Do not depend on "virtual/libc" (package not in system target).

Package-Manager: portage-2.0.53

14 files changed, 61 insertions, 47 deletions

diff --git a/sci-biology/ariadne/ChangeLog b/sci-biology/ariadne/ChangeLog
index b3dc5a0cbdde..a6374905d27a 100644
--- a/sci-biology/ariadne/ChangeLog
+++ b/sci-biology/ariadne/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/ariadne
-# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ariadne/ChangeLog,v 1.3 2005/05/13 03:08:56 ribosome Exp $
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ariadne/ChangeLog,v 1.4 2006/01/04 23:40:03 ribosome Exp $
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> ariadne-1.3-r1.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
 
   13 May 2005; Olivier Fisette <ribosome@gentoo.org> ariadne-1.3-r1.ebuild:
   Added to x86.
diff --git a/sci-biology/ariadne/ariadne-1.3-r1.ebuild b/sci-biology/ariadne/ariadne-1.3-r1.ebuild
index 39856899f95a..c1947115a6d8 100644
--- a/sci-biology/ariadne/ariadne-1.3-r1.ebuild
+++ b/sci-biology/ariadne/ariadne-1.3-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ariadne/ariadne-1.3-r1.ebuild,v 1.2 2005/05/13 03:08:56 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ariadne/ariadne-1.3-r1.ebuild,v 1.3 2006/01/04 23:40:03 ribosome Exp $
 
 inherit toolchain-funcs
 
@@ -13,8 +13,7 @@ SLOT="0"
 IUSE=""
 KEYWORDS="x86"
 
-DEPEND="virtual/libc
-	>=sci-biology/ncbi-tools-20041020-r1"
+DEPEND=">=sci-biology/ncbi-tools-20041020-r1"
 
 S=${WORKDIR}/SRC-${PV}
 
diff --git a/sci-biology/clustalw-mpi/ChangeLog b/sci-biology/clustalw-mpi/ChangeLog
index e24649b67f85..4dff7b1d64a3 100644
--- a/sci-biology/clustalw-mpi/ChangeLog
+++ b/sci-biology/clustalw-mpi/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/clustalw-mpi
-# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/ChangeLog,v 1.1 2005/11/19 17:24:29 ribosome Exp $
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/ChangeLog,v 1.2 2006/01/04 23:32:49 ribosome Exp $
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
+  clustalw-mpi-0.13.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
 
 *clustalw-mpi-0.13 (19 Nov 2005)
 
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild
index 6888d8d985e8..9fc3293e9f49 100644
--- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild,v 1.1 2005/11/19 17:24:29 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild,v 1.2 2006/01/04 23:32:49 ribosome Exp $
 
 inherit toolchain-funcs
 
@@ -13,8 +13,7 @@ SLOT="0"
 IUSE="mpi_njtree static_pairalign"
 KEYWORDS="~x86"
 
-DEPEND="virtual/libc
-	virtual/mpi"
+DEPEND="virtual/mpi"
 
 src_unpack() {
 	unpack ${A}
diff --git a/sci-biology/clustalw/ChangeLog b/sci-biology/clustalw/ChangeLog
index 3cc6c5888ee1..e168c2caa495 100644
--- a/sci-biology/clustalw/ChangeLog
+++ b/sci-biology/clustalw/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/clustalw
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/ChangeLog,v 1.8 2005/10/11 15:04:33 metalgod Exp $
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/ChangeLog,v 1.9 2006/01/04 23:37:30 ribosome Exp $
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
+  clustalw-1.83-r1.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
 
   11 Oct 2005; Luis Medinas <metalgod@gentoo.org> clustalw-1.83-r1.ebuild:
   Marked Stable on amd64.
diff --git a/sci-biology/clustalw/clustalw-1.83-r1.ebuild b/sci-biology/clustalw/clustalw-1.83-r1.ebuild
index a6f52bb48bcb..64c8a8c521c2 100644
--- a/sci-biology/clustalw/clustalw-1.83-r1.ebuild
+++ b/sci-biology/clustalw/clustalw-1.83-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-1.83-r1.ebuild,v 1.7 2005/10/11 15:04:33 metalgod Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-1.83-r1.ebuild,v 1.8 2006/01/04 23:37:30 ribosome Exp $
 
 inherit toolchain-funcs
 
@@ -13,13 +13,11 @@ SLOT="0"
 KEYWORDS="alpha amd64 ppc ppc-macos ppc64 sparc x86"
 IUSE=""
 
-DEPEND="virtual/libc"
-
-S=${WORKDIR}/${PN}${PV}
+S="${WORKDIR}"/${PN}${PV}
 
 src_unpack(){
 	unpack ${A}
-	cd ${S}
+	cd "${S}"
 	sed -i -e "s/CC	= cc/CC	= $(tc-getCC)/" \
 		-e "s/CFLAGS  = -c -O/CFLAGS  = -c ${CFLAGS}/" \
 		-e "s/LFLAGS	= -O -lm/LFLAGS	= -lm ${CFLAGS}/" makefile || die
diff --git a/sci-biology/gibbs/ChangeLog b/sci-biology/gibbs/ChangeLog
index e107af2efa75..a565decd7193 100644
--- a/sci-biology/gibbs/ChangeLog
+++ b/sci-biology/gibbs/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/gibbs
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/gibbs/ChangeLog,v 1.2 2004/12/23 20:17:57 swegener Exp $
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gibbs/ChangeLog,v 1.3 2006/01/04 23:35:08 ribosome Exp $
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> gibbs-1995.9.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
 
