[gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/

["Justin Lecher" <jlec@gentoo.org>]

commit:     cfb0869296a4156fe8c7c65c6031debaae954463
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  4 08:11:55 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb  4 08:13:00 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cfb08692

sci-biology/emboss: Drop old

Package-Manager: portage-2.2.15
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 sci-biology/emboss/ChangeLog                       |   3 +
 sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild       |  94 ------
 sci-biology/emboss/files/ax_lib_mysql.m4           | 147 ----------
 .../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch |  47 ---
 .../emboss-6.3.1_p4-r2_compilations-paths.patch    | 315 ---------------------
 .../emboss/files/emboss-6.3.1_p4-r2_libtool.patch  |  18 --
 .../emboss/files/emboss-6.3.1_p4-r2_plcol.patch    | 112 --------
 ...mboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch |  13 -
 sci-biology/emboss/files/emboss-README.Gentoo-2    |  34 ---
 9 files changed, 3 insertions(+), 780 deletions(-)

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index a8d74bc..a6558c1 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 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 $
 
+  04 Feb 2015; Justin Lecher <jlec@gentoo.org> -emboss-6.3.1_p4-r2.ebuild:
+  Drop old
+
   04 Feb 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Clean a bit, user readme.gentoo.eclass
 

diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
deleted file mode 100644
index 962d472..0000000
--- a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-inherit emboss eutils
-
-EBO_PATCH="4"
-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.bz2"
-##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz"
-
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE+=" minimal"
-
-RDEPEND+=" !sys-devel/cons"
-PDEPEND+="
-	!minimal? (
-		sci-biology/aaindex
-		sci-biology/cutg
-		sci-biology/prints
-		sci-biology/prosite
-		sci-biology/rebase
-		sci-biology/transfac
-		sci-libs/plplot
-		)"
-
-S="${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}"/${PF}.patch
-	epatch "${FILESDIR}/${PF}"_plcol.patch
-	epatch "${FILESDIR}/${PF}"_compilations-paths.patch
-	epatch "${FILESDIR}/${PF}"_rename_plwid_to_plwidth.patch
-	# cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4
-	emboss_src_prepare
-	autoreconf -vfi
-	epatch "${FILESDIR}/${PF}"_libtool.patch
-}
-
-#src_compile() {
-#	# epatch "${FILESDIR}/${PF}"_Makefile.patch
-#	sed -i -e "s#GD_LIBS = .*#GD_LIBS =#" Makefile
-#	sed -i -e "s#^LIBS = .*#LIBS =#" Makefile
-#	sed -i -e "s#^PLPLOT_LIBS = .*#PLPLOT_LIBS =#" Makefile
-#	sed -i -e "s#^libnucleus_la_LDFLAGS = .*#libnucleus_la_LDFLAGS = \$(LDFLAGS)#" Makefile
-#}
-
-src_install() {
-	default
-
-	sed -e "s:EPREFIX:${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."
-
-	# fix /usr/share/doc/emboss-6.3.1_p4-r1/html to point to /usr/share/doc/emboss-6.3.1_p4-r1/programs/html
-	# instead of /usr/share/EMBOSS/doc/html (which does not exist)
-}

