Updated course material and io_lib. Documentation now builds from source.

5 files changed, 357 insertions, 6 deletions

diff --git a/app-sci/staden/ChangeLog b/app-sci/staden/ChangeLog
index ed9ce0a61ffa..f16d13c87094 100644
--- a/app-sci/staden/ChangeLog
+++ b/app-sci/staden/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.6 2004/09/17 18:25:48 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/ChangeLog,v 1.7 2004/09/18 18:59:56 ribosome Exp $
+
+*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)
 
diff --git a/app-sci/staden/Manifest b/app-sci/staden/Manifest
index ab135f6ec412..43edd2c49271 100644
--- a/app-sci/staden/Manifest
+++ b/app-sci/staden/Manifest
@@ -1,5 +1,6 @@
+MD5 342dcc42299b6d4e8e18e7e2a454a069 staden-1.4.1-r6.ebuild 11043
 MD5 34fa9925397ab3b57f39b5d438bd20ca staden-1.4.1-r5.ebuild 7008
-MD5 ddb74640f6ba06aee9950ca41f1eb58b ChangeLog 1729
+MD5 590ef42294c4669427f1d765ee7a665d ChangeLog 1989
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
 MD5 e908bf4692dd3494ec22f07db2e7a9f5 files/staden-1.4.1-env 225
 MD5 3699a9d368068d835cbd8568d50d23e5 files/staden-1.4.1-gap4.patch 463
@@ -10,6 +11,7 @@ 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 4250ea5eac7e7f2092a797bb78e27e41 files/digest-staden-1.4.1-r5 217
+MD5 cd40ea0a473054769a0963e708257f98 files/digest-staden-1.4.1-r6 213
 MD5 708ea4c4b4cbc7e2b6b88b5a09e1b564 files/staden-1.4.1-top.patch 230
 MD5 ea4a62a1cd5070014d2c9352eeecf06a files/staden-1.4.1-tk_utils.patch 368
-MD5 12ca92a6e8763128e89ea667b4224b71 files/staden-1.4.1-emboss.patch 799
+MD5 8f13c224bf3c586a6436c39906b780ec files/staden-1.4.1-emboss.patch 1312
diff --git a/app-sci/staden/files/digest-staden-1.4.1-r6 b/app-sci/staden/files/digest-staden-1.4.1-r6
new file mode 100644
index 000000000000..f11f83bbe989
--- /dev/null
+++ b/app-sci/staden/files/digest-staden-1.4.1-r6
@@ -0,0 +1,3 @@
+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
index 7e619f0d2f5f..29639cd6c929 100644
--- a/app-sci/staden/files/staden-1.4.1-emboss.patch
+++ b/app-sci/staden/files/staden-1.4.1-emboss.patch
@@ -1,12 +1,12 @@
---- lib/spin2_emboss/create_emboss_files.tcl.old	2004-09-16 18:52:45.566400400 -0400
-+++ lib/spin2_emboss/create_emboss_files.tcl	2004-09-16 18:43:32.912416576 -0400
+--- 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
++#     $OUTDIR/lib/spin2_emboss/acdtcl/*
 +#     $OUTDIR/emboss_menu
  #
  # To run it, simply run this script. NOTE that it requires DISPLAY to be set
@@ -20,3 +20,21 @@
  
  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/staden-1.4.1-r6.ebuild b/app-sci/staden/staden-1.4.1-r6.ebuild
new file mode 100644
index 000000000000..a0d43d66b1d9
--- /dev/null
+++ b/app-sci/staden/staden-1.4.1-r6.ebuild
@@ -0,0 +1,321 @@
+# 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 1.1 2004/09/18 18:59:56 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
+	doc? mirror://sourceforge/${PN}/course-1.1.tar.gz
+	mirror://gentoo/${P}-missing-doc.tar.bz2"
+LICENSE="${PN}"
+
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="doc emboss"
+
+DEPEND="${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"
+
+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.'
+		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
+	sed -i -e 's/SHLIB_CFLAGS		= -fpic/SHLIB_CFLAGS		= -fPIC/' linux.mk \
+		&& einfo "Successfully applied sed script to patch linux.mk." \
+		|| eerror "Failed to apply sed script to patch linux.mk."
+	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.
+	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 = ${FFLAGS:-"-O2 -g3 -DNDEBUG"}/" global.mk \
+		&& einfo "Successfully applied sed script to set FFLAGS." \
+		|| eerror "Failed to apply sed script to set FFLAGS."
+}
+
+src_compile() {
+	# "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the
+	# Staden Package build process. "O" is redefined on the command line to
+	# avoid a conflict between Portage and the Staden Package build system,
+	# which both use this variable. (In Portage, its value is the directory
+	# containing the current ebuild, while in the Staden Package build system
+	# it is set to the directory containing the compiler object files.)
+	# Compiler program names also need to be specified to override the
+	# incorrect hardcoded ones.
+
+	# Compile executables and libraries.
+	make \
+		STADENROOT="${S}" \
+		SRCROOT="${S}/src" \
+		MACHINE="linux" \
+		JOB="all" \
+		O="linux-binaries" \
+		CC=${CC:-gcc} \
+		CXX=${CXX:-g++} \
+		F77=${F77:-g77} \
+		|| die "Package compilation failed."
+
+	# Build documentation.
+	cd ${S}/doc
+	make \
+		STADENROOT="${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.
+	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
+
+	# Remove the old "spin_emboss" (replaced by "spin2_emboss")
+	rm -r ${S}/lib/spin_emboss
+
+	# 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
+}