Respect LDFLAGS and CFLAGS, do not install ELF in usr/share, #297061 & 335257

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

5 files changed, 232 insertions, 23 deletions

diff --git a/sci-biology/glimmerhmm/ChangeLog b/sci-biology/glimmerhmm/ChangeLog
index ddd1db220e8c..8563d3906bb5 100644
--- a/sci-biology/glimmerhmm/ChangeLog
+++ b/sci-biology/glimmerhmm/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/glimmerhmm
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/ChangeLog,v 1.4 2009/09/22 11:33:56 maekke Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/ChangeLog,v 1.5 2011/06/20 08:32:26 jlec Exp $
+
+*glimmerhmm-3.0.1-r1 (20 Jun 2011)
+
+  20 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/3.0.1-gentoo.patch,
+  glimmerhmm-3.0.1.ebuild, +glimmerhmm-3.0.1-r1.ebuild:
+  Respect LDFLAGS and CFLAGS, do not install ELF in usr/share, #297061 & 335257
 
   22 Sep 2009; Markus Meier <maekke@gentoo.org> glimmerhmm-3.0.1.ebuild:
   x86 stable, bug #282107
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
index 8d116c29f28f..289ea64f179e 100644
--- a/sci-biology/glimmerhmm/Manifest
+++ b/sci-biology/glimmerhmm/Manifest
@@ -1,14 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
+AUX 3.0.1-gentoo.patch 4235 RMD160 743cdbe3e83e0e4486f7637c36653b93092a2abd SHA1 c2146809485e7514b2ca51aca56071fcd48f0fc0 SHA256 04eef55bb0cdb4455d143bec7fd0113491caee72fa9a6c56237024b4f18abbf4
 DIST GlimmerHMM-3.0.1.tar.gz 45475952 RMD160 273cb74458e3f444cd9f8ca9f6618335aea5465f SHA1 6caf10a3fb79660e48d88560869dee0394961f1a SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4
-EBUILD glimmerhmm-3.0.1.ebuild 1525 RMD160 1594c3a024939e089dc0dd8a8edaa535b7126459 SHA1 de4d141abbcd3436b0a64410fa85d39ad2298b46 SHA256 bfe3d891c6d22669a94aea45c8aeb29f352186d7c7cfea9fa55fac88bf1c5255
-MISC ChangeLog 652 RMD160 b94630cc8772916b459b33211efeccbfcc421d38 SHA1 a727a92e76ec19bac70543e0b8dfcbdf6c15f5f0 SHA256 d79d70eadfb7e66968859c838d1181df00a037425d2f04a920da60bccfc5f3e0
+EBUILD glimmerhmm-3.0.1-r1.ebuild 1315 RMD160 9b953765a9313361166cbb2865b25df4a0737838 SHA1 08d527cb97ced202ac9c4aa7735a4c97fe0af089 SHA256 d2b48eca44c56bb0038c857c790269c217019fe7256337638ab9dc1f2eb4a8fa
+EBUILD glimmerhmm-3.0.1.ebuild 1442 RMD160 84af70bf6da0e8f4a31e932480db53c24f287e28 SHA1 9f5b2247b4a48a76131ee33536ac65694fba1ddc SHA256 51ea3c70929df4bf0bebe802c37ea5861b079d21ac997201499da9b8fd49261e
+MISC ChangeLog 897 RMD160 42fba37c3c5b5d386206cf53e3dd51790884dfec SHA1 82c9a22897b7019f909d7c46fa2243055f9b3d1d SHA256 ad6b112b39edcb4a7aa59459de3e0522b5528ce45075bd7d012da6b2e984d1cb
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.11 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAkq4tlEACgkQkKaRLQcq0GIKagCfW/JO7QjOTGDwlQNM1AkVzzH6
-fvQAoKdtUW2BP7/VpXvft+mXyHH1uQVb
-=wl7L
+iEYEARECAAYFAk3/BaAACgkQgAnW8HDreRYc6ACfUXrYEtB8d4eOsVOhTE87FtWJ
+2OEAnRxSoMQ3XMw/vTgFLKrwHNnl8hNm
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diff --git a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
new file mode 100644
index 000000000000..949a4fe3e92d
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
@@ -0,0 +1,153 @@
+ sources/makefile |   15 +++++--------
+ train/makefile   |   59 +++++++++++++++++++++++++++++++----------------------
+ 2 files changed, 40 insertions(+), 34 deletions(-)
+
+diff --git a/sources/makefile b/sources/makefile
+index f287d71..c560f48 100644
+--- a/sources/makefile
++++ b/sources/makefile
+@@ -2,25 +2,22 @@
+ 
+ 
+ 
+-CC=g++
+-CFLAGS=-g
+-
+ all: glimmerhmm
+ 
+ glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
+-	$(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
+ 
+ glimmerhmm.o: glimmerhmm.c
+-	$(CC) $(CFLAGS) -c glimmerhmm.c
++	$(CXX) $(CXXFLAGS) -c glimmerhmm.c
+ 
+ graph.o: graph.c 
+-	$(CC) $(CFLAGS) -c graph.c
++	$(CXX) $(CXXFLAGS) -c graph.c
+ 
+ sites.o: sites.c
+-	$(CC) $(CFLAGS) -c sites.c
++	$(CXX) $(CXXFLAGS) -c sites.c
+ 
+ tree_util_prob.o: tree_util_prob.c
+-	$(CC) $(CFLAGS) -c tree_util_prob.c
++	$(CXX) $(CXXFLAGS) -c tree_util_prob.c
+ 
+ util.o: util.c
+-	$(CC) $(CFLAGS) -c util.c
++	$(CXX) $(CXXFLAGS) -c util.c
+diff --git a/train/makefile b/train/makefile
+index 2383f18..d5a7107 100644
