From f85051dc1d5a1f6e9e0351abe8c690f3861a628a Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <weaver@gentoo.org>
Date: Mon, 28 Dec 2009 19:14:27 +0000
Subject: QA fixes, including bug 298223 (Portage version: 2.2_rc30/cvs/Linux
 x86_64)

---
 sci-biology/glimmer/ChangeLog                      |  6 ++++-
 .../glimmer/files/glimmer-3.02-glibc210.patch      | 24 ++++++++++++++++++
 sci-biology/glimmer/glimmer-3.02-r1.ebuild         | 29 ++++++++++++++--------
 3 files changed, 48 insertions(+), 11 deletions(-)
 create mode 100644 sci-biology/glimmer/files/glimmer-3.02-glibc210.patch

(limited to 'sci-biology/glimmer')

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index 1dccf70808bd..5780aef0e1c4 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/glimmer
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.3 2009/01/04 01:24:22 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.4 2009/12/28 19:14:26 weaver Exp $
+
+  28 Dec 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/glimmer-3.02-glibc210.patch, glimmer-3.02-r1.ebuild:
+  QA fixes, including bug 298223
 
 *glimmer-3.02-r1 (04 Jan 2009)
 
diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
new file mode 100644
index 000000000000..f6051ec82054
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
@@ -0,0 +1,24 @@
+diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc
+--- glimmer3.02-orig/src/Common/gene.cc	2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/Common/gene.cc	2009-12-28 13:36:06.914974685 +0000
+@@ -443,7 +443,7 @@
+ //  Return a subscript corresponding to character  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (CONVERSION_STRING, tolower (ch));
+    if  (p == NULL)
+diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc
+--- glimmer3.02-orig/src/ICM/icm.cc	2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/ICM/icm.cc	2009-12-28 13:36:44.649451803 +0000
+@@ -1981,7 +1981,7 @@
+ //  model) for character  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (ALPHA_STRING, tolower (Filter (ch)));
+    if  (p == NULL)
diff --git a/sci-biology/glimmer/glimmer-3.02-r1.ebuild b/sci-biology/glimmer/glimmer-3.02-r1.ebuild
index d83c29e0e9a4..8a65fc316036 100644
--- a/sci-biology/glimmer/glimmer-3.02-r1.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02-r1.ebuild
@@ -1,10 +1,12 @@
 # Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r1.ebuild,v 1.1 2009/01/04 01:24:22 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r1.ebuild,v 1.2 2009/12/28 19:14:26 weaver Exp $
 
-inherit versionator
+EAPI="2"
 
-MY_PV=$(delete_all_version_separators)
+inherit eutils
+
+MY_PV=${PV//./}
 
 DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
 HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
@@ -16,26 +18,33 @@ IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
-RDEPEND="!app-crypt/pkcrack
+RDEPEND="app-shells/tcsh
+	!app-crypt/pkcrack
 	!media-libs/libextractor"
 
 S="${WORKDIR}/${PN}${PV}"
 
-src_compile() {
+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"
-	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh
-	cd src
-	emake || die "emake failed"
+	# 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}/${PN}-${PV}-glibc210.patch"
+}
+
+src_compile() {
+	emake -C src || die
 }
 
 src_install() {
 	rm bin/test
-	dobin bin/*
+	dobin bin/* || die
 
 	dodir /usr/share/${PN}/scripts
 	insinto /usr/share/${PN}/scripts
-	doins scripts/*
+	doins scripts/* || die
 
 	dodoc glim302notes.pdf
 }
-- 
cgit v1.2.3-65-gdbad