* [gentoo-commits] proj/sci:master commit in: sci-chemistry/molsketch/, sci-biology/embassy-clustalomega/files/, ...
@ 2013-02-22 10:40 Justin Lecher
0 siblings, 0 replies; only message in thread
From: Justin Lecher @ 2013-02-22 10:40 UTC (permalink / raw
To: gentoo-commits
commit: 0344594ee6a9fac4617b3d6c521cc215cdb47a64
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 22 10:39:59 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 22 10:39:59 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0344594e
Revert "Merge branch 'jlec' of github.com:gentoo-science/sci"
This reverts commit 62f75f52e03c91a82271472f90ef9febcc60bad1, reversing
changes made to feee3be41866e292a945d0494f9329dad2f43998.
---
.../embassy-clustalomega-0.2.0.ebuild | 11 -
.../files/embassy-clustalomega-0.2.0.patch | 336 -------------------
sci-biology/embassy-clustalomega/metadata.xml | 34 --
sci-biology/embassy/embassy-6.4.0.ebuild | 44 ---
sci-biology/emboss.new/ChangeLog | 348 --------------------
sci-biology/emboss.new/emboss-6.4.0_p24.ebuild | 75 -----
.../emboss.new/files/emboss-README.Gentoo-2 | 34 --
sci-biology/emboss.new/metadata.xml | 18 -
sci-biology/staden/files/rpath.patch | 123 -------
sci-biology/staden/staden-2.0.0_beta8.ebuild | 73 ----
sci-chemistry/molsketch/molsketch-9999.ebuild | 44 ---
sci-libs/libccp4/libccp4-6.2.20111210.ebuild | 21 --
sci-libs/libccp4/metadata.xml | 34 --
.../petsc/files/petsc-configure-pic.patch | 11 -
.../petsc/files/petsc-disable-env-warnings.patch | 13 -
.../petsc/files/petsc-disable-rpath.patch | 16 -
.../petsc/files/petsc-fix-afterimage.patch | 71 ----
sci-mathematics/petsc/files/petsc-fix-xops.patch | 21 --
18 files changed, 0 insertions(+), 1327 deletions(-)
diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-0.2.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-0.2.0.ebuild
deleted file mode 100644
index b4dd47e..0000000
--- a/sci-biology/embassy-clustalomega/embassy-clustalomega-0.2.0.ebuild
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-EBO_DESCRIPTION="wrapper to ClustalwO"
-
-inherit emboss
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-0.2.0.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-0.2.0.patch
deleted file mode 100644
index 64adabc..0000000
--- a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-0.2.0.patch
+++ /dev/null
@@ -1,336 +0,0 @@
-diff --git a/configure.in b/configure.in
-index 6c19bf0..b071401 100644
---- a/configure.in
-+++ b/configure.in
-@@ -187,16 +187,6 @@ AC_PROG_INSTALL
- AC_PROG_LN_S
- AC_PROG_MAKE_SET
-
--dnl Intel MacOSX 10.6 puts X11 in a non-standard place
--if test "${with_x}" != "no" ; then
--if test "`uname -a | grep Darwin`"; then
--OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
--if test ${OSXX} '>' '10.4'; then
--CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
--fi
--fi
--fi
--
- dnl Check for header files
- AC_PATH_XTRA
- AC_HEADER_DIRENT
-@@ -248,10 +238,10 @@ AX_LIB_MYSQL
- AX_LIB_POSTGRESQL
-
- CFLAGS="$CFLAGS $MYSQL_CFLAGS"
--LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
-+LIBS="${MYSQL_LIBS} ${LIBS}"
-
--CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
--LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
-+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
-+LIBS="$POSTGRESQL_LIBS $LIBS"
-
-
- dnl "Export" these variables for PCRE
-@@ -386,9 +376,30 @@ AC_ARG_ENABLE(systemlibs,
- AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
- if test "${enable_systemlibs}" = "yes" ; then
- have_systemlibs=yes
-+ DEFINE_USE_SYSTEM_PCRE="#define"
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd])
-+ PKG_CHECK_MODULES([ZLIB], [zlib])
-+else
-+ dnl X11 is only used by plplot
-+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
-+ if test "${with_x}" != "no" ; then
-+ if test "`uname -a | grep Darwin`"; then
-+ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
-+ if test ${OSXX} '>' '10.4'; then
-+ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
-+ fi
-+ fi
-+ fi
-+ if test "${with_x}" != "no" ; then
-+ LF_EMBOSS_PATH_XLIB
-+ fi
-+ AC_MSG_NOTICE(USING bundled LIBS)
- fi
- AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
- AC_SUBST(ESYSTEMLIBS)
-+AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
-+AC_SUBST(PLPLOT_CFLAGS)
-+AC_SUBST(PLPLOT_LIBS)
-
-
-
-diff --git a/emboss_doc/html/Makefile.am b/emboss_doc/html/Makefile.am
-index 1aa68ab..b6140b9 100644
---- a/emboss_doc/html/Makefile.am
-+++ b/emboss_doc/html/Makefile.am
-@@ -2,4 +2,4 @@ pkgdata_DATA = index.html \
- echlorop.html elipop.html enetnglyc.html enetoglyc.html enetphos.html \
- eprop.html esignalp.html etmhmm.html eyinoyang.html
-
--pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/cbstools
-+pkgdatadir=$(docdir)/html/embassy/cbstools
-diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am
-index 19a1f16..0f86f5b 100644
---- a/emboss_doc/text/Makefile.am
-+++ b/emboss_doc/text/Makefile.am
-@@ -2,4 +2,4 @@ pkgdata_DATA = echlorop.txt elipop.txt \
- enetnglyc.txt enetoglyc.txt enetphos.txt \
- eprop.txt esignalp.txt etmhmm.txt eyinoyang.txt
-
--pkgdatadir=$(prefix)/share/EMBOSS/doc/programs/text
-+pkgdatadir=$(docdir)/programs/text
-diff --git a/m4/hpdf.m4 b/m4/hpdf.m4
-index a37940f..80b329c 100644
---- a/m4/hpdf.m4
-+++ b/m4/hpdf.m4
-@@ -33,8 +33,8 @@ ALT_HOME=/usr
- #
- # Locate hpdf
- #
--if test -d "${ALT_HOME}"
--then
-+#if test -d "${ALT_HOME}"
-+#then
-
- #
- # Keep a copy if it fails
-@@ -45,13 +45,13 @@ then
- #
- # Set
- #
-- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-- CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
-+# LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-+# CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include"
-
- #
- # Check for libharu in ALT_HOME
- #
-- AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0, -L${ALT_HOME}/lib)
-+ AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0)
- #
- #
- # If everything found okay then proceed to include png driver in config.
