Fix respect of FLAGS, 334951; do not install ELF in /usr/share, 296021

Package-Manager: portage-2.2_rc79/cvs/Linux x86_64

4 files changed, 183 insertions, 3 deletions

diff --git a/sci-biology/lagan/ChangeLog b/sci-biology/lagan/ChangeLog
index 7222c8cba060..4e2f5330cc11 100644
--- a/sci-biology/lagan/ChangeLog
+++ b/sci-biology/lagan/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/lagan
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/lagan/ChangeLog,v 1.2 2009/07/21 08:12:46 weaver Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/lagan/ChangeLog,v 1.3 2010/09/12 14:20:31 jlec Exp $
+
+*lagan-2.0-r2 (12 Sep 2010)
+
+  12 Sep 2010; Justin Lecher <jlec@gentoo.org> +lagan-2.0-r2.ebuild,
+  +files/lagan-2.0-flags.patch:
+  Fix respect of FLAGS, 334951; do not install ELF in /usr/share, 296021
 
 *lagan-2.0-r1 (21 Jul 2009)
 
diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest
index c0d049c25429..d0c4c323f814 100644
--- a/sci-biology/lagan/Manifest
+++ b/sci-biology/lagan/Manifest
@@ -1,5 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX lagan-2.0-flags.patch 5848 RMD160 ab0ac777f351eb2236c2303357c9a25897857b2b SHA1 552783c0823a48b56510e6f7729771e84ae4ad96 SHA256 258c3fdcf1eddb4f2282cb45d6113d3e056f42c87442cceef24af463d0e9cf4f
 AUX lagan-2.0-gcc4.3.patch 821 RMD160 2334def85c5859c4ceabc91f997843465a2d89b6 SHA1 1aeeb1a585f70fcad08688e1fbee9e0b626337a5 SHA256 e0575359288e7de97d35a7cce7b92c5619d2f75026beefc9139042280aa20a22
 DIST lagan20.tar.gz 589115 RMD160 a55680c95efc84a4cdc21508223fd0f9bc934f98 SHA1 592ca7e92c7307861e4b2bb66820d1dce1663376 SHA256 a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe
 EBUILD lagan-2.0-r1.ebuild 1511 RMD160 680c5ef49f027bd9f53277e17c7a1a0a349ef37b SHA1 e54f1be34527d1a53da5f4bbe10177083f3f87b1 SHA256 8841f720716d88a50035c3c62e1cde556c63ccd270f0f9acf4801c064ff08718
-MISC ChangeLog 648 RMD160 53007ab8e697c001196adfc048f4dd66579e0dcf SHA1 2b8d74ab8564759064024209332c53caad35befc SHA256 336dfccfca0350ad457cff7309f2a445a615fe79a8fc6ae1511a9e3ff72b4cc1
+EBUILD lagan-2.0-r2.ebuild 1667 RMD160 5489493b9a51e9ae7916ae3bd2484810b84cb85d SHA1 f3cfab14c4c813690117941d6ccce72d89ca9263 SHA256 f9e928a092df93a7a52c4d13e6fc67627737c9d12f17720f97b7d8cad1631b8f
+MISC ChangeLog 850 RMD160 9149ca4e90ca71463372009b01a8d9a3eef8a11f SHA1 34026560569fea2f2e878e2151fc0f524bbb38e4 SHA256 d920adaf5d800b372d8ad5ff3e073e31f55863b70e065c6cffa2b4e187a653bb
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+
+iEYEARECAAYFAkyM4bQACgkQgAnW8HDreRZFLQCcDSlaDJ4NjrqB+RdoTJ7kuJNR
+WtIAn0VNapQ7y8y8e4GqkvrcHKv1lkex
+=PN1y
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-flags.patch
new file mode 100644
index 000000000000..e324ef64c4c6
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-flags.patch
@@ -0,0 +1,107 @@
+diff --git a/Makefile b/Makefile
+index fbbbe79..a1d449b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+ all:
+-	(cd src; $(MAKE))
++	$(MAKE) -C src
+ clean:
+ 	rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
+ 	(cd src; $(MAKE) clean)
+diff --git a/src/Makefile b/src/Makefile
+index 7f6b6fd..dd6309b 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
+ TRGT_DIR = ..
+ 
+ all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
+-	(cd glocal; $(MAKE))
++	$(MAKE) -C glocal
+ clean: 
+ 	rm -f *.o *~ utils/*~ mlagan.purify core
+ 	(cd glocal; $(MAKE) clean)
+ ../anchors: anchors.c skiplist.c
+-	$(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
+ ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
+ ../order: order.c diagmatrix.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
+ ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ ../utils/bin2mf: utils/bin2mf.c
+-	$(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
+ ../utils/bin2bl: utils/bin2bl.c
+-	$(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
+ ../utils/cextract: utils/cextract.c
+-	$(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
+ ../utils/cstat: utils/cstat.c
+-	$(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
+ ../utils/contigorder: utils/contigorder.c
+-	$(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
+ ../utils/getbounds: utils/getbounds.c
+-	$(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
+ ../utils/getcontigpos: utils/getcontigpos.c
+-	$(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
+ ../utils/getlength: utils/getlength.c
+-	$(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
+ ../utils/getoverlap: utils/getoverlap.c
+-	$(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
+ ../utils/rc: utils/rc.c
+-	$(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
+ ../utils/seqmerge: utils/seqmerge.c
+-	$(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
+ ../utils/scorealign: utils/scorealign.c
+-	$(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
+ ../utils/scorecontigs: utils/scorecontigs.c
+-	$(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
+ ../utils/fa2xfa: utils/fa2xfa.c
+-	$(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
+ ../utils/overlay: utils/overlay.c
+-	$(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
+ ../utils/Glue: utils/Glue.cpp
+-	$(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
+ ../utils/dotplot: utils/dotplot.cpp
+-	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
+diff --git a/src/glocal/Makefile b/src/glocal/Makefile
+index ce1421a..b82507f 100755
+--- a/src/glocal/Makefile
++++ b/src/glocal/Makefile
+@@ -10,10 +10,10 @@ TRGT = glocal
+ OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
+ 
+ .cpp.o:
+-	$(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
++	$(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
+ 
+ $(TRGT): $(OBJECTS)
+-	$(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
++	$(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+ 
+ clean :
+ 	rm -f *.o ./*~ *~ core
diff --git a/sci-biology/lagan/lagan-2.0-r2.ebuild b/sci-biology/lagan/lagan-2.0-r2.ebuild
new file mode 100644
index 000000000000..91afb6aab729
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r2.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/lagan/lagan-2.0-r2.ebuild,v 1.1 2010/09/12 14:20:31 jlec Exp $
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+MY_P="lagan20"
+
+DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die
+	# NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline
+	sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
+	epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_compile() {
+	emake \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		CXXFLAGS="${CXXFLAGS}" \
+		CFLAGS="${CFLAGS}"
+}
+
+src_install() {
+	newbin lagan.pl lagan || die
+	newbin slagan.pl slagan || die
+	dobin mlagan || die
+	rm lagan.pl slagan.pl utils/Utils.pm
+
+	insinto /usr/$(get_libdir)/${PN}/lib
+	doins Utils.pm || die
+	exeinto /usr/$(get_libdir)/${PN}/utils
+	doexe utils/* || die
+	exeinto /usr/$(get_libdir)/${PN}
+	doexe *.pl anchors chaos glocal order prolagan || die
+	insinto /usr/$(get_libdir)/${PN}
+	doins *.txt || die
+	dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
+	echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > ${S}/99${PN}
+	doenvd "${S}/99${PN}" || die
+	dodoc Readmes/README.* || die
+}