Removing EMBOSS support for now - to many issues.

4 files changed, 8 insertions, 216 deletions

diff --git a/app-sci/staden/ChangeLog b/app-sci/staden/ChangeLog
index 92ca997e5a72..49f2533a7e27 100644
--- a/app-sci/staden/ChangeLog
+++ b/app-sci/staden/ChangeLog
@@ -1,6 +1,10 @@
 # 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 1.9 2004/09/18 23:13:40 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/ChangeLog,v 1.10 2004/09/19 00:57:09 ribosome Exp $
+
+  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.
diff --git a/app-sci/staden/files/digest-staden-1.4.1-r5 b/app-sci/staden/files/digest-staden-1.4.1-r5
deleted file mode 100644
index eb3556875249..000000000000
--- a/app-sci/staden/files/digest-staden-1.4.1-r5
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 a5588b112df2071d17f256e94777def5 staden-src-rel-1-4-1.tar.gz 21889519
-MD5 c6b5f53c9962b67e5fd3554fb5f05d98 staden-1.4.1-doc.tar.bz2 9025862
-MD5 fecb02d085919e9749bb41771262e1a2 staden-1.4.1-course.tar.bz2 4856880
diff --git a/app-sci/staden/staden-1.4.1-r5.ebuild b/app-sci/staden/staden-1.4.1-r5.ebuild
deleted file mode 100644
index 5554710c45ed..000000000000
--- a/app-sci/staden/staden-1.4.1-r5.ebuild
+++ /dev/null
@@ -1,208 +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-r5.ebuild,v 1.1 2004/09/17 18:25:48 ribosome Exp $
-
-inherit eutils
-
-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
-	mirror://gentoo/${P}-doc.tar.bz2
-	doc? mirror://gentoo/${P}-course.tar.bz2"
-LICENSE="${PN}"
-
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="doc emboss ifc"
-
-DEPEND="${RDEPEND}
-	dev-lang/perl
-	ifc? ( dev-lang/ifc )"
-
-RDEPEND="app-shells/ksh
-	dev-lang/tcl
-	dev-lang/tk
-	=dev-tcltk/itcl-3.2*
-	dev-tcltk/iwidgets
-	media-libs/libpng
-	virtual/x11"
-
-PDEPEND="emboss? ( app-sci/staden-emboss )"
-
-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.'
-		elif [ ${F77} = ifc ] && ! use ifc &> /dev/null; then
-			eerror 'Please set the "ifc" "USE" flag if you want to use the Intel Fortran'
-			eerror 'Compiler to build this package. This will ensure the "dev-lang/ifc"'
-			eerror 'package gets installed on your system.'
-		elif [ ${F77} = ifc ] && use ifc &> /dev/null; then
-			eerror 'Please ensure "ifc" is in a directory referenced in "PATH".'
-		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 referenced by "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
-	echo
-
-
-
-
-	einfo "Patching Staden Package code:"
-	# "getopt" is incorrectly included as an extern (for Win32 compatibility).
-	epatch ${FILESDIR}/${P}-getopt.patch
-	# Compile libraries with fPIC.
-	cd ${S}/src/mk
-	sed -i -e 's/SHLIB_CFLAGS		= -fpic/SHLIB_CFLAGS		= -fPIC/' linux.mk
-	cd ${S}
-	echo
-	echo
-
-	# "CFLAGS" and "FFLAGS" need to be set to the user's values in the build
-	# system global Makefile.
-	einfo "Applying user-defined compilation/linking flags:"
-	cd ${S}/src/mk
-	sed -i -e "s/COPT		= -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"}/" 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 = ${FFLAGS:-"-O2 -g3 -DNDEBUG"}/" global.mk \
-		&& einfo "Successfully applied sed script to set FFLAGS." \
-		|| eerror "Failed to apply sed script to set FFLAGS."
-}
-
-src_compile() {
-	# "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the
-	# Staden Package build process. "O" is redefined on the command line to
-	# avoid a conflict between Portage and the Staden Package build system,
-	# which both use this variable. (In Portage, its value is the directory
-	# containing the current ebuild, while in the Staden Package build system
-	# it is set to the directory containing the compiler object files.)
-	# Compiler program names also need to be specified to override the
-	# incorrect hardcoded ones.
-
-	# Compiles executables and libraries.
-	make \
-		STADENROOT="${S}" \
-		SRCROOT="${S}/src" \
-		MACHINE="linux" \
-		JOB="all" \
-		O="linux-binaries" \
-		CC=${CC:-gcc} \
-		CXX=${CXX:-g++} \
-		F77=${F77:-g77} \
-		|| die "Package compilation failed."
-
-	# Moves executables in "${S}/linux-bin" and libraries to ${S}/lib.
-	make \
-		STADENROOT="${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.
-	rm ${S}/lib/linux-binaries
-	mkdir ${S}/lib/linux-binaries
-	mv ${S}/src/lib/linux-binaries/* ${S}/lib/linux-binaries
-
-	ln -s /usr/lib/libitcl3.2.so ${S}/lib/itcl3.3/libitcl3.3.so
-	ln -s /usr/lib/libitk3.2.so ${S}/lib/itk3.3/libitk3.3.so
-
-	cp ${FILESDIR}/${P}-iwidgetsrc.new ${S}/tables/iwidgetsrc
-
-	epatch ${FILESDIR}/${P}-emboss.patch
-
-	# 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.
-	cp ${FILESDIR}/${P}-staden_help.new ${S}/linux-bin/staden_help
-	chmod +x ${S}/linux-bin/staden_help
-
-	# Remove the prebuilt EMBOSS tcl/tk GUIs.
-	rm ${S}/tables/emboss_menu
-	rm -r ${S}/lib/spin2_emboss/acdtcl
-
-}
-
-src_install() {
-	# Executables and libraries
-	into /opt/${PN}
-	mkdir -p ${D}/opt/${PN}
-	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}
-
-	# Man pages
-	doman ${S}/doc/manual/man/man*/*
-
-	# Documentation
-	mv ${WORKDIR}/doc ${D}/opt/${PN}/doc
-
-	# A short course in printable format along with some data
-	use doc && mv ${WORKDIR}/course ${D}/opt/${PN}/course
-}
-
-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
-}
diff --git a/app-sci/staden/staden-1.4.1-r6.ebuild b/app-sci/staden/staden-1.4.1-r6.ebuild
index 9bd70276695c..a4c23a80ecdc 100644
--- a/app-sci/staden/staden-1.4.1-r6.ebuild
+++ b/app-sci/staden/staden-1.4.1-r6.ebuild
@@ -1,6 +1,6 @@
 # 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-r6.ebuild,v 1.3 2004/09/18 23:13:40 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/staden-1.4.1-r6.ebuild,v 1.4 2004/09/19 00:57:09 ribosome Exp $
 
 inherit eutils
 
@@ -13,7 +13,7 @@ LICENSE="${PN}"
 
 SLOT="0"
 KEYWORDS="~x86"
-IUSE="doc emboss"
+IUSE="doc"
 
 DEPEND="${RDEPEND}
 	dev-lang/perl
@@ -30,8 +30,6 @@ RDEPEND="app-shells/ksh
 	media-libs/libpng
 	virtual/x11"
 
-PDEPEND="emboss? ( app-sci/staden-emboss )"
-
 S=${WORKDIR}/${PN}-src-rel-${PV//./-}
 
 pkg_setup() {
@@ -219,6 +217,7 @@ src_compile() {
 	# 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