gentoo.org> +files/2.7-impl-dec.patch,
+  azara-2.7.ebuild, +files/2.7-prll.patch, +azara-2.8.ebuild,
+  +files/2.8-impl-dec.patch, +files/2.8-prll.patch,
+  -files/help-makefile.patch:
+  Version bump and prll make fixes
 
   11 Apr 2010; Justin Lecher <jlec@gentoo.org> azara-2.7.ebuild:
   Do not try to install not builded bins, fixed 314491
diff --git a/sci-chemistry/azara/Manifest b/sci-chemistry/azara/Manifest
index fd666284cec7..9d28c639514c 100644
--- a/sci-chemistry/azara/Manifest
+++ b/sci-chemistry/azara/Manifest
@@ -1,15 +1,20 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-AUX help-makefile.patch 4278 RMD160 1293ad23185d5d6ca6f3aa8e0429cb44635a9b91 SHA1 4220a44556b37d0b644bc829768fc42f3b1cb07d SHA256 9847738d161197912a12543b85988cbb6d6e1345181cfabb6e502af4c5d7735e
+AUX 2.7-impl-dec.patch 492 RMD160 6099d856511ae3bab803359647c774a51c2735ae SHA1 58d5179531d366c9ac6cac7ae297f7784df16fb4 SHA256 51d898d05ecf68598ea86f268a89cc9952fac1cb4f68791f6100caca6a84db05
+AUX 2.7-prll.patch 5846 RMD160 ec40e751b96a4b08b89dfe30db52cae0428254f5 SHA1 0756843126bef8287a71c698ffb54de286ca0696 SHA256 65e180c0c58ccccb05cfa85ea81499e1edaeb8cc984964fd3517b2eed6de1b87
+AUX 2.8-impl-dec.patch 254 RMD160 900412c2b1799d2a298b71bf0abfa42831864353 SHA1 3f019e2ffb558c5a781c0d83f4344b8311b23ce0 SHA256 9b05a52d1bd7b5d209aaed7116bdc01695d4c28e93ada849589203bebc446f5d
+AUX 2.8-prll.patch 6613 RMD160 0fa9c496000c695ed738468ed605f096f002429a SHA1 18412044c7fd6c799f3a08df8fd0cdb8616a4f30 SHA256 9961bf95c7434e41f2030c06cb9b549cbea21c8496ff25856bec20812756ab8f
 DIST azara-2.7-src.tar.gz 565272 RMD160 2426102dbb87984f88ec1266b72d2e307484af0c SHA1 53caa85953f700cdc4ec9ef26d2bb7d9448b77b0 SHA256 d639682d813278d2955b911c16ac0f9121cb3cf3fde6c5da4cf7bb79e478486d
-EBUILD azara-2.7.ebuild 1899 RMD160 d69a050df3e3b7f5792451fd6beeadc0156f8b4e SHA1 5b2e83ff24e6d2faf2b0e5e68ab58d6c2475d586 SHA256 64f86a42fd07f48e7fbf0ce5190deaba237a5124bd942731691efc2b69d7749d
