diff options
| -rw-r--r-- | sci-biology/glimmer/ChangeLog | 9 | ||||
| -rw-r--r-- | sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch | 22 | ||||
| -rw-r--r-- | sci-biology/glimmer/files/glimmer-3.02-ldflags.patch | 88 | ||||
| -rw-r--r-- | sci-biology/glimmer/glimmer-3.02-r2.ebuild | 51 |
4 files changed, 169 insertions, 1 deletions
diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog index 57d422652fd3..8a7763b3ff8f 100644 --- a/sci-biology/glimmer/ChangeLog +++ b/sci-biology/glimmer/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/glimmer # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.6 2010/01/03 14:17:04 pacho Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.7 2010/04/03 22:26:28 jlec Exp $ + +*glimmer-3.02-r2 (03 Apr 2010) + + 03 Apr 2010; Justin Lecher <jlec@gentoo.org> +glimmer-3.02-r2.ebuild, + +files/glimmer-3.02-jobserver-fix.patch: + jobserver fix, #299482, Thanks Myckel Habets + LDFLAGS/CFLAGS etc repected 03 Jan 2010; Pacho Ramos <pacho@gentoo.org> glimmer-3.02-r1.ebuild: amd64 stable, bug 298762 diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch new file mode 100644 index 000000000000..91498b116d12 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch @@ -0,0 +1,22 @@ +diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile +--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100 +@@ -2,12 +2,12 @@ + + + all: +- @ TGT=objs +- @ $(dosubdirs) +- @ TGT=libs +- @ $(dosubdirs) +- @ TGT=progs +- @ $(dosubdirs) ++ @+ TGT=objs ++ @+ $(dosubdirs) ++ @+ TGT=libs ++ @+ $(dosubdirs) ++ @+ TGT=progs ++ @+ $(dosubdirs) + + + install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch new file mode 100644 index 000000000000..0a04fbef1dcc --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch @@ -0,0 +1,88 @@ +diff --git a/src/c_make.gen b/src/c_make.gen +index 414dead..84c3030 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc + #### Do not redefine if (a) passed in on command line, or (b) + #### defined in an environment variable. + +-ifneq "$(origin CC)" "environment" +-CC = cc +-endif +- +-ifneq "$(origin CPPFLAGS)" "environment" +-CPPFLAGS= +-endif +- +-ifneq "$(origin CFLAGS)" "environment" +-CFLAGS = +-endif +- +-ifneq "$(origin CDEFS)" "environment" +-CDEFS = +-endif +- +-ifneq "$(origin CXX)" "environment" +-CXX = g++ +-endif +- +-ifneq "$(origin CXXFLAGS)" "environment" +-CXXFLAGS= +-endif +- +-ifneq "$(origin CXXDEFS)" "environment" +-CXXDEFS= -D__cplusplus +-endif +- +-ifneq "$(origin AR)" "environment" +-AR = ar +-endif +- +-ifneq "$(origin ARFLAGS)" "environment" +-ARFLAGS = rvs +-endif +- +-ifneq "$(origin LDFLAGS)" "environment" +-LDFLAGS = +-endif ++CC ?= cc ++CXX ?= g++ ++CXXFLAGS ?= ++CXXDEFS = -D__cplusplus ++AR ?= ar ++ARFLAGS ?= rvs + + #### Delete default suffix rules + .SUFFIXES: +@@ -359,13 +326,13 @@ $(PROGS): + cd $(LOCAL_OBJ); \ + if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + else \ + cd $(LOCAL_OBJ); \ + if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + fi ; + +diff --git a/src/c_make.glm b/src/c_make.glm +index 0decc17..b82131c 100644 +--- a/src/c_make.glm ++++ b/src/c_make.glm +@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen + + SUBDIRS = Common ICM Glimmer Util + +-CFLAGS = -g -Wall +-CXXFLAGS = -g -Wall +- +-LDFLAGS = -g -lm ++LIBS = -lm + + + #AS_BUILD_DIR =$(LOCAL_WORK) diff --git a/sci-biology/glimmer/glimmer-3.02-r2.ebuild b/sci-biology/glimmer/glimmer-3.02-r2.ebuild new file mode 100644 index 000000000000..36f088001e06 --- /dev/null +++ b/sci-biology/glimmer/glimmer-3.02-r2.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r2.ebuild,v 1.1 2010/04/03 22:26:28 jlec Exp $ + +EAPI="2" + +inherit eutils + +MY_PV=${PV//./} + +DESCRIPTION="An HMM-based microbial gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/" +SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="app-shells/tcsh + !app-crypt/pkcrack + !media-libs/libextractor" + +S="${WORKDIR}/${PN}${PV}" + +src_prepare() { + sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ + -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" + # Fix Makefile to die on failure + sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die + epatch "${FILESDIR}/${P}-glibc210.patch" + epatch "${FILESDIR}/${P}-jobserver-fix.patch" + epatch "${FILESDIR}/${P}-ldflags.patch" +} + +src_compile() { + emake -C src || die +} + +src_install() { + rm bin/test + dobin bin/* || die + + insinto /usr/share/${PN}/scripts + doins scripts/* || die + + dodoc glim302notes.pdf +} |