+--- a/train/makefile
++++ b/train/makefile
+@@ -2,9 +2,6 @@
+ 
+ # C compiler
+ 
+-C       = gcc 
+-CC      = g++ 
+-CFLAGS  = -O1 ${SEARCHDIRS}
+ #CFLAGS  = -O3 -g -Wall
+ LIBS    = -lm
+ 
+@@ -15,64 +12,76 @@ all:    build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
+ 
+ 
+ misc.o: misc.c
+-	${C} ${CFLAGS} -c misc.c
++	$(CC) $(CFLAGS) -c misc.c
+ 
+ build-icm.o: build-icm.c
+-	${C} ${CFLAGS} -c build-icm.c
++	$(CC) $(CFLAGS) -c build-icm.c
+ 
+ build-icm: build-icm.o misc.o
+-	$(C) -o $@ build-icm.o misc.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
+ 
+ build-icm-noframe.o: build-icm-noframe.c
+-	${C} ${CFLAGS} -c build-icm-noframe.c
++	$(CC) $(CFLAGS) -c build-icm-noframe.c
+ 
+ build-icm-noframe: build-icm-noframe.o misc.o
+-	$(C) -o $@ build-icm-noframe.o misc.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
+ 
+ build1: build1.o
+-	${CC} build1.c -o build1 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS)
+ 
+ build2: build2.o
+-	${CC} build2.c -o build2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS)
+ 
+ falsecomp: falsecomp.o
+-	${CC} falsecomp.c -o falsecomp $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS)
+ 
+ findsites: findsites.o
+-	${CC} findsites.c -o findsites $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS)
+ 
+ karlin: karlin.o
+-	${CC} karlin.c -o karlin $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS)
+ 
+ score: score.o
+-	${CC} score.c -o score $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS)
+ 
+ score2: score2.o
+-	${CC} score2.c -o score2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS)
+ 
+ scoreATG: scoreATG.o
+-	${CC} scoreATG.c -o scoreATG $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS)
+ 
+ scoreATG2: scoreATG2.o
+-	${CC} scoreATG2.c -o scoreATG2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS)
+ 
+ scoreSTOP: scoreSTOP.o
+-	${CC} scoreSTOP.c -o scoreSTOP $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS)
+ 
+ escoreSTOP2: scoreSTOP2.o
+-	${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS)
+ 
+-rfapp: erfapp.o
+-	${CC} erfapp.c -o erfapp $(LIBS)
++erfapp: erfapp.o
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
+ 
+ sites.o: sites.c
+-	${CC} ${CFLAGS} -c sites.c
++	$(CXX) $(CXXFLAGS) -c sites.c
++
++scoreATG.o: scoreATG.c
++	$(CXX) $(CXXFLAGS) -c scoreATG.c
++	
++scoreSTOP.o: scoreSTOP.c
++	$(CXX) $(CXXFLAGS) -c scoreSTOP.c
++
++scoreSTOP2.o: scoreSTOP2.c
++	$(CXX) $(CXXFLAGS) -c scoreSTOP2.c
++
++scoreATG2.o: scoreATG2.c
++	$(CXX) $(CXXFLAGS) -c scoreATG2.c
+ 
+ utils.o: utils.c 
+-	${CC} ${CFLAGS} -c utils.c
++	$(CXX) $(CXXFLAGS) -c utils.c
+ 
+ splicescore.o: splicescore.c
+-	${CC} ${CFLAGS} -c splicescore.c
++	$(CXX) $(CXXFLAGS) -c splicescore.c
+ 
+ splicescore: splicescore.o sites.o utils.o
+-	${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
new file mode 100644
index 000000000000..e23c43cc5867
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild,v 1.1 2011/06/20 08:32:26 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="An eukaryotic gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+src_unpack() {
+	unpack ${A}
+	mv GlimmerHMM ${P}
+}
+
+src_prepare() {
+	sed \
+		-e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \
+		-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \
+		-i "${S}/train/trainGlimmerHMM" || die
+
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	tc-export CC CXX
+}
+
+src_compile() {
+	emake -C "${S}/sources"
+	emake -C "${S}/train"
+}
+
+src_install() {
+	dobin sources/glimmerhmm train/trainGlimmerHMM
+
+	insinto /usr/share/${PN}/lib
+	doins train/*.pm
+	insinto /usr/share/${PN}/models
+	doins -r trained_dir/*
+	exeinto /usr/libexec/${PN}/training_utils
+	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
+
+	dodoc README.first train/readme.train
+}
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
index 05b93cd2689b..600a0a39b9bd 100644
--- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild
@@ -1,6 +1,6 @@
-# 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/glimmerhmm/glimmerhmm-3.0.1.ebuild,v 1.5 2009/09/22 11:33:56 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild,v 1.6 2011/06/20 08:32:26 jlec Exp $
 
