16 files changed, 0 insertions, 583 deletions
diff --git a/app-sci/staden/ChangeLog b/app-sci/staden/ChangeLog
deleted file mode 100644
index 31d77dc4b9a4..000000000000
--- a/app-sci/staden/ChangeLog
+++ /dev/null
@@ -1,74 +0,0 @@
-# ChangeLog for app-sci/staden
-# Copyright 1999-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/ChangeLog,v 1.12 2004/10/14 14:57:34 ribosome Exp $
-
-  14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> staden-1.4.1-r7.ebuild:
-  Use gcc-getCC/CXX from gcc.eclass rather than ${CC/CXX}.
-
-*staden-1.4.1-r7 (22 Sep 2004)
-
-  22 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -staden-1.4.1-r6.ebuild,
-  +staden-1.4.1-r7.ebuild:
-  Fixed the last "-fPIC" problem in mutlib.
-
-  18 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -staden-1.4.1-r5.ebuild,
-  staden-1.4.1-r6.ebuild:
-  Removing EMBOSS support until some issues are fixed.
-
-  18 Sep 2004; Olivier Fisette <ribosome@gentoo.org> staden-1.4.1-r6.ebuild:
-  Fixed an issue with the EMBOSS tcl/tk GUIs.
-
-  18 Sep 2004; Olivier Fisette <ribosome@gentoo.org> staden-1.4.1-r6.ebuild:
-  Fixed issues with "spin_emboss".
-
-*staden-1.4.1-r6 (18 Sep 2004)
-
-  18 Sep 2004; Olivier Fisette <ribosome@gentoo.org>
-  files/staden-1.4.1-emboss.patch, +staden-1.4.1-r6.ebuild:
-  Documentation builds from souce. Updated course material. Updated external
-  io_lib. Fixed some library issues.
-
-*staden-1.4.1-r5 (17 Sep 2004)
-
-  17 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -staden-1.4.1-r4.ebuild,
-  +staden-1.4.1-r5.ebuild:
-  Now compiles with -fPIC.
-
-*staden-1.4.1-r4 (16 Sep 2004)
-
-  16 Sep 2004; Olivier Fisette <ribosome@gentoo.org>
-  +files/staden-1.4.1-emboss.patch, -staden-1.4.1-r3.ebuild,
-  +staden-1.4.1-r4.ebuild:
-  Patched the "create_emboss_files" program to allow more flexibility.
-
-*staden-1.4.1-r3 (16 Sep 2004)
-
-  16 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -staden-1.4.1-r2.ebuild,
-  +staden-1.4.1-r3.ebuild:
-  Fixed problem with EMBOSS GUIs failing to compile.
-
-*staden-1.4.1-r2 (16 Sep 2004)
-
-  16 Sep 2004; Olivier Fisette <ribosome@gentoo.org>
-  +files/staden-1.4.1-top.patch, -staden-1.4.1-r1.ebuild,
-  +staden-1.4.1-r2.ebuild:
-  Provide prebuilt docs to avoid doc compilation problems and reduce the number
-  of dependencies. Made the course installation optional with the "doc" "USE"
-  flag.
-
-*staden-1.4.1-r1 (15 Sep 2004)
-
-  15 Sep 2004; Olivier Fisette <ribosome@gentoo.org> +staden-1.4.1-r1.ebuild,
-  -staden-1.4.1.ebuild:
-  Fixed the staden_help program.
-
-*staden-1.4.1 (14 Sep 2004)
-
-  14 Sep 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
-  +files/staden-1.4.1-env, +files/staden-1.4.1-gap4.patch,
-  +files/staden-1.4.1-getopt.patch, +files/staden-1.4.1-iwidgetsrc.new,
-  +files/staden-1.4.1-mutscan.patch, +files/staden-1.4.1-prefinish.patch,
-  +files/staden-1.4.1-tk_utils.patch, +files/staden-1.4.1-tracediff.patch,
-  +staden-1.4.1.ebuild:
-  Initial import.
