commit: 470054f8e4bca944eff4bed8b471a088d2927a00 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Dec 24 21:09:33 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Dec 24 21:23:36 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=470054f8
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 sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild | 45 ++++++++++++++++++++++ .../files/dialign-tx-1.0.2-fix-build-system.patch | 24 ++++++++++++ .../files/dialign-tx-1.0.2-gnu89-inline.patch | 11 ++++++ .../files/dialign-tx-1.0.2-implicits.patch | 4 +- 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);