-@@ -80,10 +80,4 @@ then
- echo "No pdf support (libhpdf) found."
- fi
-
--else
-- if test $withval != "no"; then
-- echo "Directory $ALT_HOME does not exist"
-- exit 0
-- fi
--fi
- ])
-diff --git a/m4/mysql.m4 b/m4/mysql.m4
-index 12f8fe9..5cd8b90 100644
---- a/m4/mysql.m4
-+++ b/m4/mysql.m4
-@@ -26,7 +26,7 @@
- # This macro calls:
- #
- # AC_SUBST(MYSQL_CFLAGS)
--# AC_SUBST(MYSQL_LDFLAGS)
-+# AC_SUBST(MYSQL_LIBS)
- # AC_SUBST(MYSQL_VERSION)
- #
- # And sets:
-@@ -68,7 +68,7 @@ AC_DEFUN([AX_LIB_MYSQL],
- )
-
- MYSQL_CFLAGS=""
-- MYSQL_LDFLAGS=""
-+ MYSQL_LIBS=""
- MYSQL_VERSION=""
-
- dnl
-@@ -86,7 +86,7 @@ AC_DEFUN([AX_LIB_MYSQL],
-
- dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
- MYSQL_CFLAGS="`$MYSQL_CONFIG --include`"
-- MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`"
-+ MYSQL_LIBS="`$MYSQL_CONFIG --libs`"
-
- MYSQL_VERSION=`$MYSQL_CONFIG --version`
-
-@@ -97,7 +97,7 @@ dnl not be installed
- EMBCFLAGS=$CFLAGS
- EMBLDFLAGS=$LDFLAGS
- CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS"
-- LDFLAGS="$MYSQL_LDFLAGS $EMBLDFLAGS"
-+ LIBS="${MYSQL_LIBS} ${LIBS}"
-
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
- #include "mysql.h"]],
-@@ -115,7 +115,7 @@ dnl not be installed
- AC_MSG_RESULT([yes])
- else
- MYSQL_CFLAGS=""
-- MYSQL_LDFLAGS=""
-+ MYSQL_LIBS=""
- found_mysql="no"
- AC_MSG_RESULT([no])
- fi
-@@ -172,5 +172,5 @@ dnl not be installed
-
- AC_SUBST([MYSQL_VERSION])
- AC_SUBST([MYSQL_CFLAGS])
-- AC_SUBST([MYSQL_LDFLAGS])
-+ AC_SUBST([MYSQL_LIBS])
- ])
-diff --git a/m4/pngdriver.m4 b/m4/pngdriver.m4
-index 5934321..de970ae 100644
---- a/m4/pngdriver.m4
-+++ b/m4/pngdriver.m4
-@@ -44,8 +44,8 @@ ALT_HOME=/usr
- #
- # Locate png/gd/zlib, if wanted
- #
--if test -d "${ALT_HOME}"
--then
-+#if test -d "${ALT_HOME}"
-+#then
-
- #
- # Keep a copy if it fails
-@@ -69,20 +69,26 @@ then
- fi
-
-
-+PKG_CHECK_MODULES([PNG], [libpng])
-+PKG_CHECK_MODULES([ZLIB], [zlib])
-+AC_CHECK_PROG(GD_LIBS, [gdlib-config])
-+GD_LIBS="`gdlib-config --libs` -lgd"
-+GD_CFLAGS="`gdlib-config --cflags`"
-+
-
-
-
- #
- # Check for zlib in ALT_HOME
- #
-- AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, -L${ALT_HOME}/lib -lz)
-+ AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, ${ZLIB_LIBS})
- #
-
- #
- # Check for png
- #
- if test $CHECK = "1" ; then
-- AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lz)
-+ AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , ${ZLIB_LIBS})
- fi
-
-
-@@ -92,7 +98,7 @@ then
- # Check for gd
- #
- if test $CHECK = "1"; then
-- AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lgd -lpng -lz -lm)
-+ AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , ${PNG_LIBS} ${ZLIB_LIBS} ${GD_LIBS})
- if test $CHECK = "0"; then
- echo need to upgrade gd for png driver for plplot
- fi
-@@ -101,7 +107,7 @@ then
- # If everything found okay then proceed to include png driver in config.
- #
- if test $CHECK = "1" ; then
-- LIBS="$LIBS -lgd -lpng -lz -lm"
-+ LIBS="$LIBS ${PNG_LIBS} ${ZLIB_LIBS} ${GD_LIBS}"
-
- if test $ICCHECK = "1" ; then
- LIBS="$LIBS -liconv"
-@@ -114,10 +120,11 @@ then
- AC_DEFINE(PLD_png)
- AM_CONDITIONAL(AMPNG, true)
- echo PNG libraries found
-- if test $ALT_HOME = "/usr" ; then
-+# if test $ALT_HOME = "/usr" ; then
- LDFLAGS="$ALT_LDFLAGS"
- CPPFLAGS="$ALT_CPPFLAGS"
-- fi
-+ CFLAGS="${CFLAGS} ${PNG_CFLAGS} ${ZLIB_CFLAGS} ${GD_CFLAGS}"
-+# fi
- else
- #
- # If not okay then reset FLAGS.
