[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/

[Christoph Junghans]

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 <ted.tanberry@×××××.com> bowtie-1.1.1.ebuild,
+  bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build
+  system bugs
+
   28 Sep 2013; Justin Lecher <jlec@g.o> 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