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commit: 2e9f162bea114cf4cdf1b1f37d539592b499032c |
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Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com> |
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AuthorDate: Thu Feb 2 14:35:38 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Thu Feb 2 19:18:51 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2e9f162b |
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|
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sci-biology/infernal: respect EPREFIX |
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|
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Closes: https://github.com/gentoo/gentoo/pull/3774 |
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|
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.../infernal/files/infernal-1.0.2-ldflags.patch | 4 +-- |
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.../infernal/files/infernal-1.0.2-overflows.patch | 4 +-- |
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.../files/infernal-1.0.2-parallel-build.patch | 8 ++--- |
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.../files/infernal-1.0.2-respect-DESTDIR.patch | 16 +++++++++ |
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sci-biology/infernal/infernal-1.0.2-r1.ebuild | 39 ++++++++++------------ |
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5 files changed, 42 insertions(+), 29 deletions(-) |
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|
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diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch |
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index 5bc5bd0..f688dce 100644 |
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--- a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch |
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+++ b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch |
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@@ -2,8 +2,8 @@ Respect LDFLAGS |
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|
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http://bugs.gentoo.org/show_bug.cgi?id=338177 |
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|
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---- src/Makefile.in |
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-+++ src/Makefile.in |
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+--- a/src/Makefile.in |
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++++ b/src/Makefile.in |
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@@ -86,7 +86,7 @@ |
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all: $(PROGS) |
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|
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|
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diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch |
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index b9791fa..67190c4 100644 |
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--- a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch |
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+++ b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch |
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@@ -2,8 +2,8 @@ Fix buffer overflow |
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|
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http://bugs.gentoo.org/show_bug.cgi?id=338179 |
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|
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---- easel/esl_getopts.c |
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-+++ easel/esl_getopts.c |
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+--- a/easel/esl_getopts.c |
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++++ b/easel/esl_getopts.c |
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@@ -1270,7 +1270,7 @@ |
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"Arg looks like option? Use %.24s%.24s if you really mean it.", |
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g->opt[opti].name, *ret_optarg); |
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|
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diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch |
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index 0047425..67ffa6f 100644 |
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--- a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch |
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+++ b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch |
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@@ -2,8 +2,8 @@ Fix parallel build |
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|
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http://bugs.gentoo.org/show_bug.cgi?id=311919 |
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|
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---- Makefile.in |
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-+++ Makefile.in |
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+--- a/Makefile.in |
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++++ b/Makefile.in |
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@@ -82,9 +82,10 @@ |
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all: core |
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|
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@@ -18,8 +18,8 @@ http://bugs.gentoo.org/show_bug.cgi?id=311919 |
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|
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#.PHONY: $(RIGFILTERS) |
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#$(RIGFILTERS): core |
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---- easel/Makefile.in |
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-+++ easel/Makefile.in |
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+--- a/easel/Makefile.in |
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++++ b/easel/Makefile.in |
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@@ -132,7 +132,7 @@ |
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esl_wuss.o |
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|
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|
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diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch |
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new file mode 100644 |
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index 00000000..ea465e5 |
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--- /dev/null |
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+++ b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch |
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@@ -0,0 +1,16 @@ |
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+Build system does not respect DESTDIR by default. |
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+ |
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+--- a/Makefile.in |
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++++ b/Makefile.in |
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+@@ -203,9 +203,9 @@ |
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+ # "make install" installs the programs in BINDIR |
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+ # |
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+ install: |
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+- mkdir -p ${BINDIR} |
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++ mkdir -p $(DESTDIR)${BINDIR} |
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+ for file in $(PROGS); do\ |
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+- cp src/$$file $(BINDIR)/;\ |
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++ cp src/$$file $(DESTDIR)$(BINDIR)/;\ |
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+ done |
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+ # if test -d $(RIGFILTERS); then\ |
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+ # for file in $(RFPROGS); do\ |
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|
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diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild |
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index 3c0ca9a..ad87152 100644 |
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--- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild |
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+++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild |
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@@ -1,10 +1,8 @@ |
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-# Copyright 1999-2014 Gentoo Foundation |
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+# Copyright 1999-2017 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Id$ |
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|
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-EAPI=4 |
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- |
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-inherit eutils |
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+EAPI=6 |
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|
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DESCRIPTION="Inference of RNA alignments" |
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HOMEPAGE="http://infernal.janelia.org/" |
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@@ -15,33 +13,32 @@ SLOT="0" |
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IUSE="mpi" |
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KEYWORDS="amd64 x86" |
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|
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-DEPEND="mpi? ( virtual/mpi )" |
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-RDEPEND="${DEPEND}" |
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+RDEPEND="mpi? ( virtual/mpi )" |
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+DEPEND="${RDEPEND}" |
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|
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-src_prepare() { |
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- epatch \ |
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- "${FILESDIR}"/${P}-parallel-build.patch \ |
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- "${FILESDIR}"/${P}-overflows.patch \ |
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- "${FILESDIR}"/${P}-perl-5.16-2.patch \ |
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- "${FILESDIR}"/${P}-ldflags.patch |
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-} |
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+PATCHES=( |
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+ "${FILESDIR}"/${P}-parallel-build.patch |
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+ "${FILESDIR}"/${P}-overflows.patch |
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+ "${FILESDIR}"/${P}-perl-5.16-2.patch |
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+ "${FILESDIR}"/${P}-ldflags.patch |
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+ "${FILESDIR}"/${P}-respect-DESTDIR.patch |
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+) |
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|
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src_configure() { |
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- econf \ |
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- --prefix="${D}/usr" \ |
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- $(use_enable mpi) |
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+ econf $(use_enable mpi) |
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} |
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|
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src_install() { |
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+ DOCS=( 00README* Userguide.pdf documentation/release-notes ) |
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default |
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|
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- pushd documentation/manpages > /dev/null |
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- for i in *; |
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- do newman ${i} ${i/.man/.1} |
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+ pushd documentation/manpages >/dev/null || die |
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+ local i |
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+ for i in *.man; do |
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+ newman "${i}" "${i/.man/.1}" |
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done |
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- popd > /dev/null |
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+ pushd >/dev/null || die |
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|
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insinto /usr/share/${PN} |
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doins -r benchmarks tutorial intro matrices |
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- dodoc 00README* Userguide.pdf documentation/release-notes/* |
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} |