Fixed problems with documentation. Made course installation optional.

6 files changed, 43 insertions, 95 deletions

diff --git a/app-sci/staden/ChangeLog b/app-sci/staden/ChangeLog
index d2df53fa30b5..c3ec0ff92937 100644
--- a/app-sci/staden/ChangeLog
+++ b/app-sci/staden/ChangeLog
@@ -1,6 +1,15 @@
 # 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 1.2 2004/09/15 19:09:27 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/ChangeLog,v 1.3 2004/09/16 04:12:35 ribosome Exp $
+
+*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)
 
diff --git a/app-sci/staden/Manifest b/app-sci/staden/Manifest
index 540ea3633aa5..00e7425efebc 100644
--- a/app-sci/staden/Manifest
+++ b/app-sci/staden/Manifest
@@ -1,5 +1,5 @@
-MD5 c306bebaff5d292decd309c3fa356100 staden-1.4.1-r1.ebuild 11096
-MD5 a169185d495c6ef6fc593d5eb1e207a5 ChangeLog 791
+MD5 041ff5e320f4b971dd7f6fbd56c44e71 ChangeLog 1128
+MD5 679fb754541dd95b09caca05a9827742 staden-1.4.1-r2.ebuild 8090
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
 MD5 e908bf4692dd3494ec22f07db2e7a9f5 files/staden-1.4.1-env 225
 MD5 3699a9d368068d835cbd8568d50d23e5 files/staden-1.4.1-gap4.patch 463
@@ -9,5 +9,6 @@ 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 c253634558f4beb820df20d8b109ad99 files/digest-staden-1.4.1-r1 150
+MD5 4250ea5eac7e7f2092a797bb78e27e41 files/digest-staden-1.4.1-r2 217
+MD5 708ea4c4b4cbc7e2b6b88b5a09e1b564 files/staden-1.4.1-top.patch 230
 MD5 ea4a62a1cd5070014d2c9352eeecf06a files/staden-1.4.1-tk_utils.patch 368
diff --git a/app-sci/staden/files/digest-staden-1.4.1-r1 b/app-sci/staden/files/digest-staden-1.4.1-r1
deleted file mode 100644
index c89e7f7a1c2b..000000000000
--- a/app-sci/staden/files/digest-staden-1.4.1-r1
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 a5588b112df2071d17f256e94777def5 staden-src-rel-1-4-1.tar.gz 21889519
-MD5 9550e01cd954c3f672d2a500e051fa53 staden-1.4.1-missing-doc.tar.bz2 63825
diff --git a/app-sci/staden/files/digest-staden-1.4.1-r2 b/app-sci/staden/files/digest-staden-1.4.1-r2
new file mode 100644
index 000000000000..eb3556875249
--- /dev/null
+++ b/app-sci/staden/files/digest-staden-1.4.1-r2
@@ -0,0 +1,3 @@
+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/files/staden-1.4.1-top.patch b/app-sci/staden/files/staden-1.4.1-top.patch
new file mode 100644
index 000000000000..d5e062aaef87
--- /dev/null
+++ b/app-sci/staden/files/staden-1.4.1-top.patch
@@ -0,0 +1,11 @@
+--- 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/staden-1.4.1-r1.ebuild b/app-sci/staden/staden-1.4.1-r2.ebuild
index 4d1e97482ff2..10951a49085c 100644
--- a/app-sci/staden/staden-1.4.1-r1.ebuild
+++ b/app-sci/staden/staden-1.4.1-r2.ebuild
@@ -1,24 +1,22 @@
 # 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-r1.ebuild,v 1.1 2004/09/15 19:09:27 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/staden-1.4.1-r2.ebuild,v 1.1 2004/09/16 04:12:35 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/${P}-missing-doc.tar.bz2"
+	mirror://gentoo/${P}-doc.tar.bz2
+	doc? mirror://gentoo/${P}-course.tar.bz2"
 LICENSE="${PN}"
 
 SLOT="0"
 KEYWORDS="~x86"
-IUSE="emboss ifc"
+IUSE="doc emboss ifc"
 
 DEPEND="${RDEPEND}
 	dev-lang/perl
-	media-gfx/imagemagick
-	virtual/emacs
-	virtual/tetex
 	emboss? ( app-sci/emboss )
 	ifc? ( dev-lang/ifc )"
 
@@ -74,13 +72,16 @@ pkg_setup() {
 src_unpack() {
 	unpack ${A}
 
-	# Abandon hope, all ye who enter here.
-
 	# 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.
+	# 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
@@ -93,38 +94,6 @@ src_unpack() {
 	epatch ${FILESDIR}/${P}-getopt.patch
 	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.
 	einfo "Applying user-defined compilation/linking flags:"
@@ -147,7 +116,7 @@ src_compile() {
 	# Compiler program names also need to be specified to override the
 	# incorrect hardcoded ones.
 
-	# Compiles executables and libraries, builds documentation.
+	# Compiles executables and libraries.
 	make \
 		STADENROOT="${S}" \
 		SRCROOT="${S}/src" \
@@ -196,15 +165,6 @@ src_compile() {
 	cp ${FILESDIR}/${P}-staden_help.new ${S}/linux-bin/staden_help
 	chmod +x ${S}/linux-bin/staden_help
 
-	# 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() {
@@ -223,49 +183,15 @@ src_install() {
 	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/*
+	# Documentation
+	mv ${WORKDIR}/doc ${D}/opt/${PN}/doc
 
-	# 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 some data
+	use doc && mv ${WORKDIR}/course ${D}/opt/${PN}/course
 
-	# A short course in printable format, along with example data
-	mkdir -p ${D}/opt/${PN}/course
-	mv ${S}/course/data ${D}/opt/${PN}/course
-	insinto /opt/${PN}/course
-	doins ${S}/course/README
-	newins ${S}/course/unix_docs/course_unix.pdf course_project_management.pdf
-	newins ${S}/course/unix_docs/course_unix.ps course_project_management.ps
-	newins ${S}/course/mutation_texi/notes.ps course_mutation_detection.ps
 }
 
 pkg_postinst() {