-
diff --git a/app-sci/staden/Manifest b/app-sci/staden/Manifest
deleted file mode 100644
index f9239c197c5b..000000000000
--- a/app-sci/staden/Manifest
+++ /dev/null
@@ -1,15 +0,0 @@
-MD5 54315bce4993a992c662f089dd7e3a4b staden-1.4.1-r7.ebuild 11081
-MD5 28073a1b6e1bd528e9c794279bd5259a ChangeLog 2706
-MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
-MD5 e908bf4692dd3494ec22f07db2e7a9f5 files/staden-1.4.1-env 225
-MD5 3699a9d368068d835cbd8568d50d23e5 files/staden-1.4.1-gap4.patch 463
-MD5 ccf3b22c1399cd7f80f3f6f1caec2cda files/staden-1.4.1-tracediff.patch 334
-MD5 1026629ee4b47aea8043dd7f35eb2ffe files/staden-1.4.1-staden_help.new 159
-MD5 bd82265e893628c1b46329d77e1f11d8 files/staden-1.4.1-iwidgetsrc.new 445
-MD5 8650f58c55b83838846447c89543255d files/staden-1.4.1-getopt.patch 375
-MD5 7717f77ecd800d0b3049974db3fcd0a9 files/staden-1.4.1-prefinish.patch 362
-MD5 a8ceefd2b3b2c1c0053a504561635379 files/staden-1.4.1-mutscan.patch 328
-MD5 cd40ea0a473054769a0963e708257f98 files/digest-staden-1.4.1-r7 213
-MD5 708ea4c4b4cbc7e2b6b88b5a09e1b564 files/staden-1.4.1-top.patch 230
-MD5 ea4a62a1cd5070014d2c9352eeecf06a files/staden-1.4.1-tk_utils.patch 368
-MD5 8f13c224bf3c586a6436c39906b780ec files/staden-1.4.1-emboss.patch 1312
diff --git a/app-sci/staden/files/digest-staden-1.4.1-r7 b/app-sci/staden/files/digest-staden-1.4.1-r7
deleted file mode 100644
index f11f83bbe989..000000000000
--- a/app-sci/staden/files/digest-staden-1.4.1-r7
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 a5588b112df2071d17f256e94777def5 staden-src-rel-1-4-1.tar.gz 21889519
-MD5 d6e739e823bff99e61007ded4cb71f79 course-1.1.tar.gz 5271133
-MD5 9550e01cd954c3f672d2a500e051fa53 staden-1.4.1-missing-doc.tar.bz2 63825
diff --git a/app-sci/staden/files/staden-1.4.1-emboss.patch b/app-sci/staden/files/staden-1.4.1-emboss.patch
deleted file mode 100644
index 29639cd6c929..000000000000
--- a/app-sci/staden/files/staden-1.4.1-emboss.patch
+++ /dev/null
@@ -1,40 +0,0 @@
---- src/spin2_emboss/create_emboss_files.tcl.old	2003-06-09 07:25:27.000000000 -0400
-+++ src/spin2_emboss/create_emboss_files.tcl	2004-09-18 14:18:53.782043416 -0400
-@@ -2,15 +2,15 @@
- # dialogue for each program along with the necessary menu definitions.
- #
- # These will be written to
--#     $STADENROOT/lib/spin2_emboss/acdtcl/*
--#     $STADENROOT/tables/emboss_menu
-+#     $OUTDIR/lib/spin2_emboss/acdtcl/*
-+#     $OUTDIR/emboss_menu
- #
- # To run it, simply run this script. NOTE that it requires DISPLAY to be set
- # correctly, even though no graphics are obvious. This is because certain
- # widgets are temporarily created in order to query their pathnames.
- 
--set acdtcl_dir acdtcl
--set menu_file  ../../tables/emboss_menu
-+set acdtcl_dir $env(OUTDIR)
-+set menu_file  $env(OUTDIR)/emboss_menu
- 
- tkinit
- wm withdraw .