-MISC ChangeLog 590 RMD160 b0a3379306c5414695e68b7fe8b4a459ee523a93 SHA1 b2e3d50568a044134d95da1f16f0cb8814f3d1b6 SHA256 91ca026b894c84f95719cfbb864dcb4118584c22d75fc21e90a7acec5494a5f3
+DIST azara-2.8-src.tgz 638120 RMD160 4abf47088694e2f4f2822ec2666cac6ced47f1e2 SHA1 f1ef1d06b836b68c1d8d47f2e069c161f22355d9 SHA256 1f9b86d368ca3b4818c88490c40b2055c7a6d1732e746e4c117e045a73269a98
+EBUILD azara-2.7.ebuild 2000 RMD160 8b99352cb935699e3f5f895e1685dae686b5b6f9 SHA1 59c62fef758b183a63a62253324d72071014189c SHA256 bc9e79fa52c3416f0cbbeb2e9d98d2d835dce9effda97b4331171a3a570db541
+EBUILD azara-2.8.ebuild 1811 RMD160 96387f16afe31a4c15a0bd838c962613fb4ac0b5 SHA1 5025610787c950616ad0d5bf1556ca846e77d689 SHA256 ca8e4ba9dd0828a2e7fabae4d501605fdd9fb4c164cdaed1b5172a3b3d897058
+MISC ChangeLog 870 RMD160 0c18dc261f634941b8489a2c119abbbd1ac16199 SHA1 7f4e0a172d273af34db8c9e896fea6eb1aa7cd55 SHA256 0bf25070406d8696d32125c731b571191b510a25f6ed3e84c1c51103a9027312
 MISC metadata.xml 266 RMD160 c4ea712c395727d72dcc61aad6b907800ce85df1 SHA1 ce0c21096152fff128b3f40131f8807e60f31163 SHA256 6e5273c55b0d4eab8e747f62c5a527b4e5021594f134546c8355d10d3f99c8ad
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkvCE9MACgkQgAnW8HDreRZoaQCfYMSqSNkP3BHSp28bLD109jf4
-CBcAoKuJPwDR6wI55Jrif1llyvoOWbzQ
-=OKbw
+iEYEARECAAYFAkxZfq8ACgkQgAnW8HDreRb86wCfXjld0NjdDN9f3FsjHQEDkjfS
+kJYAnRYCoyeR6SPoSHIzqvwoF0otmOuN
+=UVlX
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/azara/azara-2.7.ebuild b/sci-chemistry/azara/azara-2.7.ebuild
index ce266f94a958..ebb0b2b0415c 100644
--- a/sci-chemistry/azara/azara-2.7.ebuild
+++ b/sci-chemistry/azara/azara-2.7.ebuild
@@ -1,6 +1,6 @@
 # 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.ebuild,v 1.3 2010/04/11 18:24:13 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/azara/azara-2.7.ebuild,v 1.4 2010/08/04 14:52:26 jlec Exp $
 
