commit: 9944df7ebb74c77f354dba013b5ac9d4bdab0c8f Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> AuthorDate: Fri Feb 6 21:15:40 2015 +0000 Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org> CommitDate: Fri Feb 6 21:15:40 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9944df7e
Removed all patches, setting CXXFLAGS and such via emake now. Fixed the wrong manpage categories. --- sci-biology/bowtie/ChangeLog | 6 +++- sci-biology/bowtie/bowtie-1.1.1.ebuild | 18 ++++++----- sci-biology/bowtie/bowtie-2.2.4.ebuild | 19 +++++------ .../bowtie/files/bowtie-1.1.1-buildsystem.patch | 37 ---------------------- .../bowtie/files/bowtie-2.2.4-buildsystem.patch | 23 -------------- 5 files changed, 23 insertions(+), 80 deletions(-) diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index 1a636c5..f3d98e2 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/bowtie -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Feb 2015; Ted Tanberry <[email protected]> bowtie-1.1.1.ebuild, + bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build + system bugs + 28 Sep 2013; Justin Lecher <[email protected]> bowtie-2.1.0.ebuild: Exchange common variables, fix SRC_URI diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild index f152518..bc6d514 100644 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -19,16 +19,20 @@ IUSE="examples" DEPEND="app-arch/unzip" RDEPEND="" -PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) src_prepare() { - epatch ${PATCHES[@]} + # Suppress useless -Wall pollution + sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile } src_compile() { - unset CFLAGS emake \ - CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS}" } @@ -39,10 +43,8 @@ src_install() { exeinto /usr/libexec/${PN} doexe scripts/* - newman MANUAL ${PN} - dodoc AUTHORS NEWS TUTORIAL doc/README - docinto html - dodoc doc/{manual.html,style.css} + newman MANUAL ${PN}.1 + einstalldocs if use examples; then insinto /usr/share/${PN} diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild index 4b518ca..d8059fc 100644 --- a/sci-biology/bowtie/bowtie-2.2.4.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild @@ -23,16 +23,15 @@ DEPEND="${RDEPEND} S="${WORKDIR}/${PN}2-${PV}" -PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) - -src_prepare() { - epatch ${PATCHES[@]} -} +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) src_compile() { - unset CFLAGS emake \ - CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ EXTRA_FLAGS="${LDFLAGS}" \ RELEASE_FLAGS="${CXXFLAGS} -msse2" } @@ -43,10 +42,8 @@ src_install() { exeinto /usr/libexec/${PN}2 doexe scripts/* - newman MANUAL ${PN}2.2 - dodoc AUTHORS NEWS TUTORIAL - docinto html - dodoc doc/{manual.html,style.css} + newman MANUAL ${PN}2.1 + einstalldocs if use examples; then insinto /usr/share/${PN}2 diff --git a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch deleted file mode 100644 index 9563a33..0000000 --- a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch +++ /dev/null @@ -1,37 +0,0 @@ ---- Makefile -+++ Makefile -@@ -5,16 +5,11 @@ - SEQAN_DIR = SeqAn-1.1 - SEQAN_INC = -I $(SEQAN_DIR) - INC = $(SEQAN_INC) -I third_party --CPP = g++ --CXX = $(CPP) --CC = gcc - HEADERS = $(wildcard *.h) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = 1 - EXTRA_FLAGS = --EXTRA_CFLAGS = - EXTRA_CXXFLAGS = --CFLAGS += $(EXTRA_CFLAGS) - CXXFLAGS += $(EXTRA_CXXFLAGS) - - # Detect Cygwin or MinGW -@@ -127,7 +122,7 @@ - endif - - DEBUG_FLAGS = -O0 -g3 -m64 --RELEASE_FLAGS = -O3 -m64 -+RELEASE_FLAGS = $(CXXFLAGS) - NOASSERT_FLAGS = -DNDEBUG - FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE - -@@ -198,7 +193,7 @@ - $(MM_DEF) \ - $(SHMEM_DEF) - --ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) -+ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS) - DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\"" - RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\"" - diff --git a/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch deleted file mode 100644 index 8b9218b..0000000 --- a/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- Makefile -+++ Makefile -@@ -22,11 +22,6 @@ - # - - INC = --GCC_PREFIX = $(shell dirname `which gcc`) --GCC_SUFFIX = --CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX) --CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX) --CXX = $(CPP) - HEADERS = $(wildcard *.h) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = 0 -@@ -152,7 +147,7 @@ - - DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) - DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" --RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 -+RELEASE_FLAGS = $(CXXFLAGS) - RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" - NOASSERT_FLAGS = -DNDEBUG - FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
