jobserver fix, #299482, Thanks Myckel Habets

LDFLAGS/CFLAGS etc repected
Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

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
+}