-@@ -53,7 +53,7 @@
- 	if {$errorCode != "NONE"} {
- 	    puts "ERROR: could not parse"
- 	    puts $errorInfo
--	    continue	   
-+	    continue
- 	}
- 	if {[string match "lappend *e_menu(*" $menu_line] || \
- 	    [string match "set *e_prog(*" $menu_line]} {
-@@ -85,7 +85,7 @@
-         }
-         append out [list add_cascade "Emboss.$i"] { $::EMBOSS::init 4} \n
- 	set e_casc(Emboss.$i) 1
--	
-+
- 	if {[array names e_menu $prefix$i.*] != ""} {
- 	    set out [_do_emboss_menu $out $prefix$i.]
- 	}
diff --git a/app-sci/staden/files/staden-1.4.1-env b/app-sci/staden/files/staden-1.4.1-env
deleted file mode 100644
index 3c2697f6dc3a..000000000000
--- a/app-sci/staden/files/staden-1.4.1-env
+++ /dev/null
@@ -1,8 +0,0 @@
-STADENROOT=/opt/staden
-MACHINE=linux
-STADTABL=/opt/staden/tables
-STADLIB=/opt/staden/lib
-PATH=/opt/staden/linux-bin
-LD_LIBRARY_PATH=/opt/staden/lib/linux-binaries
-TCL_LIBRARY=/opt/staden/lib/tcl
-TK_LIBRARY=/opt/staden/lib/tk
diff --git a/app-sci/staden/files/staden-1.4.1-gap4.patch b/app-sci/staden/files/staden-1.4.1-gap4.patch
deleted file mode 100644
index 2a7773af60cf..000000000000
--- a/app-sci/staden/files/staden-1.4.1-gap4.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/gap4/Makefile.old	2003-12-01 12:30:19.000000000 -0500
-+++ src/gap4/Makefile	2004-09-12 21:52:57.275756696 -0400
-@@ -184,7 +184,7 @@
- 	$(MKDEFL) $@ $(GAPOBJS)
- 
- $(O)/gap4sh:	$(GAPOBJS) $(GAPOBJS2)
--	$(CXX) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(GAPOBJS) $(GAPOBJS2) $(GAP4SH_LIBS) $(CXX_DEP) $(F77_DEP)
-+	$(CXX) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(GAPOBJS) $(GAPOBJS2) $(GAP4SH_LIBS) $(CXX_DEP) $(F77_DEP) -L../lib/linux-binaries
- 
- COPYDBOBJS=\
-         $(GAPDB_LOW) \
diff --git a/app-sci/staden/files/staden-1.4.1-getopt.patch b/app-sci/staden/files/staden-1.4.1-getopt.patch
deleted file mode 100644
index e3aa06dcc137..000000000000
--- a/app-sci/staden/files/staden-1.4.1-getopt.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/Misc/misc.h.old	2003-06-09 07:24:36.000000000 -0400
-+++ src/Misc/misc.h	2004-09-10 10:37:54.593326848 -0400
-@@ -7,8 +7,8 @@
- 
- #include "os.h"
- #include "xalloc.h"
-+#include <getopt.h>
- 
--extern int getopt( int argc, char* const argv[], const char* optstring );
- extern int is_directory(char * fn);
- extern int is_file(char * fn);
- extern int file_exists(char * fn);
diff --git a/app-sci/staden/files/staden-1.4.1-iwidgetsrc.new b/app-sci/staden/files/staden-1.4.1-iwidgetsrc.new
deleted file mode 100644
index 1beae9513b51..000000000000
--- a/app-sci/staden/files/staden-1.4.1-iwidgetsrc.new
+++ /dev/null
@@ -1,16 +0,0 @@
-set tcl_pkgPath ""
-#if {"$tcl_platform(platform)" == "windows"} {
-#  load_package itcl33
-#  load_package itk33
-#} else {
-load_package itcl3.3
-load_package itk3.3
-#}
-load_package iwidgets
-# Can't use package require as it will still attempt to use /usr/local copy.