 EAPI="3"
 
@@ -23,19 +23,23 @@ DEPEND="${RDEPEND}"
 src_prepare() {
 	echo "" > ENVIRONMENT
 
-	epatch "${FILESDIR}"/help-makefile.patch
+#	epatch "${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 -j1 CC=$(tc-getCC) \
+	emake \
+		CC=$(tc-getCC) \
 		CFLAGS="${CFLAGS}" \
 		LFLAGS="${LDFLAGS}" \
 		MATH_LIB="-lm" \
@@ -64,7 +68,7 @@ src_install() {
 		dobin "${bin}" || die "failed to install ${bin}"
 	done
 
-	mv "${D}"/usr/bin/{,azara-}extract || die "failed to fix extract collision"
+	mv "${ED}"/usr/bin/{,azara-}extract || die "failed to fix extract collision"
 
 	dodoc CHANGES* README* || die
 	dohtml -r html/* || die
diff --git a/sci-chemistry/azara/azara-2.8.ebuild b/sci-chemistry/azara/azara-2.8.ebuild
new file mode 100644
index 000000000000..a9c511532db7
--- /dev/null
+++ b/sci-chemistry/azara/azara-2.8.ebuild
@@ -0,0 +1,79 @@
+# 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.ebuild,v 1.1 2010/08/04 14:52:26 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 ${mymake} || die
+}
+
+src_install() {
+	rm bin/pythonAzara || die
+	if ! use X; then
+		rm bin/plot* || die
+	fi
+	for bin in bin/*; do
+		dobin "${bin}" || die "failed to install ${bin}"
+	done
+
+	mv "${ED}"/usr/bin/{,azara-}extract || die "failed to fix extract collision"
+
+	dodoc CHANGES* README* || die
+	dohtml -r html/* || die
+}
+
+pkg_postinst() {
+	einfo "Due to collision we moved the extract binary to azara-extract"
+}
diff --git a/sci-chemistry/azara/files/2.7-impl-dec.patch b/sci-chemistry/azara/files/2.7-impl-dec.patch
new file mode 100644
index 000000000000..b491ec7691ec
--- /dev/null
+++ b/sci-chemistry/azara/files/2.7-impl-dec.patch
@@ -0,0 +1,24 @@
+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/help-makefile.patch b/sci-chemistry/azara/files/2.7-prll.patch
index 5a42034734da..ced64d1760e1 100644
--- a/sci-chemistry/azara/files/help-makefile.patch
+++ b/sci-chemistry/azara/files/2.7-prll.patch
@@ -1,9 +1,12 @@
---- help/makefile	2002-11-01 13:27:27.000000000 +0100
-+++ help/makefile.new	2008-12-24 14:45:56.141225333 +0100
-@@ -37,102 +37,102 @@
+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:
+-hlp:
 -	txt2hlp azara
 -	txt2hlp combine
 -	txt2hlp components
@@ -43,47 +46,8 @@
 -	txt2hlp plot1/region
 -	txt2hlp plot1/slider
 -	txt2hlp plot1/text
-+	./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:
+-
+-html:
 -	txt2html azara
 -	txt2html combine
 -	txt2html components
@@ -134,6 +98,48 @@
 -	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
@@ -194,3 +200,102 @@
 -	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-impl-dec.patch b/sci-chemistry/azara/files/2.8-impl-dec.patch
new file mode 100644
index 000000000000..644656a48e4a
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-impl-dec.patch
@@ -0,0 +1,12 @@
+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/sci-chemistry/azara/files/2.8-prll.patch b/sci-chemistry/azara/files/2.8-prll.patch
new file mode 100644
index 000000000000..20cce4534e4f
--- /dev/null
+++ b/sci-chemistry/azara/files/2.8-prll.patch
@@ -0,0 +1,312 @@
+diff --git a/DataRows/makefile b/DataRows/makefile
+index 587e710..3d49953 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) $<
+diff --git a/azara/makefile b/azara/makefile
+index 3ba0cd9..4de1857 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) $<
+ 
+diff --git a/combine/makefile b/combine/makefile
+index a855236..11891f6 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) $<
+ 
+diff --git a/connect/makefile b/connect/makefile
+index d75e7da..4769266 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) $<
+ 
+diff --git a/contours/makefile b/contours/makefile
+index 5b832b8..895fd74 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) $<
+ 
+diff --git a/deflate/makefile b/deflate/makefile
+index 4c4e02e..0b2cdc4 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) $<
+ 
+diff --git a/extract/makefile b/extract/makefile
+index 3212cb9..b786746 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) $<
+ 
+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..3cee572 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)
+ 
+ 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..77b3bac 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) $<
+diff --git a/plot1/makefile b/plot1/makefile
+index d1dce2d..73ed1ac 100644
+--- a/plot1/makefile
++++ b/plot1/makefile
+@@ -108,7 +108,7 @@ locals:
+ 	$(MAKE) local_objects
+ 
+ globals:
+-	cd $(GLOBAL_DIR); $(MAKE) plot1_objects
++	$(MAKE) -C $(GLOBAL_DIR) plot1_objects
+ 
+ .c.o:;	$(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $<
+ 
+diff --git a/plot2/makefile b/plot2/makefile
+index a6b7b4a..f1cd86c 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)
+ 
+diff --git a/process/makefile b/process/makefile
+index 22ceeed..33e811b 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
+diff --git a/project/makefile b/project/makefile
+index 78143fc..6d7745c 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) $<
+ 
+diff --git a/reflate/makefile b/reflate/makefile
+index 079a3fc..cdf8d8d 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) $<
+ 
+diff --git a/unblock/makefile b/unblock/makefile
+index 510dc9e..e006685 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) $<
+