diff options
| -rw-r--r-- | sci-biology/glimmer/ChangeLog | 9 | ||||
| -rw-r--r-- | sci-biology/glimmer/Manifest | 13 | ||||
| -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 |
5 files changed, 177 insertions, 6 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/Manifest b/sci-biology/glimmer/Manifest index 4e1fee0c35b4..6d5f82bef7ff 100644 --- a/sci-biology/glimmer/Manifest +++ b/sci-biology/glimmer/Manifest @@ -2,14 +2,17 @@ Hash: SHA1 AUX glimmer-3.02-glibc210.patch 799 RMD160 92e91e8ce9a39dd004152df712171052b726b0c5 SHA1 1a3f502692923f8b64e252c1b44f9ff68d343505 SHA256 6b0655e796a938990c29070950b36e861bdb6dd3ee1a0ae962590585976e7c5b +AUX glimmer-3.02-jobserver-fix.patch 433 RMD160 31e5cdda57f6efb27c7ccd6101f48c26555b90f9 SHA1 048aef1b2e910a8a0a9a83f9b092098d89239b5b SHA256 19f45973fa230874274d779b03aba73abbecf1344d4a0d795d70256a82036e15 +AUX glimmer-3.02-ldflags.patch 2057 RMD160 f07a863f07d22310e2bea19a07fb3eca6389e5f6 SHA1 2a0c9e52cc5cb0d586db7fc2023dc9a40ae09c9a SHA256 95d391acdbf6d84440c2f3d96791e9f97776b7a248c9546738cc9df88711a28e DIST glimmer302.tar.gz 5637075 RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 SHA1 e2f27fdab82cd8978f1452bfcd4c0287c52b77b7 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 EBUILD glimmer-3.02-r1.ebuild 1270 RMD160 c34cc41382808769b86be0687d0aa6a65564a666 SHA1 0fa5f6ab1f1f03a8629fb386fbbabb8bb4e939b6 SHA256 33e1a316e31371a6194055b7e31bb6122d446ef2352e2af9c8cbc0d945de96a0 -MISC ChangeLog 981 RMD160 a60723dde8873c400c6da693e336bff2f93ea914 SHA1 3480e4336d312265f65d5159bc1251e411dff276 SHA256 04680f86517845f646f6db321b5a7806abd03abca2addcd3a19b834312ba1867 +EBUILD glimmer-3.02-r2.ebuild 1320 RMD160 5b2b9dde910fa6508c0e605916273089e308ae05 SHA1 3db84021cea8289706380f3e0ce155cc7ba32537 SHA256 7582f3176b0580f94be6187121c4ba1e698fa49410e88acd4962cd559a593f7d +MISC ChangeLog 1205 RMD160 80bda639241ec7eba1095b609fecaaf8630bcf5c SHA1 48614baacc88039d6b77c388b535380afe0686e4 SHA256 90bc8bd4437147db7dbcd95f2474bc1b85d7708c65b306382b5cd772af60363b MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) +Version: GnuPG v2.0.14 (GNU/Linux) -iEYEARECAAYFAktApuYACgkQCaWpQKGI+9TTmQCfY6KdnZL1gcdME4xvFE5ASErt -sOwAnRDeU/DSkPeQEBZZdZvUtKtM/HFM -=p1XO +iEYEARECAAYFAku3wJkACgkQgAnW8HDreRbPTQCcDQuY9qnewUyJsQOv+z0mxY3H +3uIAn2KT1PEPQw8touL22p1viIeB5V/i +=LYOS -----END PGP SIGNATURE----- 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 +} |