-#namespace import itk::*
-#source $env(STADLIB)/itcl3.3/itcl.tcl
-source $env(STADLIB)/iwidgets/iwidgets.tcl
-package require Iwidgets
-namespace import itcl::*
-namespace import itk::*
diff --git a/app-sci/staden/files/staden-1.4.1-mutscan.patch b/app-sci/staden/files/staden-1.4.1-mutscan.patch
deleted file mode 100644
index d768bf2f39a2..000000000000
--- a/app-sci/staden/files/staden-1.4.1-mutscan.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- src/mutscan/Makefile.old	2003-06-09 07:25:30.000000000 -0400
-+++ src/mutscan/Makefile	2004-09-12 22:04:11.490260512 -0400
-@@ -19,7 +19,11 @@
- HLIBS=\
- 	$(TEXTUTILS_LIB) \
- 	$(MUT_LIB) \
--	$(IOLIB_LIB)
-+	$(IOLIB_LIB) \
-+	-lmisc \
-+	-lseq_utils \
-+	-ltk_utils \
-+	-L../lib/linux-binaries
- 
- OBJSD	= \
- 	$(MUTSCANBIN)/main.o \
diff --git a/app-sci/staden/files/staden-1.4.1-prefinish.patch b/app-sci/staden/files/staden-1.4.1-prefinish.patch
deleted file mode 100644
index bf99154c8032..000000000000
--- a/app-sci/staden/files/staden-1.4.1-prefinish.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- src/prefinish/Makefile.old	2004-01-14 05:29:14.000000000 -0500
-+++ src/prefinish/Makefile	2004-09-12 21:50:01.014552472 -0400
-@@ -53,7 +53,13 @@
- 	$(GAP_LIB) \
- 	$(TEXTUTILS_LIB) \
- 	$(MISC_LIB) \
--	$(TCL_LIB)
-+	$(TCL_LIB) \
-+	-lmutlib \
-+	-lprimer3 \
-+	-ltk_utils \
-+	-lread \
-+	-lseq_utils \
-+	-L../lib/linux-binaries
- 
- ISOBJS=\
- 	$(O)/insert_size_dist.o
diff --git a/app-sci/staden/files/staden-1.4.1-staden_help.new b/app-sci/staden/files/staden-1.4.1-staden_help.new
deleted file mode 100644
index 4e371d848ce6..000000000000
--- a/app-sci/staden/files/staden-1.4.1-staden_help.new
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-
-[ -z ${BROWSER} ] \
-	&& echo 'staden_help: "BROWSER" environment variable not set.' && exit 1 \
-	|| ${BROWSER} ${STADENROOT}/doc/documentation.html
diff --git a/app-sci/staden/files/staden-1.4.1-tk_utils.patch b/app-sci/staden/files/staden-1.4.1-tk_utils.patch
deleted file mode 100644
index b1ffa2e6e4b9..000000000000
--- a/app-sci/staden/files/staden-1.4.1-tk_utils.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/tk_utils/Makefile.old	2003-06-09 09:54:59.000000000 -0400
-+++ src/tk_utils/Makefile	2004-09-12 19:50:18.367480800 -0400
-@@ -97,7 +97,9 @@
- 
- STASH_LIBS = \
- 	$(TKUTILS_LIB) \
--	$(TK_LIB)
-+	$(TK_LIB) \
-+	$(IOLIB_LIB) \
-+	$(MISC_LIB)
- 
- $(TKUTILSBIN)/stash: $(STASH_OBJS)
- 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMWIN) $(STASH_OBJS) $(STASH_LIBS) $(LIBSC)
diff --git a/app-sci/staden/files/staden-1.4.1-top.patch b/app-sci/staden/files/staden-1.4.1-top.patch
deleted file mode 100644
index d5e062aaef87..000000000000
--- a/app-sci/staden/files/staden-1.4.1-top.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Makefile.old	2003-06-24 11:44:29.000000000 -0400
-+++ Makefile	2004-09-15 23:38:22.194325168 -0400
-@@ -30,8 +30,6 @@
- 
- all:
- 	cd src; $(MAKE) all
--	cd doc; $(MAKE) all
--	cd course; $(MAKE) all
- 
- install:
- 	cd src; $(MAKE) $@