-@@ -134,10 +141,4 @@ then
- # echo CPPFLAGS = $CPPFLAGS
-
-
--else
-- if test $withval != "no"; then
-- echo "Directory $ALT_HOME does not exist"
-- exit 0
-- fi
--fi
- ])
-diff --git a/m4/postgresql.m4 b/m4/postgresql.m4
-index e6a804d..ef4d49c 100644
---- a/m4/postgresql.m4
-+++ b/m4/postgresql.m4
-@@ -26,7 +26,7 @@
- # This macro calls:
- #
- # AC_SUBST(POSTGRESQL_CFLAGS)
--# AC_SUBST(POSTGRESQL_LDFLAGS)
-+# AC_SUBST(POSTGRESQL_LIBS)
- # AC_SUBST(POSTGRESQL_VERSION)
- #
- # And sets:
-@@ -65,7 +65,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
- )
-
- POSTGRESQL_CFLAGS=""
-- POSTGRESQL_LDFLAGS=""
-+ POSTGRESQL_LIBS=""
- POSTGRESQL_POSTGRESQL=""
-
- dnl
-@@ -82,7 +82,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
- AC_MSG_CHECKING([for PostgreSQL libraries])
-
- POSTGRESQL_CFLAGS="-I`$PG_CONFIG --includedir`"
-- POSTGRESQL_LDFLAGS="-L`$PG_CONFIG --libdir` -lpq"
-+ POSTGRESQL_LIBS="-L`$PG_CONFIG --libdir` `$PG_CONFIG --libs`"
-
- POSTGRESQL_VERSION=`$PG_CONFIG --version | sed -e 's#PostgreSQL ##'`
-
-@@ -144,5 +144,5 @@ AC_DEFUN([AX_LIB_POSTGRESQL],
-
- AC_SUBST([POSTGRESQL_VERSION])
- AC_SUBST([POSTGRESQL_CFLAGS])
-- AC_SUBST([POSTGRESQL_LDFLAGS])
-+ AC_SUBST([POSTGRESQL_LIBS])
- ])
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 7ff8b84..7a99a46 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -19,9 +19,9 @@ INCLUDES = -I../../../nucleus -I../../../ajax/pcre \
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- -I../../../ajax/acd -I../../../plplot
- else
--INCLUDES = -I${embprefix}/include -I${embprefix}/include/eplplot \
-- $(NLINCLUDES) \
-- -I${embprefix}/include/epcre
-+INCLUDES = -I${embprefix}/include $(PLPLOT_CFLAGS) \
-+ $(NLINCLUDES) -I${embprefix}/include/emboss \
-+ -I${embprefix}/include/pcre
- endif
-
- if ISSHARED
-@@ -64,6 +64,6 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
- ../../../plplot/libeplplot.la \
- $(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+ -lajax -lpcre $(NLADD) $(PLPLOT_LIBS) $(XLIB)
- endif
diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml
deleted file mode 100644
index d31449d..0000000
--- a/sci-biology/embassy-clustalomega/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!--
-This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a
-number of subelements are allowed: herd, maintainer, and
-longdescription. herd is a required subelement.
-
-For a full description look at:
-http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4
-
-
-Before committing, please remove the comments from this file. They are
-not relevant for general metadata.xml files.
--->
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>@gentoo.org</email>
-<!-- <description>Description of the maintainership</description> -->
-</maintainer>
-<longdescription>
- Long description of the package
-</longdescription>
-<!--
-<use>
- <flag name='flag'>Description of how USE='flag' affects this package</flag>
- <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this
- package</flag>
- <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking.
- Requires an installed dictionary from <cat>app-dicts</cat></flag>
-</use>
--->
-</pkgmetadata>
diff --git a/sci-biology/embassy/embassy-6.4.0.ebuild b/sci-biology/embassy/embassy-6.4.0.ebuild
deleted file mode 100644
index dd59b07..0000000
--- a/sci-biology/embassy/embassy-6.4.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/embassy-6.1.0.ebuild,v 1.2 2010/01/01 21:35:29 fauli Exp $
-
-EAPI="4"
-
-inherit emboss
-
-DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)"
-SRC_URI=""
-
-LICENSE+=" freedist"
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
-
-RDEPEND+="
- =sci-biology/embassy-cbstools-1.0.0-r3
- =sci-biology/embassy-clustalomega-0.2.0
- =sci-biology/embassy-domainatrix-0.1.0-r6
- =sci-biology/embassy-domalign-0.1.0-r5
- =sci-biology/embassy-domsearch-0.1.0-r5
- =sci-biology/embassy-emnu-1.05-r7
- =sci-biology/embassy-esim4-1.0.0-r7
- =sci-biology/embassy-hmmer-2.3.2-r4
- =sci-biology/embassy-iprscan-4.3.1-r2
- =sci-biology/embassy-memenew-4.0.0-r1
- =sci-biology/embassy-mira-2.8.2-r2
- =sci-biology/embassy-mse-3.0.0
- =sci-biology/embassy-phylipnew-3.69
- =sci-biology/embassy-signature-0.1.0-r5
- =sci-biology/embassy-structure-0.1.0-r5
- =sci-biology/embassy-topo-2.0.0
- =sci-biology/embassy-vienna-1.7.2-r2"
-
-DOCS=""
-
-S="${WORKDIR}"
-
-src_prepare() {
-:
-}
-
-src_configure() {
-:
-}
diff --git a/sci-biology/emboss.new/ChangeLog b/sci-biology/emboss.new/ChangeLog
deleted file mode 100644
index 9e8a431..0000000
--- a/sci-biology/emboss.new/ChangeLog
+++ /dev/null
@@ -1,348 +0,0 @@
-# ChangeLog for sci-biology/emboss
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $
-
- 24 Sep 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
- Use Fedora hosting because unpstream removed the patches
-
- 27 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild,
- -files/emboss-6.3.1_p4-r1.patch:
- Last fix for 64bitness
-
- 22 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch:
- Fix compile correctly against postgresql, #359959
-
- 21 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch:
- Implicit decs fix, thanks bicatali for help
-
- 21 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild,
- files/emboss-6.3.1_p4-r1.patch:
- Fixed for reviewed eclass
-
- 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
- Straighten ENV
-
- 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
- New emboss_src_install used
-
- 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
- Naming of eclass changed
-
- 14 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild:
- Ebov not needed to be set anymore
-
-*emboss-6.3.1_p4-r1 (11 Mar 2011)
-
- 11 Mar 2011; Justin Lecher <jlec@gentoo.org> -emboss-6.3.1_p4.ebuild,
- +emboss-6.3.1_p4-r1.ebuild, +files/emboss-6.3.1_p4-r1.patch,
- -files/emboss-6.3.1_p4.patch:
- Rev bump, to ahead of the tree ebuild
-
- 10 Mar 2011; Justin Lecher <jlec@gentoo.org> -files/6.3.1_p4.patch,
- emboss-6.3.1_p4.ebuild, +files/emboss-6.3.1_p4.patch:
- Correct naming of patch
-
- 10 Mar 2011; Justin Lecher <jlec@gentoo.org> metadata.xml:
- Removed largefile from local USE description
-
- 10 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
- Move to new embassy-ng.eclass
-
- 09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
- Move to new embassy-ng.eclass
-
- 09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
- EAPI=4 takes three arguments on use_with
-
-*emboss-6.3.1_p4 (09 Mar 2011)
-
- 09 Mar 2011; Justin Lecher <jlec@gentoo.org>
- +files/6.3.1_p4-unbundle-libs.patch, -files/6.3.1-unbundle-libs.patch,
- -emboss-6.3.1.ebuild, +emboss-6.3.1_p4.ebuild:
- Bump to latest upstream patches
-
-*emboss-6.3.1 (09 Mar 2011)
-
- 09 Mar 2011; Justin Lecher <jlec@gentoo.org>
- +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2,
- emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild,
- +emboss-6.3.1.ebuild, metadata.xml:
- Version Bump #335603, Unbundled libs, removed old, fix clash with
- /usr/bin/digest, #330507
-
- 18 Jul 2010; <nixnut@gentoo.org> emboss-6.0.1.ebuild:
- ppc stable #325457
-
- 09 Jul 2010; Samuli Suominen <ssuominen@gentoo.org> emboss-6.0.1.ebuild:
- ppc64 stable wrt #325457
-
- 23 Jun 2010; Justin Lecher <jlec@gentoo.org> emboss-4.0.0.ebuild,
- emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild:
- Blocking sys-devel/cons, bug 248792
-
-*emboss-6.1.0-r1 (07 Mar 2010)
-
- 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
- +emboss-6.1.0-r1.ebuild:
- Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay,
- keyworded as in overlay
-
- 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
- Giving up maintainership of this package.
