Respecting *FLAGS, #335447; added real 64bit support, #351502

Package-Manager: portage-2.2.0_alpha15/cvs/Linux x86_64

5 files changed, 115 insertions, 14 deletions

diff --git a/sci-biology/mummer/ChangeLog b/sci-biology/mummer/ChangeLog
index b1f172be9428..de9899e90447 100644
--- a/sci-biology/mummer/ChangeLog
+++ b/sci-biology/mummer/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/mummer
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/ChangeLog,v 1.11 2009/10/29 02:21:12 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/ChangeLog,v 1.12 2011/01/13 09:14:52 jlec Exp $
+
+*mummer-3.22-r1 (13 Jan 2011)
+
+  13 Jan 2011; Justin Lecher <jlec@gentoo.org> +files/3.22-ldflags.patch,
+  +files/3.22-prll.patch, -mummer-3.22.ebuild, +mummer-3.22-r1.ebuild:
+  Respecting *FLAGS, #335447; added real 64bit support, #351502
 
   28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> mummer-3.22.ebuild:
   Set EAPI
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
index 166d330bcf2e..3023d5595653 100644
--- a/sci-biology/mummer/Manifest
+++ b/sci-biology/mummer/Manifest
@@ -1,9 +1,21 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 3.22-ldflags.patch 590 RMD160 d1d38a90f2cd12096b5325d18a0f1c36fcb1a8f8 SHA1 74767e627092fc185910c700dd596e96962f2628 SHA256 b30dfc0af0cf296b3fe11413cf4f9ac9d54ac7ae88dd42f8dda39c537fc76f21
+AUX 3.22-prll.patch 1192 RMD160 e9c05ad1de874f5a3ea175eac0864c34ef24ec2f SHA1 c6636577d0a98c8d4cb6325044c8cd06dc6885f0 SHA256 aca40e446ceb0d1f774e55b23ff09a8f4de982b80142983b4ea3915e9258f9be
 AUX mummer-3.20-gcc43.patch 258 RMD160 4d04d0d51ac3a0e5281474acc6ede7f32e332bc1 SHA1 6a1d7928652fc118b11435265d99827836d36d83 SHA256 8496c80683bd938b56bf8308768f56c034a18fd7dbfc30df1a68119e53155134
 DIST MUMmer3.20.tar.gz 3155446 RMD160 7e5fefef359c6a6ee49f2ebf14dc18caa19f48fb SHA1 68d6742de93d8524236ccf538f32ba8bb4edf7cc SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260
 DIST MUMmer3.21.tar.gz 3155965 RMD160 3a112ee3bc92c1585d42f4df72751a50548002d1 SHA1 228a5c283bef90d97d90d2dee12dd892a9f54c42 SHA256 7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8
 DIST MUMmer3.22.tar.gz 3156338 RMD160 f3c20f8458318dcf3251fb68bfd54c9513bf09ae SHA1 c763649fa12b3bdf4598bde4f292f9460bf2d47c SHA256 429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da
 EBUILD mummer-3.20.ebuild 1831 RMD160 8c82cd10d8e5041f0bbd34d2660a2d02e1a69f19 SHA1 d73f49319cff98368413584e4704206bdde2cc50 SHA256 d30b9d867a5a61404771777ec96b600612f861150339382a1b2cadd46fb22832
 EBUILD mummer-3.21.ebuild 1599 RMD160 43fe1b77a89931117d25d890f16cd8bda1aad0cd SHA1 4d9dea25c79a6dfc99f95f7cfcd881ada85b7700 SHA256 31f9e38c96a541caf12165217679097c8c119c1be97dcb1aa98e4deaf5232036
-EBUILD mummer-3.22.ebuild 1595 RMD160 0549eac539281b934282384b31420560718db196 SHA1 15485dee53df82413c411947ca6231f2ffac0614 SHA256 dde9dce02cd4e014e9c91f637b25be8c5a82ed20037c4fa10378b9924a93a201
-MISC ChangeLog 1616 RMD160 fec496875fddec5212d412725446629202d09939 SHA1 0d45afe0488fe58c29a1e3a45c13cb34c191262c SHA256 6bf4e6dfd3e6f99b28e96c7e8b8f578e3b287a74c5f7e6324636d799b71560fd
+EBUILD mummer-3.22-r1.ebuild 1687 RMD160 f92cfb83200d1bba431b7734cc6dcffb7d587bd6 SHA1 90724cddb819685b2c4b6f64d2c638c9a45f32c0 SHA256 4e555285168093c1861c3e0b9d8803d3766367bf4e6609903b74bb90415de0bc
+MISC ChangeLog 1855 RMD160 8d9cd685c9c6f8611d33ce4a8e2729aea38c237e SHA1 00495485d121cfcba0f1f3e2f77dc6b14b3753af SHA256 1e0f8e18bd93e2e4a3099bbf9d6f3479128597c0427ad0e71a8f3c4012fff2d8
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+
+iEYEARECAAYFAk0uwoYACgkQgAnW8HDreRZNrQCgiv2bWSztKVjXJ0/BGm2N4q/z
+1AoAoJDwNSyFaxnb4DEIPhyGldlZhjeC
+=qaJ3
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/mummer/files/3.22-ldflags.patch b/sci-biology/mummer/files/3.22-ldflags.patch
new file mode 100644
index 000000000000..d3c4a60a1adb
--- /dev/null
+++ b/sci-biology/mummer/files/3.22-ldflags.patch
@@ -0,0 +1,16 @@
+diff --git a/src/tigr/Makefile b/src/tigr/Makefile
+index cf6b9ca..5b28d1e 100644
+--- a/src/tigr/Makefile
++++ b/src/tigr/Makefile
+@@ -9,9 +9,9 @@ AUX_BIN_DIR := $(CURDIR)
+ endif
+ 
+ OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
+-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
++BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
+            chmod 755 $(BIN_DIR)/$@
+-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
++AUX_BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
+            chmod 755 $(AUX_BIN_DIR)/$@
+ VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
+ 
diff --git a/sci-biology/mummer/files/3.22-prll.patch b/sci-biology/mummer/files/3.22-prll.patch
new file mode 100644
index 000000000000..3b24ee40214a
--- /dev/null
+++ b/sci-biology/mummer/files/3.22-prll.patch
@@ -0,0 +1,56 @@
+diff --git a/Makefile b/Makefile
+index 4db4977..bbd00ed 100644
+--- a/Makefile
++++ b/Makefile
+@@ -114,15 +114,15 @@ install: all
+ 
+ 
+ kurtz:
+-	cd $(KURTZ_SRC_DIR); $(MAKE) mummer
++	$(MAKE) -C $(KURTZ_SRC_DIR) mummer
+ 
+ 
+ scripts:
+-	cd $(SCRIPT_DIR); $(MAKE) all
++	$(MAKE) -C $(SCRIPT_DIR) all
+ 
+ 
+ tigr:
+-	cd $(TIGR_SRC_DIR); $(MAKE) all
++	$(MAKE) -C $(TIGR_SRC_DIR) all
+ 
+ 
+ uninstall: clean
+diff --git a/src/kurtz/Makefile b/src/kurtz/Makefile
+index 85dfc16..5bff793 100644
+--- a/src/kurtz/Makefile
++++ b/src/kurtz/Makefile
+@@ -1,7 +1,7 @@
+ all:
+-	cd libbasedir; $(MAKE) all
+-	cd streesrc; $(MAKE) all
+-	cd mm3src; $(MAKE) all
++	$(MAKE) -C libbasedir all
++	$(MAKE) -C streesrc all
++	$(MAKE) -C mm3src all
+ 
+ clean:
+ 	rm -f *~
+@@ -10,11 +10,11 @@ clean:
+ 	cd mm3src; $(MAKE) clean
+ 
+ mummer:
+-	cd libbasedir; $(MAKE) libbase.a
+-	cd streesrc; $(MAKE) libstree.a
+-	cd mm3src; $(MAKE) mummer
++	$(MAKE) -C libbasedir libbase.a
++	$(MAKE) -C streesrc libstree.a
++	$(MAKE) -C mm3src mummer
+ 
+ splintall:
+-	cd libbasedir; ${MAKE} splintall
+-	cd streesrc; ${MAKE} splintall
+-	cd mm3src; ${MAKE} splintall
++	$(MAKE) -C libbasedir splintall
++	$(MAKE) -C streesrc splintall
++	$(MAKE) -C mm3src splintall
diff --git a/sci-biology/mummer/mummer-3.22.ebuild b/sci-biology/mummer/mummer-3.22-r1.ebuild
index ddeec39e649e..0c6ee771ac4c 100644
--- a/sci-biology/mummer/mummer-3.22.ebuild
+++ b/sci-biology/mummer/mummer-3.22-r1.ebuild
@@ -1,8 +1,10 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/mummer-3.22.ebuild,v 1.2 2009/10/29 02:21:12 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/mummer-3.22-r1.ebuild,v 1.1 2011/01/13 09:14:52 jlec Exp $
 
