sci-biology/shrimp: Do not install elf in usr/share, #438652

Package-Manager: portage-2.2.0_alpha141/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

5 files changed, 49 insertions, 79 deletions

diff --git a/sci-biology/shrimp/ChangeLog b/sci-biology/shrimp/ChangeLog
index ece2fc2bd12a..4f57d4aba634 100644
--- a/sci-biology/shrimp/ChangeLog
+++ b/sci-biology/shrimp/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/shrimp
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.14 2011/03/07 15:33:02 tomka Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.15 2012/10/18 18:00:44 jlec Exp $
+
+  18 Oct 2012; Justin Lecher <jlec@gentoo.org> -shrimp-1.3.1.ebuild,
+  shrimp-2.0.1.ebuild, shrimp-2.1.0.ebuild:
+  Do not install elf in usr/share, #438652
 
   07 Mar 2011; Thomas Kahle <tomka@gentoo.org> shrimp-2.0.1.ebuild:
   x86 stable per bug 353563
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
index 9c5612b03b62..687e7e972b6d 100644
--- a/sci-biology/shrimp/Manifest
+++ b/sci-biology/shrimp/Manifest
@@ -1,18 +1,17 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
-DIST SHRiMP_1_3_1.src.tar.gz 120929 RMD160 399455b93be51047958945c767a3bdd31dada88e SHA1 ce571eb23ce3172fd1303ffd71deee652e9d395e SHA256 a0847d1e05ca4c277d7be95f315b5f7d12fad0852324985660fe9ea1820487b9
-DIST SHRiMP_2_0_1.src.tar.gz 158535 RMD160 9153bb3b1cb8648a74df431537b38efa4267929a SHA1 b6b54a2990fc5193b72f2a08f47f95b527fabde3 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
-DIST SHRiMP_2_1_0.src.tar.gz 189121 RMD160 846b9c014c5d961f1c86e7c169a14e9be01c25e7 SHA1 52afe3673f2205cb79000999daf247cef808e003 SHA256 72a414fcbc528e98af70967942ecf32b377df0582c8076a0bf32c95fa8a8c39e
-EBUILD shrimp-1.3.1.ebuild 845 RMD160 dbabe4f8787f2be0d9afeb5704d34815e2cb32a6 SHA1 cc36b8fbf230f6d460a162785c05beccf7a534b8 SHA256 148eee6a913bb3806918369c26c876b6d4bcd81b65de4ad65d49c95d738c305e
-EBUILD shrimp-2.0.1.ebuild 1199 RMD160 3c856b924d19db6b366e5be0e282587883e328a3 SHA1 0a0aed2e377c22922f5b634e839c5cce1f5de6f3 SHA256 bf85c77a4db683a33613b1a1565662e9f73f0e7b335fb9047c5a4c00a343fd94
-EBUILD shrimp-2.1.0.ebuild 1215 RMD160 2fc65900b3b0357932d9a5056b0cc20b510b9d7c SHA1 2f9e83cc7e26db66d0853c7f587a14bb0f354d0e SHA256 35b4799dd3431956998974831d27703081c0019f94343770885d29db1c9ef81e
-MISC ChangeLog 2050 RMD160 95ff28f8e067ae5289c8eb2db7d5b0c7058099a8 SHA1 3d50b5642e3b99b84de2a39991be5b121ae4305e SHA256 cd052118c03eb896b620bc9286aedf37ade797bf67294f515e29c2d17a69c7f7
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
+DIST SHRiMP_2_1_0.src.tar.gz 189121 SHA256 72a414fcbc528e98af70967942ecf32b377df0582c8076a0bf32c95fa8a8c39e SHA512 01a54dbcb645bfa55ec280d932cc947cab9b6f5266d273d8ea4103cb298e747da00aa04b56753f880d6de11663d9c4219b2402f84d5c15ebe4f1c5bb94e80a8a WHIRLPOOL d0f87dbad1a61c83527be166181eabd491fc3e5a2bd6e22aacd4b369146940e2d843b44ab6e6e9b7c092afe6c08b1cb7b060e3944e47f3d3c87acc634a2c7f36
+EBUILD shrimp-2.0.1.ebuild 1267 SHA256 4685094dae4cd65bffa0da56634350599c5ec4748111e3ce81942b1eea2b63d0 SHA512 96698ffcabc0f57c763e080e935ebb89b19499786c9dc6cdda1cc04f71224cfd9745965ca48f396da501b099781c1fa66405332fac0c534eb969d2dcd7462ed4 WHIRLPOOL 042167c616f661495139539dc2936c3e75389da400f02400d85771375014c510b25f7d4645db667c78790d1ffd7df723ce1dd58532e3fcd42f68a4076b8fd3d0
+EBUILD shrimp-2.1.0.ebuild 1258 SHA256 fd9cb865e3fc3afec5ffd40134f94be6fe72d8c9be7ea211eff27a1298770b31 SHA512 6a7a4e416b9b00d1973e810a4026aa926516a7ba5046959bb90dbbc574ceb8fd34293f9995bd6cc55322612b10d4f2cca681ee0cde9541e2b903d3f685a56bad WHIRLPOOL 05205feb28fab7159797d51e539e67f55c3676836890fda8e984740828867b2c5a4d26468a22552350c968e4948ac05e4d633e31d42c1b95a9f33bf26d2ed920
+MISC ChangeLog 2206 SHA256 43d33b3de640d125afc013ae32e2ea29d46012de485d4fa4a85d14b34f0e0fc3 SHA512 dbb02d052f48e1f7b12ca04941a34fd36238cc8fb0c2c868fb16da523c16ca62974d02eb85701db4aa92479df6857bb053c865ecc4574b5aa01b56522f13b46a WHIRLPOOL ffc4aea77a8886891e57a1f3b0d217ca2ec3cba106cf7fab66aaff80e710e6d652cd2e6e419c997183942d54df779f01114ef2a3387b752155b48b9fa39e766d
+MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
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diff --git a/sci-biology/shrimp/shrimp-1.3.1.ebuild b/sci-biology/shrimp/shrimp-1.3.1.ebuild
deleted file mode 100644
index 5723168881ea..000000000000
--- a/sci-biology/shrimp/shrimp-1.3.1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-1.3.1.ebuild,v 1.3 2010/01/03 14:19:01 pacho Exp $
-
-EAPI="2"
-
-MY_PV=${PV//./_}
-
-DESCRIPTION="SHort Read Mapping Package"
-HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
-SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
-
-LICENSE="as-is"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/SHRiMP_${MY_PV}"
-
-src_prepare() {
-	sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die
-	sed -i -e '1 a CXXFLAGS+= -O3 -mmmx -msse -msse2' \
-		-e 's/-static//' "${S}/Makefile" || die
-}
-
-src_install() {
-	rm bin/README
-	dobin bin/* || die
-	insinto /usr/share/${PN}
-	doins -r utils || die
-	dodoc HISTORY README TODO MEMORY
-}
diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild
index c8d8c0072874..81f1bb11185d 100644
--- a/sci-biology/shrimp/shrimp-2.0.1.ebuild
+++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.5 2011/03/07 15:33:02 tomka Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.6 2012/10/18 18:00:44 jlec Exp $
 