-
- 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.1.0.ebuild:
- Remove documentation that conflicts with EMBASSY phylipnew.
-
-*emboss-6.1.0 (01 Sep 2009)
-
- 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +emboss-6.1.0.ebuild:
- New upstream version.
-
- 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.0.1.ebuild:
- Stabilised on x86 and amd64.
-
- 31 Aug 2009; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild,
- emboss-6.0.1.ebuild:
- Q.A. fixes, including better dependency on ClustalW.
-
- 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -emboss-5.0.0.ebuild:
- Pruning version that will never be stabilised.
-
- 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild:
- Depend on ClustalW 1.83 since version 2.x will soon be added to Portage
- and is incompatible with EMBOSS wrapper programs.
-
-*emboss-6.0.1 (26 Aug 2008)
-
- 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +emboss-6.0.1.ebuild:
- New upstream version.
-
- 25 Jan 2008; Markus Dittrich <markusle@gentoo.org>
- +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild,
- emboss-5.0.0.ebuild:
- Fixed unresolved symbols with as-needed (see bug #207304).
-
- 22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; emboss-4.0.0.ebuild:
- Drop virtual/x11 references.
-
- 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org>
- +files/emboss-README.Gentoo-1:
- Added updated Gentoo README file in reStructuredText format.
-
-*emboss-5.0.0 (18 Jul 2007)
-
- 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +emboss-5.0.0.ebuild:
- New upstream version.
-
- 09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/22emboss,
- -files/22emboss-r1, emboss-4.0.0.ebuild:
- Fixed to use doenvd wrt bug #173884
-
- 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org>
- -emboss-3.0.0-r1.ebuild, emboss-4.0.0.ebuild:
- Pruned old version. Removed ppc-macos keyword, as grobian said the
- package and its dependencies were fully moved into "prefix".
-
- 20 Nov 2006; <blubb@gentoo.org> emboss-4.0.0.ebuild:
- stable on amd64
-
- 15 Nov 2006; Markus Rothe <corsair@gentoo.org> emboss-4.0.0.ebuild:
- Stable on ppc64; bug #153766
-
- 03 Nov 2006; nixnut <nixnut@gentoo.org> emboss-4.0.0.ebuild:
- Stable on ppc wrt bug 153766
-
- 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> emboss-3.0.0-r1.ebuild:
- Added ~sparc to emboss-3 for embassy-phylip-3.6b.
-
- 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild:
- Added to x86.
-
- 18 Aug 2006; Jason Wever <weeve@gentoo.org> emboss-4.0.0.ebuild:
- Added ~sparc keyword wrt bug #144241.
-
-*emboss-4.0.0 (21 Jul 2006)
-
- 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +emboss-4.0.0.ebuild:
- New upstream version. See change log:
- "http://emboss.sourceforge.net/developers/changelog.html".
-
- 20 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -emboss-3.0.0.ebuild:
- Removed old revision.
-
- 08 Apr 2006; Simon Stelling <blubb@gentoo.org> emboss-3.0.0-r1.ebuild:
- stable on amd64
-
- 22 Feb 2006; Fabian Groffen <grobian@gentoo.org> ChangeLog:
- Marked ppc-macos stable (bug #123332)
-
- 22 Feb 2006; <nixnut@gentoo.org> emboss-3.0.0-r1.ebuild:
- Stable on ppc. bug 123332
-
- 21 Feb 2006; Markus Rothe <corsair@gentoo.org> emboss-3.0.0-r1.ebuild:
- Stable on ppc64; bug #123332
-
- 20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> emboss-3.0.0-r1.ebuild:
- Stable on x86; bug #123332
-
- 19 Feb 2006; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0-r1.ebuild:
- Block old versions of pscan to avoid file collisions (see bug #116236).
-
- 23 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +files/README.Gentoo:
- Added missing README file (fixes bug #120071).
-
-*emboss-3.0.0-r1 (21 Jan 2006)
-
- 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
- +emboss-3.0.0-r1.ebuild:
- Install codons and restriction enzyme equivalence files in alternative
- directories. This avoids file collisions on case insensitive filesystems
- (see bug #115446), allows the installation of an updated enzyme prototypes
- file that will give more consistent results (see bug #118832).
-
- 14 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; emboss-3.0.0.ebuild:
- Add modular X dependencies.
-
- 19 Nov 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
- stable on amd64
-
- 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.10.0.ebuild:
- Removed obsolete version.
-
- 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild:
- Stable on ppc-macos (with j4rg0n's permission, bug #102420).
-
- 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-3.0.0.ebuild:
- Stable on ppc.
-
- 24 Sep 2005; Markus Rothe <corsair@gentoo.org> emboss-3.0.0.ebuild:
- Stable on ppc64
-
- 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild:
- Added to x86.
-
- 04 Sep 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
- added ~amd64 keyword
-
- 13 Aug 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild,
- emboss-2.10.0.ebuild:
- Fixed Prosite dependency.
-
-*emboss-3.0.0 (06 Aug 2005)
-
- 06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-3.0.0.ebuild:
- New version.
-
- 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.9.0.ebuild:
- Removed old version.
-
- 25 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.10.0.ebuild:
- Stable ppc-macos
-
- 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> emboss-2.10.0.ebuild:
- Marked ppc stable for bug #96819.
-
- 19 Jun 2005; Markus Rothe <corsair@gentoo.org> emboss-2.10.0.ebuild:
- Stable on ppc64
-
- 13 May 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.10.0.ebuild:
- Added to x86.
-
- 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> emboss-2.10.0.ebuild:
- Added ~ppc64
-
- 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-2.9.0.ebuild:
- Stable on ppc.
