Respect LDFLAGS wrt bug 336196. Thanks to Diego for the report. Fix install and implicit function declaration. Drop old.

(Portage version: 2.2_rc73/cvs/Linux x86_64)

5 files changed, 125 insertions, 45 deletions

diff --git a/sci-biology/rnaview/ChangeLog b/sci-biology/rnaview/ChangeLog
index 7419dff16e9b..cf3cc33e592a 100644
--- a/sci-biology/rnaview/ChangeLog
+++ b/sci-biology/rnaview/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-biology/rnaview
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/ChangeLog,v 1.11 2008/08/26 18:08:55 ribosome Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/ChangeLog,v 1.12 2010/09/06 12:24:45 xarthisius Exp $
+
+*rnaview-20040713-r2 (06 Sep 2010)
+
+  06 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org>
+  -rnaview-20040713-r1.ebuild, +rnaview-20040713-r2.ebuild,
+  +files/rnaview-20040713-implicit.patch,
+  +files/rnaview-20040713-makefile.patch:
+  Respect LDFLAGS wrt bug 336196. Thanks to Diego for the report. Fix
+  install and implicit function declaration. Drop old.
 
 *rnaview-20040713-r1 (26 Aug 2008)
 
diff --git a/sci-biology/rnaview/files/rnaview-20040713-implicit.patch b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch
new file mode 100644
index 000000000000..009f6e79ae86
--- /dev/null
+++ b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch
@@ -0,0 +1,13 @@
+Fix implicit function declaration
+
+--- src/xml2ps.c
++++ src/xml2ps.c
+@@ -36,7 +36,7 @@
+ void read_sugar_syn(char *inpfile, long **sugar_syn);
+ void get_sugar_syn(FILE *inp, char *value_ch);
+ void get_chain_broken(long nres, double **a, double **b, long *chain_broken);
+-
++extern void get_BDIR(char *BDIR, char *filename);
+ 
+ 
+ FILE  *psfile; 
diff --git a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
new file mode 100644
index 000000000000..5d9ecd99cf25
--- /dev/null
+++ b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
@@ -0,0 +1,67 @@
+Fix install paths, respect LDFLAGS, CFLAGS
+
+http://bugs.gentoo.org/show_bug.cgi?id=336196
+
+--- rnaml2ps/Makefile
++++ rnaml2ps/Makefile
+@@ -5,16 +5,21 @@
+ RNADRAW = rnaml2ps
+ OBJS_RNADRAW = rnaml2ps.o nrutil.o 
+ 
++all: $(RNADRAW)
++
+ $(RNADRAW):   $(OBJS_RNADRAW)
+-	$(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
++	$(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
+ 
+ nrutil.o : nrutil.c 
+-	cc -c  nrutil.c
++	$(CC) $(CFLAGS) -c  nrutil.c
+ 
+ rnaml2ps.o :  rnaml2ps.c
+-	cc -c  rnaml2ps.c
++	$(CC) $(CFLAGS) -c  rnaml2ps.c
+ 
+ 
+-.PHONY : clean
++.PHONY : clean all install
+ clean:
+-	rm *.o
++	rm -f *.o
++
++install:
++	install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW)
+--- Makefile
++++ Makefile
+@@ -56,9 +56,14 @@
+            $(OBJ)/multiple.o \
+            $(OBJ)/statistics.o
+ 
++.PHONY: clean all install
++
++SUBDIRS = rnaml2ps
++
+ all: $(RNAVIEW)
++	for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} all ) ; done
+ 
+-CFLAGS  =  $(LINCLUDES) 
++CFLAGS  +=  $(LINCLUDES)
+ 
+ $(RNAVIEW) : $(HFILES) $(OBJ_FILE) 
+ 	$(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB)
+@@ -111,6 +116,15 @@
+ clean:
+ 	@rm -f $(OBJ)/*.o
+ 	@rm -f $(ALLTARGETS)
++	for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} clean ) ; done
++
++install:
++	install -D -m 0755 bin/rnaview $(DESTDIR)/usr/bin/rnaview
++	mkdir -p $(DESTDIR)/usr/share/rnaview/BASEPARS
++	install -m 0644 BASEPARS/* $(DESTDIR)/usr/share/rnaview/BASEPARS
++	mkdir -p $(DESTDIR)/usr/share/rnaview/test
++	install -m 0644 test/* $(DESTDIR)/usr/share/rnaview/test
++	for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} install ) ; done
+ 
+ export:
+ 	mkdir -p $(EXPORT_DIR)
diff --git a/sci-biology/rnaview/rnaview-20040713-r1.ebuild b/sci-biology/rnaview/rnaview-20040713-r1.ebuild
deleted file mode 100644
index 4bdf64dfd6c1..000000000000
--- a/sci-biology/rnaview/rnaview-20040713-r1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/rnaview-20040713-r1.ebuild,v 1.1 2008/08/26 18:08:55 ribosome Exp $
-
-inherit toolchain-funcs
-
-DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions"
-HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-LICENSE="public-domain"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	sed -e "s/CC        = cc/CC        = $(tc-getCC)/" \
-		-e "s/CFLAGS  =/CFLAGS  = ${CFLAGS}/" \
-		-i Makefile || die
-}
-
-src_compile() {
-	make clean
-	make || die "Failed to build programs."
-	cd "${S}"/rnaml2ps
-	make clean
-	make || die "Failed to build rnaml2ps."
-	cd "${S}"/test
-	rm '.#t'
-}
-
-src_install() {
-	dobin bin/rnaview rnaml2ps/rnaml2ps || die "Failed to install programs."
-	dodoc README || die "Failed to install documentation."
-	mkdir -p "${D}"/usr/share/${PN}
-	cp -r BASEPARS test "${D}"/usr/share/${PN}
-	cat <<- EOF > 22rnaview
-		RNAVIEW="/usr/share/rnaview"
-	EOF
-	doenvd 22rnaview || die "Failed to install environment file."
-}
diff --git a/sci-biology/rnaview/rnaview-20040713-r2.ebuild b/sci-biology/rnaview/rnaview-20040713-r2.ebuild
new file mode 100644
index 000000000000..e2bdbf053f08
--- /dev/null
+++ b/sci-biology/rnaview/rnaview-20040713-r2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/rnaview-20040713-r2.ebuild,v 1.1 2010/09/06 12:24:45 xarthisius Exp $
+
+EAPI=2
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions"
+HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+LICENSE="public-domain"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-makefile.patch \
+		"${FILESDIR}"/${P}-implicit.patch
+	cat <<- EOF > 22rnaview
+		RNAVIEW="/usr/share/${PN}"
+	EOF
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" || die
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+	dodoc README || die
+	doenvd 22rnaview || die
+}