New version

8 files changed, 378 insertions, 12 deletions

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index a86abe16c659..66aa899fe0d9 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -1,6 +1,14 @@
 # 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 1.6 2005/01/09 11:39:13 swegener Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.7 2005/01/15 02:37:04 ribosome Exp $
+
+*staden-1.5.3 (14 Jan 2005)
+
+  14 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
+  +files/staden-1.5.3-getopt.patch, +files/staden-1.5.3-text_utils.patch,
+  +files/staden-1.5.3-tk_utils.patch, +files/staden-1.5.3-top.patch,
+  +staden-1.5.3.ebuild:
+  New version.
 
   09 Jan 2005; Sven Wegener <swegener@gentoo.org> staden-1.4.1-r7.ebuild:
   Added missing parentheses in SRC_URI/*DEPEND/LICENSE.
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
index 63b4f4e2f1d2..4b9039890d6d 100644
--- a/sci-biology/staden/Manifest
+++ b/sci-biology/staden/Manifest
@@ -1,24 +1,20 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
+MD5 900e6d2666d723e0354fc7c334cdc9e4 staden-1.5.3.ebuild 9903
 MD5 fe19fbd7368ca77e37fab8ee461dddda staden-1.4.1-r7.ebuild 9894
-MD5 84a0707094ea555a0375ea854b7e326b ChangeLog 3264
+MD5 47b7572195599c28701e1ad577f035a8 ChangeLog 3529
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
+MD5 6ce4d77a48d0377a1ada09f1990fb2af files/staden-1.5.3-text_utils.patch 478
 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 0857e0bf79953bfa46b1224f6218701a files/staden-1.5.3-top.patch 230
 MD5 7717f77ecd800d0b3049974db3fcd0a9 files/staden-1.4.1-prefinish.patch 362
+MD5 daf40c222b80ffc48d9a2ac2544ab631 files/staden-1.5.3-getopt.patch 367
 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 1ead6fa1e26351872c3404ab9da21416 files/staden-1.5.3-tk_utils.patch 547
+MD5 e3ce8053514641a26df3ca33f2962e55 files/digest-staden-1.5.3 338
 MD5 ea4a62a1cd5070014d2c9352eeecf06a files/staden-1.4.1-tk_utils.patch 368
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diff --git a/sci-biology/staden/files/digest-staden-1.5.3 b/sci-biology/staden/files/digest-staden-1.5.3
new file mode 100644
index 000000000000..e56ba566e848
--- /dev/null
+++ b/sci-biology/staden/files/digest-staden-1.5.3
@@ -0,0 +1,5 @@
+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/files/staden-1.5.3-getopt.patch b/sci-biology/staden/files/staden-1.5.3-getopt.patch
new file mode 100644
index 000000000000..bc5da3f26275
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-getopt.patch
@@ -0,0 +1,14 @@
+--- src/Misc/misc.h.old	2004-11-09 04:53:23.000000000 -0500
++++ src/Misc/misc.h	2005-01-08 22:25:42.487088768 -0500
+@@ -7,10 +7,7 @@
+ 
+ #include "os.h"
+ #include "xalloc.h"
+-
+-#ifdef _MSC_VER
+-extern int getopt( int argc, char* const argv[], const char* optstring );
+-#endif
++#include <getopt.h>
+ 
+ extern int is_directory(char * fn);
+ extern int is_file(char * fn);
diff --git a/sci-biology/staden/files/staden-1.5.3-text_utils.patch b/sci-biology/staden/files/staden-1.5.3-text_utils.patch
new file mode 100644
index 000000000000..315860248dfc
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-text_utils.patch
@@ -0,0 +1,17 @@
+--- src/text_utils/Makefile.old	2004-11-09 04:53:27.000000000 -0500
++++ src/text_utils/Makefile	2005-01-08 23:17:12.196381560 -0500
+@@ -41,14 +41,6 @@
+ 
+ .PRECIOUS:	.links
+ .links:
+-	ln -s ../licence/boxes.h .
+-	ln -s ../licence/licence.h .
+-	ln -s ../licence/check_licence.c .
+-	ln -s ../licence/licence_utils.c .
+-	ln -s ../licence/licence_utils.h .
+-	ln -s ../licence/md52.c .
+-	ln -s ../licence/md52.h .
+-	ln -s ../licence/valid_seq.c .
+ 	touch .links
+ 	$(MAKE) $(MFLAGS)
+ 
diff --git a/sci-biology/staden/files/staden-1.5.3-tk_utils.patch b/sci-biology/staden/files/staden-1.5.3-tk_utils.patch
new file mode 100644
index 000000000000..58aa79afa9b3
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-tk_utils.patch
@@ -0,0 +1,19 @@
+--- src/tk_utils/Makefile.old	2004-11-09 04:53:26.000000000 -0500
++++ src/tk_utils/Makefile	2005-01-08 22:47:41.659544072 -0500
+@@ -105,16 +105,6 @@
+ 
+ .PRECIOUS:	.links
+ .links:
+-	ln -s ../licence/boxes.h .
+-	ln -s ../licence/licence.h .
+-	ln -s ../licence/check_licence.c .
+-	ln -s ../licence/licence_utils.c .
+-	ln -s ../licence/licence_utils.h .
+-	ln -s ../licence/md52.c .
+-	ln -s ../licence/md52.h .
+-	ln -s ../licence/valid_seq.c .
+-	ln -s ../tcl8.4.6/unix/tclAppInit.c .
+-	ln -s ../tk8.4.6/winMain.c .
+ 	touch .links
+ 	$(MAKE) $(MFLAGS)
+ 
diff --git a/sci-biology/staden/files/staden-1.5.3-top.patch b/sci-biology/staden/files/staden-1.5.3-top.patch
new file mode 100644
index 000000000000..049dfa9f9458
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-top.patch
@@ -0,0 +1,11 @@
+--- Makefile.old	2004-11-09 04:53:22.000000000 -0500
++++ Makefile	2005-01-08 21:22:35.561788920 -0500
+@@ -30,8 +30,6 @@
+ 
+ all:
+ 	cd src; $(MAKE) all
+-	cd doc; $(MAKE) all
+-	cd course; $(MAKE) all
+ 
+ install:
+ 	cd src; $(MAKE) $@
diff --git a/sci-biology/staden/staden-1.5.3.ebuild b/sci-biology/staden/staden-1.5.3.ebuild
new file mode 100644
index 000000000000..50b9c9a937ff
--- /dev/null
+++ b/sci-biology/staden/staden-1.5.3.ebuild
@@ -0,0 +1,296 @@
+# 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 1.1 2005/01/15 02:37:04 ribosome 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="~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 "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).
+	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
+	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
+	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 ${FILESDIR}/${PN}-1.4.1-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 ${FILESDIR}/${PN}-1.4.1-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
+
+	# 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}
+	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
+
+	# 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 -i -e "s/COPT		= -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk
+	sed -i -e "s/FOPT		= -O2 -g3 -DNDEBUG/FOPT = ${FFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk
+}
+
+src_compile() {
+	# "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the
+	# Staden Package build process. "O" is redefined on the command line to
+	# avoid a conflict between Portage and the Staden Package build system,
+	# which both use this variable. (In Portage, its value is the directory
+	# containing the current ebuild, while in the Staden Package build system
+	# it is set to the directory containing the compiler object files.)
+	# Compiler program names also need to be specified to override the
+	# incorrect hardcoded ones.
+
+	# Compile executables and libraries.
+	make \
+		STADENROOT="${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 ${FILESDIR}/${PN}-1.4.1-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
+}