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authorDavid Seifert <soap@gentoo.org>2017-12-24 22:09:33 +0100
committerDavid Seifert <soap@gentoo.org>2017-12-24 22:23:36 +0100
commit470054f8e4bca944eff4bed8b471a088d2927a00 (patch)
tree8a08951650076a955cca1bfb62228a12c687e658 /sci-biology
parentsys-auth/polkit: hppa stable wrt bug #632492 (diff)
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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
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild45
-rw-r--r--sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch24
-rw-r--r--sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch11
-rw-r--r--sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch4
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 00000000000..123977916f0
--- /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 00000000000..cbfd458043c
--- /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 00000000000..21f576f0705
--- /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 a8388d03232..d82a5bf4be3 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);