diff --git a/app-sci/staden/files/staden-1.4.1-tracediff.patch b/app-sci/staden/files/staden-1.4.1-tracediff.patch
deleted file mode 100644
index ae24721986d0..000000000000
--- a/app-sci/staden/files/staden-1.4.1-tracediff.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- src/tracediff/Makefile.old	2003-06-09 07:25:23.000000000 -0400
-+++ src/tracediff/Makefile	2004-09-12 21:58:06.157799488 -0400
-@@ -19,7 +19,11 @@
- HLIBS=\
- 	$(TEXTUTILS_LIB) \
- 	$(MUT_LIB) \
--	$(IOLIB_LIB)
-+	$(IOLIB_LIB) \
-+	-lmisc \
-+	-lseq_utils \
-+	-ltk_utils \
-+	-L../lib/linux-binaries
- 
- OBJSD	= \
- 	$(TRACEDIFFBIN)/main.o \
diff --git a/app-sci/staden/metadata.xml b/app-sci/staden/metadata.xml
deleted file mode 100644
index e9391a41a838..000000000000
--- a/app-sci/staden/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>ribosome@gentoo.org</email>
-		<name>Olivier Fisette</name>
-	</maintainer>
-	<herd>sci</herd>
-</pkgmetadata>
diff --git a/app-sci/staden/staden-1.4.1-r7.ebuild b/app-sci/staden/staden-1.4.1-r7.ebuild
deleted file mode 100644
index f0b87076a164..000000000000
--- a/app-sci/staden/staden-1.4.1-r7.ebuild
+++ /dev/null
@@ -1,319 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/staden-1.4.1-r7.ebuild,v 1.2 2004/10/14 14:57:34 ribosome Exp $
-
-inherit eutils gcc
-
-DESCRIPTION="The Staden Package - Biological sequence handling and analysis"
-HOMEPAGE="http://${PN}.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${PN}-src-rel-${PV//./-}.tar.gz
-	doc? mirror://sourceforge/${PN}/course-1.1.tar.gz
-	mirror://gentoo/${P}-missing-doc.tar.bz2"
-LICENSE="${PN}"
-
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="doc"
-
-DEPEND="${RDEPEND}
-	dev-lang/perl
-	media-gfx/imagemagick
-	virtual/emacs
-	virtual/tetex"
-
-RDEPEND="app-shells/ksh
-	dev-lang/tcl
-	dev-lang/tk
-	dev-libs/io_lib
-	=dev-tcltk/itcl-3.2*
-	dev-tcltk/iwidgets
-	media-libs/libpng
-	virtual/x11"
-
-S=${WORKDIR}/${PN}-src-rel-${PV//./-}
-
-pkg_setup() {
-	# Check for a Fortran compiler.
-	if ! which ${F77:-g77} &> /dev/null; then
-		echo
-		eerror "The Fortran compiler \"${F77:-g77}\" could not be found on your system."
-		if [ -z ${F77} ] || [ ${F77} = g77 ]; then
-			eerror 'Please reinstall "sys-devel/gcc" with the "f77" "USE" flag enabled.'
-		else
-			eerror 'Please make sure the variable ${F77} is set to the name of a valid'
-			eerror 'Fortran compiler installed on your system. Make sure this executable'
-			eerror 'is in a directory included in "PATH", and that the corresponding'
-			eerror '"USE" flag is set if applicable (for example "ifc" if you use the'
-			eerror 'Intel Fortran Compiler).'
-		fi
-		die "Fortran compiler not found."
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-
-	# The following Makefiles are more or less broken. Libraries are missing,
-	# or their directories are not included, or the variables are not set
-	# correctly and must be replaced by hardcoded library names. The
-	# top-level Makefile is also changed to avoid compiling documentation
-	# (which is provided prebuilt because of numerous compilation/dead links
-	# problems).