-
-*emboss-2.10.0 (22 Mar 2005)
-
- 22 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-2.10.0.ebuild:
- New version.
-
- 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
- Added support for minimal build.
-
- 09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
- Stable ppc-macos
-
- 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
- Ebuild cleanup.
-
- 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
- Unstable ppc-macos.
-
-*emboss-2.9.0 (23 Dec 2004)
-
- 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
- +files/22emboss-r1, +emboss-2.9.0.ebuild:
- Moved from app-sci/emboss to sci-biology/emboss.
-
- 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild,
- -emboss-2.8.0-r3.ebuild:
- Removed old version. Added 2.9.0 to x86.
-
- 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org>
- emboss-2.8.0-r3.ebuild:
- Added to x86.
- emboss-2.8.0-r2.ebuild:
- Removed obsolete ebuild.
-
- 21 Jul 2004; David Holm <dholm@gentoo.org> emboss-2.9.0.ebuild:
- Added to ~ppc.
-
- 20 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
- emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild:
- Removed icc support since no patching is needed.
-
- 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
- Version bump. Changed the configuration and install steps a bit to
- reflect the fact that header files are now installed automatically.
-
- 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
- emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png
- USE flags independent; Added support for icc; Added primer3 and clustalw
- to the dependencies since some EMBOSS programs won't work without them;
- Added support for the biological databases aaindex, cutg, prints, prosite,
- rebase and transfac, which are needed for many EMBOSS programs (the databases
- are PDEPENDencies since they all must be indexed with an EMBOSS program before
- use) (this database support is optional); Added header files installation for
- EMBOSS development.
- emboss-2.8.0-r2.ebuild: Added to x86.
- emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files.
- metadata.xml: Added long description; Set myself as maintainer.
-
- 02 Jun 2004; Aron Griffis <agriffis@gentoo.org> emboss-2.8.0-r1.ebuild,
- emboss-2.8.0-r2.ebuild:
- Fix use invocation
-
- 12 May 2004; David Holm <dholm@gentoo.org> emboss-2.8.0-r2.ebuild:
- Added to ~ppc.
-
-*emboss-2.8.0-r2 (11 May 2004)
-
- 11 May 2004; Patrick Kursawe <phosphan@gentoo.org> emboss-2.8.0-r2.ebuild,
- files/22emboss-r1:
- Adjusted value of PLPLOT_LIB, see bug #50176
-
-*emboss-2.8.0-r1 (30 Jan 2004)
-
- 30 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0-r1.ebuild:
- Modified to use X and png properly for servers
-
- 28 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0.ebuild:
- Modified 2.8.0 ebuild to require X not just USE it.
-
-*emboss-2.8.0 (13 Dec 2003)
-
- 13 Dec 2003; Stephen Diener <sediener@gentoo.org> emboss-2.7.1.ebuild,
- emboss-2.8.0.ebuild:
- Version bump...
-
- 20 Oct 2003; George Shapovalov <george@gentoo.org> metdata.xml :
- added metadata.xml, marked ebuild stable
-
-*emboss-2.7.1 (03 Sep 2003)
-
- 03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild:
- Initial ebuild
-
diff --git a/sci-biology/emboss.new/emboss-6.4.0_p24.ebuild b/sci-biology/emboss.new/emboss-6.4.0_p24.ebuild
deleted file mode 100644
index 7f85061..0000000
--- a/sci-biology/emboss.new/emboss-6.4.0_p24.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $
-
-EAPI=4
-
-inherit emboss
-
-EBO_PATCH="24"
-EBOV=${PV/_p*}
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-SRC_URI="
- ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
- http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.xz"
-[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE+=" minimal"
-
-RDEPEND+=" !sys-devel/cons"
-PDEPEND+="
- !minimal? (
- sci-biology/aaindex
- sci-biology/cutg
- sci-biology/prints
- sci-biology/prosite
- sci-biology/rebase
- sci-biology/transfac
- )"
-
-S="${WORKDIR}"/EMBOSS-${EBOV}
-
-EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
-
-DOCS+=" FAQ THANKS"
-
-src_prepare() {
- [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch
- epatch "${WORKDIR}"/${PF}.patch
- emboss_src_prepare
-}
-
-src_install() {
- default
-
- sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
- dodoc README.Gentoo
-
- # Install env file for setting libplplot and acd files path.
- cat <<- EOF > 22emboss
- # ACD files location
- EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
- EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
- EOF
- doenvd 22emboss
-
- # Clashes #330507, resolved upstream
- mv "${ED}"/usr/bin/{digest,pepdigest} || die
-
- # Remove useless dummy files from the image.
- find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files."
-
- # Move the provided codon files to a different directory. This will avoid
- # user confusion and file collisions on case-insensitive file systems (see
- # bug #115446). This change is documented in "README.Gentoo".
- mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
- die "Failed to move CODON directory."
-
- # Move the provided restriction enzyme prototypes file to a different name.
- # This avoids file collisions with versions of rebase that install their
- # own enzyme prototypes file (see bug #118832).
- mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
- die "Failed to move enzyme equivalence file."
-}
diff --git a/sci-biology/emboss.new/files/emboss-README.Gentoo-2 b/sci-biology/emboss.new/files/emboss-README.Gentoo-2
deleted file mode 100644
index 72fa366..0000000
--- a/sci-biology/emboss.new/files/emboss-README.Gentoo-2
+++ /dev/null
@@ -1,34 +0,0 @@
-Administrating EMBOSS on Gentoo systems
-=======================================
-
-
-Codon data files location
--------------------------
-
-The codon data files that are distributed with EMBOSS are installed in the
-``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
-``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
-these codon files and those installed with the CUTG database. The names of
-these files sometimes vary only by their case. Having both sets of files in
-the same directory is also impossible on systems such as MacOSX, where the
-root filesystem is case insensitive. If you do not have the CUTG database
-installed and want to use the codon files distributed with EMBOSS, you can
-symlink the ``CODONS.orig`` directory to ``CODONS``::
-
- # cd EPREFIX/usr/share/EMBOSS/data
- # ln -s CODONS.orig CODONS
-
-
-Restriction enzymes equivalence file location
----------------------------------------------
-
-The restriction enzymes equivalence file distributed with EMBOSS is installed
-as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
-``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
-collision with the equivalence file provided by the Rebase database. If you do
-not have the Rebase database installed and want to use the equivalence file
-distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
-``embossre.equ``::
-
- # cd EPREFIX/usr/share/EMBOSS/data
- # ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss.new/metadata.xml b/sci-biology/emboss.new/metadata.xml
deleted file mode 100644
index b85761d..0000000
--- a/sci-biology/emboss.new/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
- <longdescription>
- EMBOSS is "The European Molecular Biology Open Software Suite".
