[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/

[Justin Lecher]

commit:     2b64eb561a6fb14fd4af81a272d17ac9590f0a23
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  1 13:26:22 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  1 13:26:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2b64eb56

sci-biology/ncbi-tools++: Some Prefix love

Package-Manager: portage-2.2.0_alpha170
RepoMan-Options: --force

---
 sci-biology/ncbi-tools++/ChangeLog                 |    7 ++
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   87 +++++++++++---------
 2 files changed, 55 insertions(+), 39 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index ab4e4ea..234411a 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  01 Apr 2013; Justin Lecher <jlec@g.o> ncbi-tools++-9.0.0-r1.ebuild:
+  Some Prefix love
+
+  01 Apr 2013; Justin Lecher <jlec@g.o> ncbi-tools++-9.0.0-r1.ebuild:
+  Some Prefix love
+
+
   03 Mar 2013; Justin Lecher <jlec@g.o> metadata.xml:
   Document USE
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index eada94b..9a2f8da 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -104,6 +104,8 @@ src_prepare() {
 	epatch ${PATCHES[@]}
 
 	tc-export CXX CC
+
+
 #	cd src/build-system || die
 #	eaclocal -I.
 #	eautoconf
@@ -184,9 +186,9 @@ src_configure() {
 #	--with-sssutils
 #	--with-sssdb
 #	--with-included-sss
-	--with-z="${EPREFIX}"/usr
-	--with-bz2="${EPREFIX}"/usr
-	--with-muparser="${EPREFIX}"/usr
+	--with-z="${EPREFIX}/usr"
+	--with-bz2="${EPREFIX}/usr"
+	--with-muparser="${EPREFIX}/usr"
 	--without-sybase
 	--with-autodep
 #	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
@@ -199,41 +201,41 @@ src_configure() {
 	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
 	$(use_with test check)
 	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}"/usr)
-	$(use_with pcre pcre "${EPREFIX}"/usr)
-	$(use_with gnutls gnutls "${EPREFIX}"/usr)
-	$(use_with ssl openssl "${EPREFIX}"/usr)
-	$(use_with ftds ftds "${EPREFIX}"/usr)
-	$(use_with mysql mysql "${EPREFIX}"/usr)
-	$(use_with fltk fltk "${EPREFIX}"/usr)
-	$(use_with opengl opengl "${EPREFIX}"/usr)
-	$(use_with mesa mesa "${EPREFIX}"/usr)
-	$(use_with opengl glut "${EPREFIX}"/usr)
-	$(use_with opengl glew "${EPREFIX}"/usr)
+	$(use_with lzo lzo "${EPREFIX}/usr")
+	$(use_with pcre pcre "${EPREFIX}/usr")
+	$(use_with gnutls gnutls "${EPREFIX}/usr")
+	$(use_with ssl openssl "${EPREFIX}/usr")
+	$(use_with ftds ftds "${EPREFIX}/usr")
+	$(use_with mysql mysql "${EPREFIX}/usr")
+	$(use_with fltk fltk "${EPREFIX}/usr")
+	$(use_with opengl opengl "${EPREFIX}/usr")
+	$(use_with mesa mesa "${EPREFIX}/usr")
+	$(use_with opengl glut "${EPREFIX}/usr")
+	$(use_with opengl glew "${EPREFIX}/usr")
 	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}"/usr)
+	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
 	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}"/usr)
-	$(use_with fastcgi fastcgi "${EPREFIX}"/usr)
-	$(use_with berkdb bdb "${EPREFIX}"/usr)
-	$(use_with odbc odbc "${EPREFIX}"/usr)
-	$(use_with python python "${EPREFIX}"/usr)
-	$(use_with boost boost "${EPREFIX}"/usr)
-	$(use_with sqlite sqlite3 "${EPREFIX}"/usr)
-	$(use_with icu icu "${EPREFIX}"/usr)
-	$(use_with expat expat "${EPREFIX}"/usr)
-	$(use_with xml libxml "${EPREFIX}"/usr)
-	$(use_with xml libxslt "${EPREFIX}"/usr)
-	$(use_with xerces xerces "${EPREFIX}"/usr)
-	$(use_with hdf5 hdf5 "${EPREFIX}"/usr)
-	$(use_with xalan xalan "${EPREFIX}"/usr)
-#	$(use_with gif gif "${EPREFIX}"/usr)
-	$(use_with jpeg jpeg "${EPREFIX}"/usr)
-	$(use_with tiff tiff "${EPREFIX}"/usr)
-	$(use_with png png "${EPREFIX}"/usr)
-	$(use_with xpm xpm "${EPREFIX}"/usr)
-	$(use_with curl curl "${EPREFIX}"/usr)
-#	$(use_with X x "${EPREFIX}"/usr)
+	$(use_with freetype freetype "${EPREFIX}/usr")
+	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
+	$(use_with berkdb bdb "${EPREFIX}/usr")
+	$(use_with odbc odbc "${EPREFIX}/usr")
+	$(use_with python python "${EPREFIX}/usr")
+	$(use_with boost boost "${EPREFIX}/usr")
+	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
+	$(use_with icu icu "${EPREFIX}/usr")
+	$(use_with expat expat "${EPREFIX}/usr")
+	$(use_with xml libxml "${EPREFIX}/usr")
+	$(use_with xml libxslt "${EPREFIX}/usr")
+	$(use_with xerces xerces "${EPREFIX}/usr")
+	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
+	$(use_with xalan xalan "${EPREFIX}/usr")
+#	$(use_with gif gif "${EPREFIX}/usr")
+	$(use_with jpeg jpeg "${EPREFIX}/usr")
+	$(use_with tiff tiff "${EPREFIX}/usr")
+	$(use_with png png "${EPREFIX}/usr")
+	$(use_with xpm xpm "${EPREFIX}/usr")
+	$(use_with curl curl "${EPREFIX}/usr")
+#	$(use_with X x "${EPREFIX}/usr")
 	$(use_with X x)
 	)
 
@@ -244,14 +246,14 @@ src_configure() {
 	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
 	# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
 
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}"/usr --libdir=/usr/lib64 ${myconf[@]}"
+	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
 
 #	bash \
 #		./src/build-system/configure \
 #	cd src/build-system || die
 	econf \
 		--srcdir="${S}" \
-		--prefix="${EPREFIX}"/usr \
+		--prefix="${EPREFIX}/usr" \
 		--libdir=/usr/lib64 \
 		${myconf[@]} || die
 #--without-debug \
@@ -278,7 +280,14 @@ src_compile() {
 }
 
 src_install() {
-	emake install || die
+	rm -rvf "${S}"_build/lib/ncbi || die
+	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+
+#	dobin "${S}"_build/bin/*
+#	dolib.so "${S}"_build/lib/*so*
+#	dolib.a "${S}"_build/lib/*.a
+#	doheader "${S}"_build/inc/*
+
 	# File collisions with sci-biology/ncbi-tools
 	rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
 	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2