-	cd ${S}
-	einfo "Patching Staden Package Makefiles:"
-	epatch ${FILESDIR}/${P}-top.patch
-	epatch ${FILESDIR}/${P}-gap4.patch
-	epatch ${FILESDIR}/${P}-mutscan.patch
-	epatch ${FILESDIR}/${P}-prefinish.patch
-	epatch ${FILESDIR}/${P}-tk_utils.patch
-	epatch ${FILESDIR}/${P}-tracediff.patch
-	cd ${S}/src/mk
-	# Remove the "-fpic" flag. This will be replaced by "-fPIC".
-	sed -i -e 's/SHLIB_CFLAGS		= -fpic/SHLIB_CFLAGS		= /' linux.mk \
-		&& einfo "Successfully applied sed script to patch linux.mk." \
-		|| eerror "Failed to apply sed script to patch linux.mk."
-	cd ${S}/src/mutlib
-	cd ${S}
-	echo
-
-
-	einfo "Patching Staden Package code:"
-
-	# "getopt" is incorrectly included as an extern (for Win32 compatibility).
-	epatch ${FILESDIR}/${P}-getopt.patch
-
-	# The "create_emboss_files" program needs more flexibility to respect the
-	# Gentoo FSH.
-	epatch ${FILESDIR}/${P}-emboss.patch
-
-	# The original iwidgetsrc crashes...
-	einfo 'Replacing broken iwidgetsrc'
-	cp ${FILESDIR}/${P}-iwidgetsrc.new ${S}/tables/iwidgetsrc
-
-	# Netscape is not a good default browser (security masked in Portage).
-	# Use documentation.html rather than staden_home.html as the top-level
-	# hypertext documentation file.
-	einfo 'Replacing old staden_help script'
-	cp ${FILESDIR}/${P}-staden_help.new ${S}/src/scripts/staden_help
-	chmod +x ${S}/src/scripts/staden_help
-	echo
-
-	# The documentation building process is broken on Gentoo, mainly because
-	# incorrect program locations are assumed.
-	einfo "Patching Staden Package documentation build system:"
-
-	# Documentation build process cannot find "update-nodes.el".
-	cd ${S}/doc/manual/tools
-	sed -i -e 's%emacs -batch $1 -l ${DOCDIR:-.}/tools/update-nodes.el%emacs -batch $1 -l ${DOCDIR:-..}/manual/tools/update-nodes.el%' update-nodes \
-		&& einfo "Successfully applied sed script to patch update-nodes." \
-		|| eerror "Failed to apply sed script to patch update-nodes."
-
-	# Perl scripts search for "pearl" in "/usr/local".
-	for SCRIPT in *.pl texi2html; do
-		sed -i -e 's%/usr/local/bin/perl%/usr/bin/perl%' ${SCRIPT} \
-			&& einfo "Successfully applied sed script to patch ${SCRIPT}." \
-			|| eerror "Failed to apply sed script to patch ${SCRIPT}."
-	done
-
-	# The "convert" tool from Imagemagick is searched for in "/usr/X11R6".
-	sed -i -e 's%/usr/X11R6/bin/convert%/usr/bin/convert%' make_ps \
-		&& einfo "Successfully applied sed script to patch make.ps." \
-		|| eerror "Failed to apply sed script to patch make.ps."
-
-	# Solves issues with images in the exercise* texi files.
-	cd ${S}/course/texi
-	for FILE in exercise*.texi; do
-		sed -i -e 's/,,8in}/,,8in,,eps}/' ${FILE} && \
-			sed -i -e 's/,6in}/,6in,,,eps}/' ${FILE} \
-			&& einfo "Successfully applied sed scripts to patch ${FILE}." \
-			|| eerror "Failed to apply sed scripts to patch ${FILE}."
-	done
-	echo
-
-	# "CFLAGS" and "FFLAGS" need to be set to the user's values in the build
-	# system global Makefile. We also want only "-fPIC" shared libraries.
-	einfo "Applying user-defined compilation/linking flags:"
-	cd ${S}/src/mk
-	sed -i -e "s/COPT		= -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk \
-		&& einfo "Successfully applied sed script to set CFLAGS." \
-		|| eerror "Failed to apply sed script to set CFLAGS."
