Removed obsolete version

(Portage version: 2.0.53)

3 files changed, 5 insertions, 308 deletions

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index d29a778476ce..7989337feb0b 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/staden
-# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.16 2005/12/15 03:57:49 tsunam Exp $
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.17 2006/01/21 18:33:09 ribosome Exp $
+
+  21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -staden-1.5.3.ebuild:
+  Removed obsolete version.
 
   15 Dec 2005; Joshua Jackson <tsunam@gentoo.org> staden-1.5.3-r1.ebuild:
   Stable on x86; bug #115438
diff --git a/sci-biology/staden/files/digest-staden-1.5.3 b/sci-biology/staden/files/digest-staden-1.5.3
deleted file mode 100644
index e56ba566e848..000000000000
--- a/sci-biology/staden/files/digest-staden-1.5.3
+++ /dev/null
@@ -1,5 +0,0 @@
-MD5 8f0ab94abe48972aecda69a1828d59ea staden-src-1-5-3.tar.gz 19670216
-MD5 9550e01cd954c3f672d2a500e051fa53 staden-1.4.1-missing-doc.tar.bz2 63825
-MD5 9009a92dc648775fb8a9b0789b995756 tcl8.4.6-src.tar.gz 3448711
-MD5 24b7774d54c1c568cabe16f3498ddccd tk8.4.6-src.tar.gz 3230760
-MD5 d6e739e823bff99e61007ded4cb71f79 course-1.1.tar.gz 5271133
diff --git a/sci-biology/staden/staden-1.5.3.ebuild b/sci-biology/staden/staden-1.5.3.ebuild
deleted file mode 100644
index 2772f841ef1e..000000000000
--- a/sci-biology/staden/staden-1.5.3.ebuild
+++ /dev/null
@@ -1,301 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/staden-1.5.3.ebuild,v 1.9 2005/08/26 19:12:57 r3pek Exp $
-
-inherit eutils toolchain-funcs
-
-TCLV=8.4.6
-TKV=8.4.6
-
-DESCRIPTION="The Staden Package - Biological sequence handling and analysis"
-HOMEPAGE="http://staden.sourceforge.net"
-SRC_URI="mirror://sourceforge/${PN}/${PN}-src-${PV//./-}.tar.gz
-	mirror://gentoo/${PN}-1.4.1-missing-doc.tar.bz2
-	mirror://sourceforge/tcl/tcl${TCLV}-src.tar.gz
-	mirror://sourceforge/tcl/tk${TKV}-src.tar.gz
-	doc? ( mirror://sourceforge/${PN}/course-1.1.tar.gz )"
-LICENSE="${PN}"
-
-SLOT="0"
-KEYWORDS="~amd64 x86"
-IUSE="doc"
-
-DEPEND="${RDEPEND}
-	dev-lang/perl
-	media-gfx/imagemagick
-	virtual/emacs
-	virtual/tetex"
-
-RDEPEND="app-shells/ksh
-	dev-lang/tcl
-	dev-lang/tk
-	sci-libs/io_lib
-	=dev-tcltk/itcl-3.2*
-	dev-tcltk/iwidgets
-	media-libs/libpng
-	virtual/x11"
-
-S=${WORKDIR}/${PN}-src-${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 "fortran" "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).
-	mv ${WORKDIR}/tcl${TCLV} ${S}/src
-	mv ${WORKDIR}/tk${TKV} ${S}/src
-	cd ${S}
-	epatch ${FILESDIR}/${P}-top.patch
-	epatch ${FILESDIR}/${P}-text_utils.patch
-	epatch ${FILESDIR}/${P}-tk_utils.patch
-	epatch ${FILESDIR}/${P}-prefinish.patch
-	epatch ${FILESDIR}/${P}-tracediff.patch
-	epatch ${FILESDIR}/${P}-mutscan.patch
-	epatch ${FILESDIR}/${P}-mutlib-gcc-3.4.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 || die
-	cd ${S}
-
-	# "getopt" is incorrectly included as an extern (for Win32 compatibility).
-	epatch ${FILESDIR}/${P}-getopt.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
-
-	# 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 || die
-
-	# 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} || die
-	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 | die
-
-	# 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}
-	done
-
-	# "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 -e "s/COPT		= -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" \
-		-e "s/FOPT		= -O2 -g3 -DNDEBUG/FOPT = ${FFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" \
-		-i global.mk || die
-}
-
-src_compile() {
-	# "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the
-	# Staden Package build process. "O" is redefined on the command line to
-	# avoid a conflict between Portage and the Staden Package build system,
-	# which both use this variable. (In Portage, its value is the directory
-	# containing the current ebuild, while in the Staden Package build system
-	# it is set to the directory containing the compiler object files.)
-	# Compiler program names also need to be specified to override the
-	# incorrect hardcoded ones.
-
-	# Compile executables and libraries.
-	make \
-		STADENROOT="${S}" \
-		SRCROOT="${S}/src" \
-		MACHINE="linux" \
-		JOB="all" \
-		O="linux-binaries" \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		F77=${F77:-g77} \
-		|| die "Package compilation failed."
-
-	# Build documentation.
-	cd ${S}/doc
-	make \
-		STADENROOT="${S}" \
-		SRCROOT="${S}/src" \
-		MACHINE="linux" \
-		JOB="all" \
-		O="linux-binaries" \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		F77=${F77:-g77} \
-		|| die "Package compilation failed."
-
-
-	# The install process will copy the libraries in ${S}/lib/linux-binaries,
-	# but this directory is in fact a symlink to the source directory.
-	rm ${S}/lib/linux-binaries
-	mkdir ${S}/lib/linux-binaries
-
-	# Moves executables in "${S}/linux-bin" and libraries to
-	# ${S}/lib/linux-binaries.
-	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 libread since an updated version is included in "sci-libs/io_lib".
-	rm ${S}/lib/linux-binaries/libread.so
-	# Delete the binaries already included in "sci-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 (broken) 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 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}/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}/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 ${S}/doc/manual/*unix*.{png,html,index}
-	insinto /opt/${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 ${WORKDIR}/${PN}-1.4.1-missing-doc/documentation.html
-	insinto /opt/${PN}/doc/misc
-	doins ${WORKDIR}/${PN}-1.4.1-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.pdf manual.pdf
-	newins ${S}/doc/manual/mini_unix.pdf mini_manual.pdf
-	newins ${S}/doc/scripting_manual/scripting.pdf scripting_manual.pdf
-
-	# 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
-}