 inherit toolchain-funcs
 
@@ -15,19 +15,18 @@ SLOT="0"
 IUSE=""
 KEYWORDS="amd64 x86"
 
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/${MY_P}"
-
 src_unpack() {
 	unpack ${A}
-	sed -i -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/share/'${PN}'/training_utils"|' \
-		-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' "${S}/train/trainGlimmerHMM" || die
-	sed -i -e 's/^CFLAGS[ ]*=.*//' \
+	mv GlimmerHMM ${P}
+	sed \
+		-e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/share/'${PN}'/training_utils"|' \
+		-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \
+		-i "${S}/train/trainGlimmerHMM" || die
+	sed \
+		-e 's/^CFLAGS[ ]*=.*//' \
 		-e 's/C *=.*/C='$(tc-getCC)'/' \
 		-e 's/CC *=.*/CC='$(tc-getCXX)'/' \
-		"${S}"/*/makefile || die
+		-i "${S}"/*/makefile || die
 }
 
 src_compile() {
@@ -38,14 +37,12 @@ src_compile() {
 src_install() {
 	dobin sources/glimmerhmm train/trainGlimmerHMM || die
 
-	dodir /usr/share/${PN}/{lib,models,training_utils}
 	insinto /usr/share/${PN}/lib
 	doins train/*.pm || die
 	insinto /usr/share/${PN}/models
 	doins -r trained_dir/* || die
-	insinto /usr/share/${PN}/training_utils
-	insopts -m755
-	doins train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} || die
+	exeinto /usr/share/${PN}/training_utils
+	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} || die
 
 	dodoc README.first train/readme.train
 }