diff options
author | Olivier Fisette <ribosome@gentoo.org> | 2005-01-03 01:49:47 +0000 |
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committer | Olivier Fisette <ribosome@gentoo.org> | 2005-01-03 01:49:47 +0000 |
commit | b01e235e33f572b4c2b0d3ed0e5470d7e73ec678 (patch) | |
tree | 364f67b33c777dff8222831bdcbfa50eb8bb50a4 /sci-biology | |
parent | Marked ~ppc for bug #76376." (diff) | |
download | historical-b01e235e33f572b4c2b0d3ed0e5470d7e73ec678.tar.gz historical-b01e235e33f572b4c2b0d3ed0e5470d7e73ec678.tar.bz2 historical-b01e235e33f572b4c2b0d3ed0e5470d7e73ec678.zip |
Use the toolchain-funcs rather than the gcc eclass. Removed useless patch.
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/staden/ChangeLog | 6 | ||||
-rw-r--r-- | sci-biology/staden/Manifest | 5 | ||||
-rw-r--r-- | sci-biology/staden/files/staden-1.4.1-emboss.patch | 40 | ||||
-rw-r--r-- | sci-biology/staden/staden-1.4.1-r7.ebuild | 60 |
4 files changed, 26 insertions, 85 deletions
diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog index b9f4c4d81123..fd1c17263ff4 100644 --- a/sci-biology/staden/ChangeLog +++ b/sci-biology/staden/ChangeLog @@ -1,6 +1,10 @@ # 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 1.4 2005/01/02 15:34:38 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.5 2005/01/03 01:49:46 ribosome Exp $ + + 02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + -files/staden-1.4.1-emboss.patch, staden-1.4.1-r7.ebuild: + Use the toolchain-funcs rather than the gcc eclass. Removed useless patch. 02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> staden-1.4.1-r7.ebuild: Added to x86. diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest index 0b282fa6fb5e..a51f1ba9c1da 100644 --- a/sci-biology/staden/Manifest +++ b/sci-biology/staden/Manifest @@ -1,5 +1,5 @@ -MD5 5ed6580cd1d49d118d99f6702fed21a1 staden-1.4.1-r7.ebuild 11086 -MD5 3e5bf8ea267739c5a509bc725e27ceb8 ChangeLog 2942 +MD5 153c13c839cdeeb534736bd3049c7624 staden-1.4.1-r7.ebuild 9890 +MD5 33a4d27174abad5150898e934216a6f1 ChangeLog 3133 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254 MD5 e908bf4692dd3494ec22f07db2e7a9f5 files/staden-1.4.1-env 225 MD5 3699a9d368068d835cbd8568d50d23e5 files/staden-1.4.1-gap4.patch 463 @@ -12,4 +12,3 @@ 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 ea4a62a1cd5070014d2c9352eeecf06a files/staden-1.4.1-tk_utils.patch 368 -MD5 8f13c224bf3c586a6436c39906b780ec files/staden-1.4.1-emboss.patch 1312 diff --git a/sci-biology/staden/files/staden-1.4.1-emboss.patch b/sci-biology/staden/files/staden-1.4.1-emboss.patch deleted file mode 100644 index 29639cd6c929..000000000000 --- a/sci-biology/staden/files/staden-1.4.1-emboss.patch +++ /dev/null @@ -1,40 +0,0 @@ ---- 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.] - } diff --git a/sci-biology/staden/staden-1.4.1-r7.ebuild b/sci-biology/staden/staden-1.4.1-r7.ebuild index 58e391d201ed..7237b00cb8a6 100644 --- a/sci-biology/staden/staden-1.4.1-r7.ebuild +++ b/sci-biology/staden/staden-1.4.1-r7.ebuild @@ -1,8 +1,8 @@ # 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/" @@ -55,10 +55,7 @@ src_unpack() { # 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 @@ -69,23 +66,16 @@ src_unpack() { 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 @@ -104,29 +94,21 @@ src_unpack() { # 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 @@ -134,12 +116,8 @@ src_unpack() { # 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 = ${FFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk } src_compile() { @@ -159,9 +137,9 @@ src_compile() { MACHINE="linux" \ JOB="all" \ O="linux-binaries" \ - CC=$(gcc-getCC) \ - CXX=$(gcc-getCXX) \ - F77=${F77:-g77} \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + F77=g77 \ || die "Package compilation failed." # Build documentation. @@ -172,10 +150,10 @@ src_compile() { 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 ${S} @@ -216,12 +194,12 @@ src_compile() { ln -s /usr/$(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} |