+++ /dev/null
---- 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/lib/spin2_emboss/acdtcl/*
-+# $OUTDIR/emboss_menu
- #
- # To run it, simply run this script. NOTE that it requires DISPLAY to be set
- # correctly, even though no graphics are obvious. This is because certain
- # widgets are temporarily created in order to query their pathnames.
-
--set acdtcl_dir acdtcl
--set menu_file ../../tables/emboss_menu
-+set acdtcl_dir $env(OUTDIR)
-+set menu_file $env(OUTDIR)/emboss_menu
-
- tkinit
- wm withdraw .
-@@ -53,7 +53,7 @@
- if {$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.]
- }
# 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-1.4.1-r7.ebuild,v 1.3 2005/01/02 15:34:38 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/staden-1.4.1-r7.ebuild,v 1.4 2005/01/03 01:49:46 ribosome Exp $
-inherit eutils gcc
+inherit eutils toolchain-funcs
DESCRIPTION="The Staden Package - Biological sequence handling and analysis"
HOMEPAGE="http://staden.sourceforge.net/"
# 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).
+ # correctly and must be replaced by hardcoded library names.
cd ${S}
einfo "Patching Staden Package Makefiles:"
epatch ${FILESDIR}/${P}-top.patch
epatch ${FILESDIR}/${P}-tracediff.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 \
- && einfo "Successfully applied sed script to patch linux.mk." \
- || eerror "Failed to apply sed script to patch linux.mk."
+ sed -i -e 's/SHLIB_CFLAGS = -fpic/SHLIB_CFLAGS = /' linux.mk
cd ${S}/src/mutlib
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
# 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."
+ 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} \
- && einfo "Successfully applied sed script to patch ${SCRIPT}." \
- || eerror "Failed to apply sed script to patch ${SCRIPT}."
+ 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 \
- && einfo "Successfully applied sed script to patch make.ps." \
- || eerror "Failed to apply sed script to patch make.ps."
+ 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} \
- && einfo "Successfully applied sed scripts to patch ${FILE}." \
- || eerror "Failed to apply sed scripts to patch ${FILE}."
+ sed -i -e 's/,6in}/,6in,,,eps}/' ${FILE}
done
echo
# 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 \
- && 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"} -fPIC/" global.mk \
- && einfo "Successfully applied sed script to set FFLAGS." \
- || eerror "Failed to apply sed script to set FFLAGS."
+ 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 = ${FFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk
}
src_compile() {
MACHINE="linux" \
JOB="all" \
O="linux-binaries" \
- CC=$(gcc-getCC) \
- CXX=$(gcc-getCXX) \
- F77=${F77:-g77} \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ F77=g77 \
|| die "Package compilation failed."
# Build documentation.
MACHINE="linux" \
JOB="all" \
O="linux-binaries" \
- CC=$(gcc-getCC) \
- CXX=$(gcc-getCXX) \
- F77=${F77:-g77} \
- || die "Package compilation failed."
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ F77=g77 \
+ || die "Document compilation failed."
# Moves executables in "${S}/linux-bin" and libraries to ${S}/lib.
cd ${S}
ln -s /usr/$(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.
+ # 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 just built hypertext documentation.
+ # 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}
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