-	sed -i -e "s/FOPT		= -O2 -g3 -DNDEBUG/FOPT = ${FFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk \
-		&& einfo "Successfully applied sed script to set FFLAGS." \
-		|| eerror "Failed to apply sed script to set FFLAGS."
-}
-
-src_compile() {
-	# "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the
-	# Staden Package build process. "O" is redefined on the command line to
-	# avoid a conflict between Portage and the Staden Package build system,
-	# which both use this variable. (In Portage, its value is the directory
-	# containing the current ebuild, while in the Staden Package build system
-	# it is set to the directory containing the compiler object files.)
-	# Compiler program names also need to be specified to override the
-	# incorrect hardcoded ones.
-
-	# Compile executables and libraries.
-	make \
-		STADENROOT="${S}" \
-		SRCROOT="${S}/src" \
-		MACHINE="linux" \
-		JOB="all" \
-		O="linux-binaries" \
-		CC=$(gcc-getCC) \
-		CXX=$(gcc-getCXX) \
-		F77=${F77:-g77} \
-		|| die "Package compilation failed."
-
-	# Build documentation.
-	cd ${S}/doc
-	make \
-		STADENROOT="${S}" \
-		SRCROOT="${S}/src" \
-		MACHINE="linux" \
-		JOB="all" \
-		O="linux-binaries" \
-		CC=$(gcc-getCC) \
-		CXX=$(gcc-getCXX) \
-		F77=${F77:-g77} \
-		|| die "Package compilation failed."
-
-	# Moves executables in "${S}/linux-bin" and libraries to ${S}/lib.
-	cd ${S}
-	make \
-		STADENROOT="${S}" \
-		SRCROOT="${S}/src" \
-		MACHINE="linux" \
-		JOB="all" \
-		O="linux-binaries" \
-		install || die "Package pre-installation failed."
-
-	# Remove Makefiles from directories which will be manually installed.
-	rm ${S}/lib/Makefile
-	rm ${S}/demo/Makefile
-	rm ${S}/tables/Makefile
-	rm ${S}/userdata/Makefile
-
-	# Remove trashed "linux-binaries" file and replace it by a directory
-	# containing the appropriate libraries. Remove libread since an updated
-	# version is included in "dev-libs/io_lib".
-	rm ${S}/lib/linux-binaries
-	rm ${S}/src/lib/linux-binaries/libread.so
-	mkdir ${S}/lib/linux-binaries
-	cp ${S}/src/lib/linux-binaries/* ${S}/lib/linux-binaries
-
-	# Delete the binaries already included in "dev-libs/io_lib".
-	for FILE in convert_trace \
-		extract_seq \
-		get_comment \
-		index_tar \
-		makeSCF \
-		scf_{dump,info,update} \
-		trace_dump; do
-		rm ${S}/linux-bin/${FILE}
-	done
-
-	# These won't be found if they are not symlinked in the lib dir.
-	ln -s /usr/$(get_libdir)/libitcl3.2.so ${S}/lib/itcl3.3/libitcl3.3.so
-	ln -s /usr/$(get_libdir)/libitk3.2.so ${S}/lib/itk3.3/libitk3.3.so
-
-	# Remove the prebuilt EMBOSS tcl/tk GUIs.
-	rm ${S}/tables/emboss_menu
-	rm -r ${S}/lib/spin2_emboss/acdtcl
-	rm -r ${S}/lib/spin_emboss/acdtcl
-
-	# Patch just built hypertext documentation.