- EMBOSS is a free Open Source software analysis package specially
- developed for the needs of the molecular biology (e.g. EMBnet) user
- community. The software automatically copes with data in a variety
- of formats and even allows transparent retrieval of sequence data
- from the web. Also, as extensive libraries are provided with the
- package, it is a platform to allow other scientists to develop and
- release software in true open source spirit. EMBOSS also integrates
- a range of currently available packages and tools for sequence
- analysis into a seamless whole. EMBOSS breaks the historical trend
- towards commercial software packages.
- </longdescription>
-</pkgmetadata>
diff --git a/sci-biology/staden/files/rpath.patch b/sci-biology/staden/files/rpath.patch
deleted file mode 100644
index 7bda217..0000000
--- a/sci-biology/staden/files/rpath.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-diff -cr staden-2.0.0b8-src/ac_stubs/tcl.m4 staden-2.0.0b8-src.orig/ac_stubs/tcl.m4
-*** staden-2.0.0b8-src/ac_stubs/tcl.m4 Wed Feb 9 11:40:00 2011
---- staden-2.0.0b8-src.orig/ac_stubs/tcl.m4 Tue Feb 15 15:12:37 2011
-***************
-*** 2245,2250 ****
---- 2245,2252 ----
-
- AC_SUBST(LD_LIBRARY_PATH_VAR)
-
-+ AC_SUBST(CC_SEARCH_FLAGS)
-+
- # These must be called after we do the basic CFLAGS checks and
- # verify any possible 64-bit or similar switches are necessary
- TEA_TCL_EARLY_FLAGS
-diff -cr staden-2.0.0b8-src/configure staden-2.0.0b8-src.orig/configure
-*** staden-2.0.0b8-src/configure Wed Feb 9 11:39:59 2011
---- staden-2.0.0b8-src.orig/configure Tue Feb 15 15:12:37 2011
-***************
-*** 745,750 ****
---- 745,751 ----
- SHLIB_LD_LIBS
- SHLIB_CFLAGS
- LD_LIBRARY_PATH_VAR
-+ CC_SEARCH_FLAGS
- TCL_INCLUDES
- TCL_TOP_DIR_NATIVE
- TK_INCLUDES
-***************
-*** 13888,13893 ****
---- 13889,13896 ----
-
-
-
-+
-+
- # These must be called after we do the basic CFLAGS checks and
- # verify any possible 64-bit or similar switches are necessary
-
-***************
-*** 15886,15891 ****
---- 15889,15895 ----
- SHLIB_LD_LIBS!$SHLIB_LD_LIBS$ac_delim
- SHLIB_CFLAGS!$SHLIB_CFLAGS$ac_delim
- LD_LIBRARY_PATH_VAR!$LD_LIBRARY_PATH_VAR$ac_delim
-+ CC_SEARCH_FLAGS!$CC_SEARCH_FLAGS$ac_delim
- TCL_INCLUDES!$TCL_INCLUDES$ac_delim
- TCL_TOP_DIR_NATIVE!$TCL_TOP_DIR_NATIVE$ac_delim
- TK_INCLUDES!$TK_INCLUDES$ac_delim
-***************
-*** 15905,15911 ****
- LTLIBOBJS!$LTLIBOBJS$ac_delim
- _ACEOF
-
-! if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 53; then
- break
- elif $ac_last_try; then
- { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
---- 15909,15915 ----
- LTLIBOBJS!$LTLIBOBJS$ac_delim
- _ACEOF
-
-! if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 54; then
- break
- elif $ac_last_try; then
- { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
-diff -cr staden-2.0.0b8-src/staden.profile staden-2.0.0b8-src.orig/staden.profile
-*** staden-2.0.0b8-src/staden.profile Wed Feb 9 11:40:00 2011
---- staden-2.0.0b8-src.orig/staden.profile Tue Feb 15 15:12:37 2011
-***************
-*** 46,54 ****
- then
- [ x"$STADEN_PREPEND" != "x" ] \
- && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
-! || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB
- else
-! LD_LIBRARY_PATH=$STADLIB
- fi
- export LD_LIBRARY_PATH
- fi
---- 46,54 ----
- then
- [ x"$STADEN_PREPEND" != "x" ] \
- && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
-! || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB:$STADENROOT/lib
- else
-! LD_LIBRARY_PATH=$STADLIB:$STADENROOT/lib
- fi
- export LD_LIBRARY_PATH
- fi
-diff -cr staden-2.0.0b8-src/system.mk.in staden-2.0.0b8-src.orig/system.mk.in
-*** staden-2.0.0b8-src/system.mk.in Wed Feb 9 11:40:00 2011
---- staden-2.0.0b8-src.orig/system.mk.in Tue Feb 15 15:12:37 2011
-***************
-*** 61,66 ****
---- 61,67 ----
- # How else do we get commas in a subst text or pattern?
