commit: 4344861bbf45ec0e259a986b19942ce284f93fc9 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Nov 1 18:35:50 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Nov 1 18:35:50 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4344861b
sci-biology/dialign-tx: Fix -fno-common Closes: https://bugs.gentoo.org/707008 Closes: https://bugs.gentoo.org/727966 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild | 13 +++++++------ .../files/dialign-tx-1.0.2-fno-common.patch | 22 ++++++++++++++++++++++ .../files/dialign-tx-1.0.2-gnu89-inline.patch | 20 ++++++++++++++++++++ 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.