-	cd ${S}/doc/manual
-	for FILE in *.html; do
-		sed -i -e 's%<a href="../staden_home.html"><img src="i/nav_home.gif" alt="home"></a>%%' ${FILE}
-	done
-	cd ${S}/doc/scripting_manual
-	for FILE in *.html; do
-		sed -i -e 's%<a href="../staden_home.html"><img src="i/nav_home.gif" alt="home"></a>%%' ${FILE}
-	done
-}
-
-src_install() {
-	# Executables and libraries
-	mkdir -p ${D}/opt/${PN}
-
-	for FILE in ${S}/src/lib/linux-binaries/*; do
-		dolib ${FILE}
-	done
-
-	mv ${S}/linux-bin ${D}/opt/${PN}/linux-bin
-	mv ${S}/lib ${D}/opt/${PN}/lib
-
-	# Shared files
-	mv ${S}/demo ${D}/opt/${PN}
-	mv ${S}/tables ${D}/opt/${PN}
-	mv ${S}/userdata ${D}/opt/${PN}
-
-	# "env" file for setting paths to Staden Package root, libraries, tables...
-	insinto /etc/env.d
-	newins ${FILESDIR}/${P}-env 27${PN}
-
-	# Basic documentation
-	insinto /opt/${PN}/doc
-	doins ${S}/{ChangeLog,doc/Acknowledgements}
-	newins ${S}/doc/emboss.txt README.emboss
-
-	# Man pages
-	doman ${S}/doc/manual/man/man*/*
-
-	# Hypertext documentation
-	insinto /opt/${PN}/doc/manual
-	doins ${S}/doc/manual/*unix*.{gif,html,index}
-	insinto /opt/${PN}/doc/scripting_manual
-	doins ${S}/doc/scripting_manual/*.html
-	insinto /opt/${PN}/doc/manual/i
-	doins ${S}/doc/manual/i/*
-	insinto /opt/${PN}/doc/scripting_manual/i
-	doins ${S}/doc/scripting_manual/i/*
-
-	# Missing hypertext documentation
-	insinto /opt/${PN}/doc
-	doins ${WORKDIR}/${P}-missing-doc/documentation.html
-	insinto /opt/${PN}/doc/misc
-	doins ${WORKDIR}/${P}-missing-doc/misc/*
-	insinto /opt/${PN}/doc/misc/i
-	doins ${S}/doc/manual/i/*
-
-	# Printable manuals and articles
-	insinto /opt/${PN}/doc
-	newins ${S}/doc/gkb547_gml.pdf Staden1998.pdf
-	newins ${S}/doc/manual/manual_unix.dvi manual.dvi
-	newins ${S}/doc/manual/manual_unix.ps manual.ps
-	newins ${S}/doc/manual/mini_unix.ps mini_manual.ps
-	newins ${S}/doc/scripting_manual/scripting.dvi scripting_manual.dvi
-	newins ${S}/doc/scripting_manual/scripting.ps scripting_manual.ps
-
-	# A short course in printable format, along with example data
-	if use doc; then
-		mkdir -p ${D}/opt/${PN}/course
-		mv ${WORKDIR}/course-1.1/data ${D}/opt/${PN}/course/data
-		insinto /opt/${PN}/course
-		doins ${WORKDIR}/course-1.1/README
-		newins ${WORKDIR}/course-1.1/unix_docs/mutation_talk.ppt course_mutation_detection_diapos.pdf
-		newins ${WORKDIR}/course-1.1/unix_docs/course_unix.pdf course_project_management.pdf
-		newins ${WORKDIR}/course-1.1/unix_docs/mutation_notes.pdf course_mutation_detection.pdf
-	fi
-}
-
-pkg_postinst() {
-	echo
-	ewarn 'Known issues:'
-	ewarn
-	ewarn 'The help browser integrated in the GUI applications reports missing'
-	ewarn 'files when following hyperlinks on the main documentation page. This'
-	ewarn 'seems to be a problem in the Staden Package help browser. You might'
-	ewarn 'want to use your favorite browser instead of the integrated one to'
-	ewarn 'read the documentation.'
-	ewarn
-	ewarn 'The GUI programs may crash when bringing up the font selection'
-	ewarn 'dialog. This problem is related to the presence of certain'
-	ewarn 'fonts in "FontPath". If you experience this problem, try using'
-	ewarn '"strace" to identify the problematic font(s) and either uninstall'
-	ewarn 'them or remove the directory they are in from "FontPath" by'
-	ewarn 'editing your X server configuration file.'
-	echo
-}