- comma = ,
-
-+ LIB_RUNTIME_DIR = ${prefix}/lib/staden
- CC = @CC@
- #CDEBUG = -Wall -Wno-sign-compare -Wno-pointer-sign -Wno-parentheses -Wno-unused -Wno-char-subscripts -Wno-pointer-to-int-cast -Wno-int-to-pointer-cast
- CFLAGS = @CFLAGS@ $(DEFINES) $(INCLUDES)
-***************
-*** 68,76 ****
- CXXFLAGS = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
- CPP = @CPP@
- CPPFLAGS = @CPPFLAGS@
-! LDFLAGS = -L$(L) @LDFLAGS@
- #CLDFLAGS = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
-! CLDFLAGS = -L$(L)
- CXXLDFLAGS = $(CLDFLAGS)
- F77 = @F77@
- FFLAGS = @FFLAGS@
---- 69,77 ----
- CXXFLAGS = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
- CPP = @CPP@
- CPPFLAGS = @CPPFLAGS@
-! LDFLAGS = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
- #CLDFLAGS = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
-! CLDFLAGS = -L$(L) @CC_SEARCH_FLAGS@
- CXXLDFLAGS = $(CLDFLAGS)
- F77 = @F77@
- FFLAGS = @FFLAGS@
diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
deleted file mode 100644
index 88a6147..0000000
--- a/sci-biology/staden/staden-2.0.0_beta8.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit base eutils flag-o-matic fortran-2 multilib
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden/"
-SRC_URI="
- http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz
- http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="curl debug fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-DEPEND="
- app-arch/xz-utils
- dev-lang/tk
- dev-tcltk/tklib
- >=media-libs/libpng-1.2
- sci-biology/samtools
- >=sci-libs/io_lib-1.12.2
- >=sys-libs/zlib-1.2
- virtual/fortran"
-RDEPEND="${DEPEND}
- >=dev-tcltk/iwidgets-4.0
- tcl? ( >=dev-tcltk/itcl-3.2 )
- tk? ( >=dev-tcltk/itk-3.2 )"
-
-S="${WORKDIR}"/staden-2.0.0b8-src
-
-src_prepare() {
- unpack ${A} || die
- cd "${S}" || die "Cannot cd ${WORKDIR}/staden-2.0.0b8-src"
- epatch "${FILESDIR}"/rpath.patch || die "failed to apply -rpath=/usr/lib/staden patch"
- ./bootstrap || die "bootstrap failed"
-}
-
-src_configure(){
- local myconf
- use X && myconf=" --with-x"
- myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK
- use amd64 && myconf="${myconf} --enable-64bit"
- use debug && append-cflags "-DCACHE_REF_DEBUG"
- econf ${myconf}
-}
-
-src_install() {
- # TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
- emake install DESTDIR="${D}" || die "make install failed"
- #cd "${WORKDIR}"/staden_doc-2.0.0b8-src || die "failed to cd "${WORKDIR}"/staden_doc-2.0.0b8-src"
- #make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
-
- # install the LDPATH so that it appears in /etc/ld.so.conf after env-update
- # subsequently, apps linked against /usr/lib/staden can be run because
- # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
- # somehow for gap2caf, for example
- cat >> "${T}"/99staden <<- EOF
- LDPATH=/usr/$(get_libdir)/staden
- EOF
- doenvd 99staden
-}
diff --git a/sci-chemistry/molsketch/molsketch-9999.ebuild b/sci-chemistry/molsketch/molsketch-9999.ebuild
deleted file mode 100644
index b131269..0000000
--- a/sci-chemistry/molsketch/molsketch-9999.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molsketch/molsketch-0.2.0-r1.ebuild,v 1.2 2011/03/26 22:26:30 jlec Exp $
-
-EAPI=3
-
-inherit cmake-utils git-2 multilib
-
-MY_P=${P/m/M}-Source
-
-DESCRIPTION="A drawing tool for 2D molecular structures"
-HOMEPAGE="http://molsketch.sourceforge.net/"
-SRC_URI=""
-EGIT_REPO_URI="git://molsketch.git.sourceforge.net/gitroot/molsketch/molsketch"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
- =sci-chemistry/openbabel-2.2*
- x11-libs/qt-core:4
- x11-libs/qt-gui:4
- x11-libs/qt-test:4
- || (
- >=x11-libs/qt-assistant-4.7.0:4[compat]
- <x11-libs/qt-assistant-4.7.0:4 )"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/${MY_P}
-
-src_prepare() {
- sed -e "/LIBRARY DESTINATION/ s/lib/$(get_libdir)/g" \
- -i libmolsketch/src/CMakeLists.txt || die #351246
- sed -e "s:doc/molsketch:doc/${PF}:g" \
- -i molsketch/src/{CMakeLists.txt,mainwindow.cpp} || die
-}
-
-src_configure() {
- local mycmakeargs=(
- -DOPENBABEL2_INCLUDE_DIR="${EPREFIX}/usr/include/openbabel-2.0" )
- cmake-utils_src_configure
-}
diff --git a/sci-libs/libccp4/libccp4-6.2.20111210.ebuild b/sci-libs/libccp4/libccp4-6.2.20111210.ebuild
deleted file mode 100644
index ecb0a4c..0000000
--- a/sci-libs/libccp4/libccp4-6.2.20111210.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-inherit autotools-utils
-
-DESCRIPTION="Main function library of the Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="LGPL-3"
-IUSE="static-libs"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-
diff --git a/sci-libs/libccp4/metadata.xml b/sci-libs/libccp4/metadata.xml
deleted file mode 100644
index d31449d..0000000
--- a/sci-libs/libccp4/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!--
-This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a
-number of subelements are allowed: herd, maintainer, and
-longdescription. herd is a required subelement.
-
-For a full description look at:
-http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4
-
-
-Before committing, please remove the comments from this file. They are
-not relevant for general metadata.xml files.
--->
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>@gentoo.org</email>
-<!-- <description>Description of the maintainership</description> -->
-</maintainer>
-<longdescription>
- Long description of the package
-</longdescription>
-<!--
-<use>
- <flag name='flag'>Description of how USE='flag' affects this package</flag>
- <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this
- package</flag>
- <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking.
- Requires an installed dictionary from <cat>app-dicts</cat></flag>
-</use>
--->
-</pkgmetadata>
diff --git a/sci-mathematics/petsc/files/petsc-configure-pic.patch b/sci-mathematics/petsc/files/petsc-configure-pic.patch
deleted file mode 100644
index bbfdae1..0000000
--- a/sci-mathematics/petsc/files/petsc-configure-pic.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- config/BuildSystem/config/setCompilers.py.old 2010-09-07 21:41:32.693103846 +0200
-+++ config/BuildSystem/config/setCompilers.py 2010-09-07 21:41:45.322093881 +0200
-@@ -875,7 +875,7 @@
- languages.append('FC')
- for language in languages:
- self.pushLanguage(language)
-- for testFlag in ['-PIC', '-fPIC', '-KPIC','-qpic']:
-+ for testFlag in ['-fPIC', '-PIC', '-KPIC', '-qpic']:
- try:
- self.framework.logPrint('Trying '+language+' compiler flag '+testFlag)
- if not self.checkLinkerFlag(testFlag):
diff --git a/sci-mathematics/petsc/files/petsc-disable-env-warnings.patch b/sci-mathematics/petsc/files/petsc-disable-env-warnings.patch
deleted file mode 100644
index d2ee44e..0000000
--- a/sci-mathematics/petsc/files/petsc-disable-env-warnings.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: petsc-3.2-p6/config/BuildSystem/config/setCompilers.py
-===================================================================
---- petsc-3.2-p6.orig/config/BuildSystem/config/setCompilers.py
-+++ petsc-3.2-p6/config/BuildSystem/config/setCompilers.py
-@@ -1463,7 +1463,7 @@ This way - mpi compilers from '''+self.a
- 'LDFLAGS','LIBS','MPI_DIR']
- for envVal in ignoreEnv:
- if envVal in os.environ:
-- self.logPrintBox('***** WARNING: '+envVal+' found in enviornment variables - ignoring ******')
-+ #self.logPrintBox('***** WARNING: '+envVal+' found in enviornment variables - ignoring ******')
- del os.environ[envVal]
- return
-
diff --git a/sci-mathematics/petsc/files/petsc-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-disable-rpath.patch
deleted file mode 100644
index 3c443b2..0000000
--- a/sci-mathematics/petsc/files/petsc-disable-rpath.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- config/BuildSystem/config/setCompilers.py 2010-11-24 18:01:17.110124425 +0100
-+++ config/BuildSystem/config/setCompilers.py 2010-11-24 18:02:28.710104226 +0100
-@@ -1186,12 +1186,7 @@
- for language in languages:
- flag = '-L'
- self.pushLanguage(language)
-- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
-- if not Configure.isDarwin():
-- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,']
-- else:
-- testFlags = []
-- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not.