-EAPI="2"
+EAPI=4
 
 inherit flag-o-matic toolchain-funcs
 
@@ -14,20 +14,20 @@ SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.g
 
 LICENSE="as-is"
 SLOT="0"
-IUSE=""
 KEYWORDS="amd64 x86"
-
-DEPEND=">=sys-devel/gcc-4.3[openmp]"
-RDEPEND="${DEPEND}"  # -lgomp
+IUSE="custom-cflags"
 
 S=${WORKDIR}/SHRiMP_${MY_PV}
 
 pkg_setup() {
-	tc-has-openmp || die "At least gcc-4.3 is required for openmp support."
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
 }
 
 src_prepare() {
-	sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die #294811
+	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
 	# respect LDFLAGS wrt 331823
 	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
 		-e 's/-static//' Makefile || die
@@ -35,14 +35,15 @@ src_prepare() {
 
 src_compile() {
 	append-flags -fopenmp
+	use custom-cflags || append-flags -O3 # per instructions in BUILDING
 	tc-export CXX
-	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
 }
 
 src_install() {
-	rm bin/README || die
-	dobin bin/* || die
+	rm bin/README
+	dobin bin/*
 	insinto /usr/share/${PN}
-	doins -r utils || die
-	dodoc HISTORY README TODO SPLITTING_AND_MERGING || die
+	doins -r utils
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING
 }
diff --git a/sci-biology/shrimp/shrimp-2.1.0.ebuild b/sci-biology/shrimp/shrimp-2.1.0.ebuild
index b6e235263f49..17e3a7398a5f 100644
--- a/sci-biology/shrimp/shrimp-2.1.0.ebuild
+++ b/sci-biology/shrimp/shrimp-2.1.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.1.0.ebuild,v 1.1 2011/02/03 00:13:49 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.1.0.ebuild,v 1.2 2012/10/18 18:00:44 jlec Exp $
 
-EAPI="2"
+EAPI=4
 
 inherit flag-o-matic toolchain-funcs
 
@@ -14,34 +14,35 @@ SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.g
 
 LICENSE="as-is"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=sys-devel/gcc-4.3[openmp]"
-RDEPEND="${DEPEND}"  # -lgomp
+IUSE="custom-cflags"
 
 S=${WORKDIR}/SHRiMP_${MY_PV}
 
 pkg_setup() {
-	tc-has-openmp || die "At least gcc-4.3 is required for openmp support."
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
 }
 
 src_prepare() {
-	sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die #294811
+	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
 	# respect LDFLAGS wrt 331823
 	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
 		-e 's/-static//' Makefile || die
 }
 
 src_compile() {
-	append-flags -fopenmp -O3 # per instructions in BUILDING
+	append-flags -fopenmp
+	use custom-cflags || append-flags -O3 # per instructions in BUILDING
 	tc-export CXX
-	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
 }
 
 src_install() {
-	dobin bin/* || die
-	insinto /usr/share/${PN}
-	doins -r utils || die
-	dodoc HISTORY README TODO SPLITTING_AND_MERGING || die
+	dobin bin/*
+	insinto /usr/libexec/${PN}
+	doins -r utils/*
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING
 }