-EAPI="2"
+EAPI="3"
+
+inherit eutils flag-o-matic
 
 DESCRIPTION="A rapid whole genome aligner"
 HOMEPAGE="http://mummer.sourceforge.net/"
@@ -18,11 +20,18 @@ RDEPEND="app-shells/tcsh"
 
 S="${WORKDIR}/MUMmer${PV}"
 
-src_unpack() {
-	unpack ${A}
-	# Warning: package uses CPPFLAGS on c as well as cpp, despite the name
-	sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
-		-e 's/LDFLAGS  =$//' "${S}/Makefile" || die
+src_prepare() {
+	use amd64 && append-flags -DSIXTYFOURBITS
+
+	epatch \
+		"${FILESDIR}"/${PV}-prll.patch \
+		"${FILESDIR}"/${PV}-ldflags.patch
+
+	sed \
+		-e '/^CFLAGS/d' \
+		-e '/^CXXFLAGS/d' \
+		-e '/^LDFLAGS/d' \
+		-i Makefile || die
 }
 
 src_compile() {
@@ -47,7 +56,9 @@ src_install() {
 	insinto /usr/share/${PN}/lib
 	doins scripts/Foundation.pm || die
 
-	dodoc ACKNOWLEDGEMENTS ChangeLog README
+	dodoc ACKNOWLEDGEMENTS ChangeLog README || die
 	insinto /usr/share/doc/${PF}
-	use doc && doins -r docs
+	if use doc; then
+		doins -r docs || die
+	fi
 }