-+ testFlags = []
- if self.isSun(self.framework.getCompiler()):
- testFlags.insert(0,'-R')
- for testFlag in testFlags:
diff --git a/sci-mathematics/petsc/files/petsc-fix-afterimage.patch b/sci-mathematics/petsc/files/petsc-fix-afterimage.patch
deleted file mode 100644
index 27f4d3b..0000000
--- a/sci-mathematics/petsc/files/petsc-fix-afterimage.patch
+++ /dev/null
@@ -1,71 +0,0 @@
-
-# HG changeset patch
-# User Jed Brown <jed@59A2.org>
-# Date 1330818004 21600
-# Node ID fb79e104b74267c74aa64f125e7eb6a64bce4b14
-# Parent 8242202a123dd2cbfea7a4a2a9a1797951306f8d
-Fixes for libAfterImage compilation, ImageMagick is still just a stub
-
-diff -r 8242202a123d -r fb79e104b742 config/PETSc/packages/afterimage.py
---- a/config/PETSc/packages/afterimage.py Sat Mar 03 16:05:00 2012 -0600
-+++ b/config/PETSc/packages/afterimage.py Sat Mar 03 17:40:04 2012 -0600
-@@ -9,6 +9,7 @@
- self.includedir = ''
- self.libdir = '../../lib'
- self.double = 0
-+ self.complex = 1
-
- def setupDependencies(self, framework):
- PETSc.package.NewPackage.setupDependencies(self, framework)
-diff -r 8242202a123d -r fb79e104b742 config/PETSc/packages/imagemagick.py
---- a/config/PETSc/packages/imagemagick.py Sat Mar 03 16:05:00 2012 -0600
-+++ b/config/PETSc/packages/imagemagick.py Sat Mar 03 17:40:04 2012 -0600
-@@ -4,8 +4,8 @@
- def __init__(self, framework):
- PETSc.package.NewPackage.__init__(self, framework)
- self.functions = ['IsMagickInstantiated']
-- self.includes = ['MagicCore/MagickCore.h']
-- self.liblist = [['libMagicCore.a']]
-+ self.includes = ['magick/MagickCore.h']
-+ self.liblist = [['libMagickCore.a']]
-
-
-
-diff -r 8242202a123d -r fb79e104b742 src/sys/draw/impls/x/xinit.c
---- a/src/sys/draw/impls/x/xinit.c Sat Mar 03 16:05:00 2012 -0600
-+++ b/src/sys/draw/impls/x/xinit.c Sat Mar 03 17:40:04 2012 -0600
-@@ -291,7 +291,7 @@
- #include <afterimage.h>
- #undef __FUNCT__
- #define __FUNCT__ "PetscDrawSave_X"
--PetscErrorCode PetscDrawSave_X(PetscDraw draw,PetscViewer viewer)
-+PetscErrorCode PetscDrawSave_X(PetscDraw draw)
- {
- PetscDraw_X *drawx = (PetscDraw_X*)draw->data;
- XImage *image;
-@@ -328,10 +328,10 @@
- void deflateEnd(void) {;}
-
- #elif defined(PETSC_HAVE_IMAGEMAGICK)
--#include <MagicCore/MagickCore.h>
-+#include <magick/MagickCore.h>
- #undef __FUNCT__
- #define __FUNCT__ "PetscDrawSave_X"
--PetscErrorCode PetscDrawSave_X(PetscDraw draw,PetscViewer viewer)
-+PetscErrorCode PetscDrawSave_X(PetscDraw draw)
- {
- PetscDraw_X *drawx = (PetscDraw_X*)draw->data;
- Image *image;
-diff -r 8242202a123d -r fb79e104b742 src/sys/draw/impls/x/xops.c
---- a/src/sys/draw/impls/x/xops.c Sat Mar 03 16:05:00 2012 -0600
-+++ b/src/sys/draw/impls/x/xops.c Sat Mar 03 17:40:04 2012 -0600
-@@ -551,7 +551,7 @@
- PetscFunctionReturn(0);
- }
-
--PetscErrorCode PetscDrawSave_X(PetscDraw,PetscViewer);
-+PetscErrorCode PetscDrawSave_X(PetscDraw);
- PetscErrorCode PetscDrawSetSave_X(PetscDraw,const char*);
-
- static struct _PetscDrawOps DvOps = { PetscDrawSetDoubleBuffer_X,
-
diff --git a/sci-mathematics/petsc/files/petsc-fix-xops.patch b/sci-mathematics/petsc/files/petsc-fix-xops.patch
deleted file mode 100644
index cd2edeb..0000000
--- a/sci-mathematics/petsc/files/petsc-fix-xops.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# HG changeset patch
-# User Jed Brown <jed@59A2.org>
-# Date 1330812300 21600
-# Node ID 8242202a123dd2cbfea7a4a2a9a1797951306f8d
-# Parent 759927945bb3cdd30ff4265c043264db5286d263
-Fix declaration of PetscDrawSave_X()
-
-diff -r 759927945bb3 -r 8242202a123d src/sys/draw/impls/x/xops.c
---- a/src/sys/draw/impls/x/xops.c Fri Mar 02 11:10:34 2012 -0600
-+++ b/src/sys/draw/impls/x/xops.c Sat Mar 03 16:05:00 2012 -0600
-@@ -551,7 +551,7 @@
- PetscFunctionReturn(0);
- }
-
--PetscErrorCode PetscDrawSave_X(PetscDraw);
-+PetscErrorCode PetscDrawSave_X(PetscDraw,PetscViewer);
- PetscErrorCode PetscDrawSetSave_X(PetscDraw,const char*);
-
- static struct _PetscDrawOps DvOps = { PetscDrawSetDoubleBuffer_X,
-
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