sci-biology/dialign-tx: Fix C99 inline semantics

* Also port to EAPI 6
Closes: https://bugs.gentoo.org/640188
Package-Manager: Portage-2.3.19, Repoman-2.3.6

4 files changed, 82 insertions, 2 deletions

diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
new file mode 100644
index 000000000000..123977916f06
--- /dev/null
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+MY_P=${PN^^}_${PV}
+
+DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment"
+HOMEPAGE="http://dialign-tx.gobics.de/"
+SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S=${WORKDIR}/${MY_P}
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-build-system.patch
+	"${FILESDIR}"/${P}-implicits.patch
+	"${FILESDIR}"/${P}-modernize.patch
+	"${FILESDIR}"/${P}-gnu89-inline.patch
+)
+
+src_configure() {
+	tc-export CC
+}
+
+src_compile() {
+	emake -C source clean
+	emake -C source
+}
+
+src_install() {
+	dobin source/dialign-tx
+	insinto /usr/$(get_libdir)/${PN}/conf
+	doins -r conf/.
+}
+
+pkg_postinst() {
+	einfo "The configuration directory is"
+	einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf"
+	einfo "You will need to pass this to ${PN} on every run."
+}
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch
new file mode 100644
index 000000000000..cbfd458043c5
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch
@@ -0,0 +1,24 @@
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -1,4 +1,3 @@
+-CC=gcc

+ # debug

+ #CPPFLAGS=-g -O0 -Q -v -da

+ #CPPFLAGS=-g -O0 -fstack-check -Q -v -da

+@@ -8,7 +7,6 @@
+ # THIS IS FOR THE OPTIMIZED ONE

+ #CPPFLAGS=-g 

+ #CPPFLAGS=-O3 -march=i686 -funroll-loops

+-CPPFLAGS=-O3 -funroll-loops -march=i686 -mfpmath=sse -msse  -mmmx

+ #CPPFLAGS=-march=athlon-mp -g -O0 -Wall -D_USE_XOPEN -D__unix__

+ 

+ OBJ_DIR=.

+@@ -33,7 +31,7 @@
+ 

+ museq:	$(OBJ)

+ 	rm -f $(TARGET)/$@

+-	$(CC) -o $(TARGET)/$@ \

++	$(CC) $(LDFLAGS) -o $(TARGET)/$@ \

+ 	$(OBJ) \

+ 	-pipe -Wall -lm 

+ 	mv museq dialign-tx

diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch
new file mode 100644
index 000000000000..21f576f07052
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch
@@ -0,0 +1,11 @@
+--- a/source/diag.c
++++ b/source/diag.c
+@@ -958,7 +958,7 @@
+  * The pointer returned (and the ones included in the struct)  
+  * has to be deallocted explicitely from memory. 
+  */ 
+-inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
++static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
+ 				struct prob_dist *pdist, struct seq* seq1,  
+ 				struct seq* seq2, struct alignment *algn, 
+ 				 long double **tmp_dist, int round) { 
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
index a8388d03232f..d82a5bf4be33 100644
--- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
@@ -1,5 +1,5 @@
---- source/museq.c
-+++ source/museq.c
+--- a/source/museq.c
++++ b/source/museq.c
 @@ -38,6 +38,7 @@
  //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
  //		 struct prob_dist *pdist);