Fix tests that use gsl. Make repoman happy.

(Portage version: 2.1.8.3/cvs/Linux x86_64)

5 files changed, 47 insertions, 18 deletions

diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
index ffdbdb428829..42334f40b8ec 100644
--- a/sci-biology/hmmer/ChangeLog
+++ b/sci-biology/hmmer/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/hmmer
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.29 2010/07/16 21:56:53 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.30 2010/07/18 10:20:59 xarthisius Exp $
+
+  18 Jul 2010; Kacper Kowalik <xarthisius@gentoo.org> hmmer-2.3.2-r1.ebuild,
+  hmmer-2.3.2-r2.ebuild, hmmer-3.0.ebuild, +files/hmmer-3.0-fix_tests.patch:
+  Fix tests that use gsl. Make repoman happy.
 
   16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> hmmer-3.0.ebuild:
   Stable on amd64 wrt bug #328419
diff --git a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch
new file mode 100644
index 000000000000..983827b0bd46
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch
@@ -0,0 +1,23 @@
+--- easel/Makefile.in
++++ easel/Makefile.in
+@@ -26,8 +26,7 @@
+ LDFLAGS  = @LDFLAGS@
+ SIMDFLAGS= @SIMD_CFLAGS@
+ CPPFLAGS = @CPPFLAGS@
+-LIBGSL   = @LIBGSL@
+-LIBS     = @LIBS@ @PTHREAD_LIBS@
++LIBS     = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@
+ 
+ # Other tools
+ #
+@@ -252,8 +251,8 @@
+         else \
+            DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+         fi;\
+-	echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm;\
+-	${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm
++	echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS};\
++	${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+ 
+ 
+ # install:   installs libeasel.a in ${libdir}/
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
index 41c59662726c..b186e1e6a093 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild,v 1.11 2008/02/07 14:39:22 grobian Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild,v 1.12 2010/07/18 10:20:59 xarthisius Exp $
 
 DESCRIPTION="Sequence analysis using profile hidden Markov models"
 LICENSE="GPL-2"
@@ -16,9 +16,9 @@ DEPEND="pvm? ( sys-cluster/pvm )"
 src_compile() {
 	./configure \
 		--host=${CHOST} \
-		--prefix=${D}/usr \
-		--exec_prefix=${D}/usr \
-		--mandir=${D}/usr/share/man \
+		--prefix="${D}"/usr \
+		--exec_prefix="${D}"/usr \
+		--mandir="${D}"/usr/share/man \
 		--enable-lfs \
 		$(use_enable pvm) \
 		$(use_enable threads) || die
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
index ec8cd3e0ded0..64ece5e99184 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild,v 1.7 2008/02/07 14:39:22 grobian Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild,v 1.8 2010/07/18 10:20:59 xarthisius Exp $
 
 DESCRIPTION="Sequence analysis using profile hidden Markov models"
 LICENSE="GPL-2"
@@ -16,9 +16,9 @@ DEPEND="pvm? ( sys-cluster/pvm )"
 src_compile() {
 	econf \
 		--host=${CHOST} \
-		--prefix=${D}/usr \
-		--exec_prefix=${D}/usr \
-		--mandir=${D}/usr/share/man \
+		--prefix="${D}"/usr \
+		--exec_prefix="${D}"/usr \
+		--mandir="${D}"/usr/share/man \
 		--enable-lfs \
 		$(use_enable pvm) \
 		$(use_enable threads) || die
diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild
index f8e3c212be6e..8611cccff9fc 100644
--- a/sci-biology/hmmer/hmmer-3.0.ebuild
+++ b/sci-biology/hmmer/hmmer-3.0.ebuild
@@ -1,9 +1,11 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.2 2010/07/16 21:56:53 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.3 2010/07/18 10:20:59 xarthisius Exp $
 
 EAPI="2"
 
+inherit eutils
+
 DESCRIPTION="Sequence analysis using profile hidden Markov models"
 HOMEPAGE="http://hmmer.janelia.org/"
 SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz"
@@ -17,22 +19,22 @@ DEPEND="mpi? ( virtual/mpi )
 	gsl? ( >=sci-libs/gsl-1.12 )"
 RDEPEND="${DEPEND}"
 
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-fix_tests.patch
+}
+
 src_configure() {
 	econf $(use_enable sse) \
 		$(use_enable mpi) \
 		$(use_enable threads) \
-		$(use_with gsl) || die
+		$(use_with gsl)
 }
 
 src_install() {
-	einstall || die
+	emake DESTDIR="${D}" install || die
 	dolib src/libhmmer.a || die
 	dolib easel/libeasel.a || die
 	insinto /usr/share/${PN}
 	doins -r tutorial || die
 	dodoc RELEASE-NOTES Userguide.pdf
 }
-
-src_test() {
-	emake check || die
-}