 *gibbs-1995.9 (23 Dec 2004)
 
diff --git a/sci-biology/gibbs/gibbs-1995.9.ebuild b/sci-biology/gibbs/gibbs-1995.9.ebuild
index 5fdc58fc8e75..a38be2db4a07 100644
--- a/sci-biology/gibbs/gibbs-1995.9.ebuild
+++ b/sci-biology/gibbs/gibbs-1995.9.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2004 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/gibbs/gibbs-1995.9.ebuild,v 1.1 2004/12/23 18:39:57 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gibbs/gibbs-1995.9.ebuild,v 1.2 2006/01/04 23:35:08 ribosome Exp $
 
 DESCRIPTION="A Gibbs sampling algorithm for local alignment of subtle sequence signals in multiple protein sequences."
 
@@ -15,18 +15,16 @@ SLOT="0"
 KEYWORDS="x86"
 IUSE=""
 
-DEPEND="virtual/libc"
-
-S=${WORKDIR}/${SRC_NAME}/code
+S="${WORKDIR}"/${SRC_NAME}/code
 
 src_compile() {
 	LIBS="-lm" make -e || die
 }
 
 src_install() {
-	cd ${WORKDIR}/${SRC_NAME}
+	cd "${WORKDIR}"/${SRC_NAME}
 	dobin gibbs purge scan
-	dobin ${FILESDIR}/gibbs-demo
+	dobin "${FILESDIR}"/gibbs-demo
 
 	dodoc README
 
diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
index 94512a3c7217..e5cba4b9c7c0 100644
--- a/sci-biology/hmmer/ChangeLog
+++ b/sci-biology/hmmer/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/hmmer
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.8 2005/09/19 02:36:36 ribosome Exp $
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.9 2006/01/04 23:36:18 ribosome Exp $
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> hmmer-2.3.2-r1.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
 
   19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
   Maintainer changed from Stephen Diener (MIA) to Olivier Fisette.
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
index 965820f5f4b2..4b4f07bc25dd 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild,v 1.5 2005/08/26 19:24:54 r3pek Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild,v 1.6 2006/01/04 23:36:18 ribosome Exp $
 
 DESCRIPTION="Sequence analysis using profile hidden Markov models"
 LICENSE="GPL-2"
@@ -11,8 +11,7 @@ SLOT="0"
 IUSE="pvm threads"
 KEYWORDS="amd64 ~ppc ~ppc-macos ~sparc x86"
 
-DEPEND="virtual/libc
-	pvm? ( sys-cluster/pvm )"
+DEPEND="pvm? ( sys-cluster/pvm )"
 
 src_compile() {
 	./configure \
diff --git a/sci-biology/qrna/ChangeLog b/sci-biology/qrna/ChangeLog
index 87d940609c54..590d7c1381dd 100644
--- a/sci-biology/qrna/ChangeLog
+++ b/sci-biology/qrna/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/qrna
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/ChangeLog,v 1.9 2005/10/17 17:43:24 ribosome Exp $
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/ChangeLog,v 1.10 2006/01/04 23:31:45 ribosome Exp $
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> qrna-2.0.3c.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
 
   17 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -qrna-2.0.3b.ebuild:
   Pruning old version.
diff --git a/sci-biology/qrna/qrna-2.0.3c.ebuild b/sci-biology/qrna/qrna-2.0.3c.ebuild
index 6ec4f356c0d1..02d8e3506552 100644
--- a/sci-biology/qrna/qrna-2.0.3c.ebuild
+++ b/sci-biology/qrna/qrna-2.0.3c.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/qrna-2.0.3c.ebuild,v 1.4 2005/10/17 05:17:02 josejx Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/qrna-2.0.3c.ebuild,v 1.5 2006/01/04 23:31:45 ribosome Exp $
 
 inherit toolchain-funcs
 
@@ -13,8 +13,7 @@ SLOT="0"
 KEYWORDS="amd64 ppc x86"
 IUSE=""
 
-DEPEND="dev-lang/perl
-	virtual/libc"
+DEPEND="dev-lang/perl"
 
 src_compile () {
 	sed -e "s/CC = gcc/CC = $(tc-getCC)/" \
diff --git a/sci-biology/tree-puzzle/ChangeLog b/sci-biology/tree-puzzle/ChangeLog
index 8d50953d8162..02413ad78c63 100644
--- a/sci-biology/tree-puzzle/ChangeLog
+++ b/sci-biology/tree-puzzle/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/tree-puzzle
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/ChangeLog,v 1.8 2005/02/08 01:39:30 j4rg0n Exp $
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/ChangeLog,v 1.9 2006/01/04 23:38:46 ribosome Exp $
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> tree-puzzle-5.2.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
 
   07 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> tree-puzzle-5.1.ebuild,
   tree-puzzle-5.2.ebuild:
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
index f7a85e04d831..870630805c7f 100644
--- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild,v 1.6 2005/02/08 01:39:30 j4rg0n Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild,v 1.7 2006/01/04 23:38:46 ribosome Exp $
 
 inherit toolchain-funcs
 
@@ -13,8 +13,7 @@ SLOT="0"
 KEYWORDS="x86 ~amd64 ~ppc-macos"
 IUSE="mpi"
 
-DEPEND="virtual/libc
-	mpi? ( sys-cluster/lam-mpi )"
+DEPEND="mpi? ( sys-cluster/lam-mpi )"
 
 pkg_setup () {
 	use mpi && [ $(tc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc.