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-rw-r--r--sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild13
-rw-r--r--sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch22
-rw-r--r--sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch20
3 files changed, 49 insertions, 6 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
index 123977916f0..78681265a0b 100644
--- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit toolchain-funcs
@@ -15,12 +15,13 @@ LICENSE="LGPL-2.1"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-S=${WORKDIR}/${MY_P}
+S="${WORKDIR}/${MY_P}"
PATCHES=(
"${FILESDIR}"/${P}-fix-build-system.patch
"${FILESDIR}"/${P}-implicits.patch
"${FILESDIR}"/${P}-modernize.patch
"${FILESDIR}"/${P}-gnu89-inline.patch
+ "${FILESDIR}"/${P}-fno-common.patch
)
src_configure() {
@@ -34,12 +35,12 @@ src_compile() {
src_install() {
dobin source/dialign-tx
- insinto /usr/$(get_libdir)/${PN}/conf
+ insinto /usr/$(get_libdir)/dialign-tx/conf
doins -r conf/.
}
pkg_postinst() {
einfo "The configuration directory is"
- einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf"
- einfo "You will need to pass this to ${PN} on every run."
+ einfo "${EROOT}/usr/$(get_libdir)/dialign-tx/conf"
+ einfo "You will need to pass this to dialign-tx on every run."
}
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
new file mode 100644
index 00000000000..de3104fa0eb
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
@@ -0,0 +1,22 @@
+--- a/source/parameters.c
++++ b/source/parameters.c
+@@ -26,6 +26,8 @@
+
+ extern char *optarg;
+ extern int optind, opterr, optopt;
++
++struct parameters* para;
+ /****************************
+ * PROTEIN DEFAULT VALUES! *
+ ****************************/
+--- a/source/parameters.h
++++ b/source/parameters.h
+@@ -138,7 +138,7 @@
+ /* global variable */
+ /* */
+ /************************************************/
+-struct parameters* para;
++extern struct parameters* para;
+
+
+
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
index 21f576f0705..fc8d0284e6a 100644
--- 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
@@ -1,5 +1,25 @@
+--- a/source/assemble.c
++++ b/source/assemble.c
+@@ -574,7 +574,7 @@
+ * returns a value <0 if there is an non-conflicting overlap
+ * returns 0 in all other non-conflicting cases
+ */
+-inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
++static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
+ // if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!");
+ int s1_1 = dg1->seq_p1.num;
+ int s1_2 = dg1->seq_p2.num;
--- a/source/diag.c
+++ b/source/diag.c
+@@ -312,7 +312,7 @@
+ /**
+ * calculates the overlap weight for the given diag
+ */
+-inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
++void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
+ struct prob_dist *pdist) {
+ int sn1 = dg->seq_p1.num;
+ int sn2 = dg->seq_p2.num;
@@ -958,7 +958,7 @@
* The pointer returned (and the ones included in the struct)
* has to be deallocted explicitely from memory.