diff --git a/sci-biology/emboss/files/ax_lib_mysql.m4 b/sci-biology/emboss/files/ax_lib_mysql.m4
deleted file mode 100644
index e27d755..0000000
--- a/sci-biology/emboss/files/ax_lib_mysql.m4
+++ /dev/null
@@ -1,147 +0,0 @@
-# ===========================================================================
-#       http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-#   AX_LIB_MYSQL([MINIMUM-VERSION])
-#
-# DESCRIPTION
-#
-#   This macro provides tests of availability of MySQL client library of
-#   particular version or newer.
-#
-#   AX_LIB_MYSQL macro takes only one argument which is optional. If there
-#   is no required version passed, then macro does not run version test.
-#
-#   The --with-mysql option takes one of three possible values:
-#
-#   no - do not check for MySQL client library
-#
-#   yes - do check for MySQL library in standard locations (mysql_config
-#   should be in the PATH)
-#
-#   path - complete path to mysql_config utility, use this option if
-#   mysql_config can't be found in the PATH
-#
-#   This macro calls:
-#
-#     AC_SUBST(MYSQL_CFLAGS)
-#     AC_SUBST(MYSQL_LDFLAGS)
-#     AC_SUBST(MYSQL_VERSION)
-#
-#   And sets:
-#
-#     HAVE_MYSQL
-#
-# LICENSE
-#
-#   Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
-#
-#   Copying and distribution of this file, with or without modification, are
-#   permitted in any medium without royalty provided the copyright notice
-#   and this notice are preserved. This file is offered as-is, without any
-#   warranty.
-
-#serial 12
-
-AC_DEFUN([AX_LIB_MYSQL],
-[
-    AC_ARG_WITH([mysql],
-        AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
-            [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
-        ),
-        [
-        if test "$withval" = "no"; then
-            want_mysql="no"
-        elif test "$withval" = "yes"; then
-            want_mysql="yes"
-        else
-            want_mysql="yes"
-            MYSQL_CONFIG="$withval"
-        fi
-        ],
-        [want_mysql="yes"]
-    )
-    AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
-
-    MYSQL_CFLAGS=""
-    MYSQL_LDFLAGS=""
-    MYSQL_VERSION=""
-
-    dnl
-    dnl Check MySQL libraries
-    dnl
-
-    if test "$want_mysql" = "yes"; then
-
-        if test -z "$MYSQL_CONFIG" ; then
-            AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
-        fi
-
-        if test "$MYSQL_CONFIG" != "no"; then
-            MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
-            MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`"
-
-            MYSQL_VERSION=`$MYSQL_CONFIG --version`
-
-            found_mysql="yes"
-        else
-            found_mysql="no"
-        fi
-    fi
-
-    dnl
-    dnl Check if required version of MySQL is available
-    dnl
-
-
-    mysql_version_req=ifelse([$1], [], [], [$1])
-
-    if test "$found_mysql" = "yes" -a -n "$mysql_version_req"; then
-
-        AC_MSG_CHECKING([if MySQL version is >= $mysql_version_req])
-
-        dnl Decompose required version string of MySQL
-        dnl and calculate its number representation
-        mysql_version_req_major=`expr $mysql_version_req : '\([[0-9]]*\)'`
-        mysql_version_req_minor=`expr $mysql_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
-        mysql_version_req_micro=`expr $mysql_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
-        if test "x$mysql_version_req_micro" = "x"; then
-            mysql_version_req_micro="0"
-        fi
-
-        mysql_version_req_number=`expr $mysql_version_req_major \* 1000000 \
-                                   \+ $mysql_version_req_minor \* 1000 \
-                                   \+ $mysql_version_req_micro`
-
-        dnl Decompose version string of installed MySQL
-        dnl and calculate its number representation
-        mysql_version_major=`expr $MYSQL_VERSION : '\([[0-9]]*\)'`
-        mysql_version_minor=`expr $MYSQL_VERSION : '[[0-9]]*\.\([[0-9]]*\)'`
-        mysql_version_micro=`expr $MYSQL_VERSION : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
-        if test "x$mysql_version_micro" = "x"; then
-            mysql_version_micro="0"
-        fi
-
-        mysql_version_number=`expr $mysql_version_major \* 1000000 \
-                                   \+ $mysql_version_minor \* 1000 \
-                                   \+ $mysql_version_micro`
-
-        mysql_version_check=`expr $mysql_version_number \>\= $mysql_version_req_number`
-        if test "$mysql_version_check" = "1"; then
-            AC_MSG_RESULT([yes])
-        else
-            AC_MSG_RESULT([no])
-        fi
-    fi
-
-    if test "$found_mysql" = "yes" ; then
-        AC_DEFINE([HAVE_MYSQL], [1],
-                  [Define to 1 if MySQL libraries are available])
-    fi
-
-    AC_SUBST([MYSQL_VERSION])
-    AC_SUBST([MYSQL_CFLAGS])
-    AC_SUBST([MYSQL_LDFLAGS])
-])

diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch
deleted file mode 100644
index 419369e..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch
+++ /dev/null
@@ -1,47 +0,0 @@
---- EMBOSS-6.3.1/nucleus/Makefile	2013-09-11 14:50:25.140219756 +0200
-+++ nucleus/Makefile	2013-09-11 14:52:00.920220006 +0200
-@@ -165,7 +165,7 @@
- ESYSTEMLIBS = 
- EXEEXT = 
- FGREP = /bin/grep -F
--GD_LIBS = -ljpeg -lfontconfig -lfreetype -lz -lm -lgd
-+GD_LIBS = 
- GREP = /bin/grep
- HAVE_MEMMOVE = 
- HAVE_STRERROR = 
-@@ -180,7 +180,7 @@
- LD = /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
- LDFLAGS = -Wl,--as-needed
- LIBOBJS = 
--LIBS =   -L/usr/lib64/mysql -lmysqlclient -lpthread -lz -lm -lrt -lssl -lcrypto -ldl -lm  -lhpdf -lpng16  -L/usr/lib64 -lz  -ljpeg -lfontconfig -lfreetype -lz -lm -lgd
-+LIBS =   
- LIBTOOL = $(SHELL) $(top_builddir)/libtool
- LIPO = 
- LN_S = ln -s
-@@ -219,7 +219,7 @@
- # zap the crap
- PLPLOT_CFLAGS = 
- PLPLOT_CPPFLAGS = 
--PLPLOT_LIBS = -lplplotd -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lSM -lICE -lX11 -lXext -lgd -lpng -lz -ljpeg -lfreetype -lSM -lICE -lX11 -lXext -lpthread -lLASi -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfreetype -lfontconfig -lhpdf -lm -lcsirocsa -lnistcd -lqsastime -lfreetype 
-+PLPLOT_LIBS = 
- PNG_CFLAGS = -I/usr/include/libpng16 
- PNG_LIBS = -lpng16 
- POSIX_MALLOC_THRESHOLD = -DPOSIX_MALLOC_THRESHOLD=10
-@@ -336,7 +336,7 @@
- VERS_INF = -version-info 6:3:0
- LINKFLAGS = $(VERS_INF)
- #LINKFLAGS = $(VERS_INF) $(CYGWIN_LDFLAGS) $(CYGWIN_LIBS)
--libnucleus_la_LDFLAGS = $(LINKFLAGS)
-+libnucleus_la_LDFLAGS = $(LDFLAGS)
- libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd
- all: all-am
- 
-@@ -407,7 +407,7 @@
- 	  rm -f $${locs}; \
- 	}
- libnucleus.la: $(libnucleus_la_OBJECTS) $(libnucleus_la_DEPENDENCIES) $(EXTRA_libnucleus_la_DEPENDENCIES) 
--	$(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(libnucleus_la_LIBADD) $(LIBS)
-+	$(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(LIBS)
- 
- mostlyclean-compile:
- 	-rm -f *.$(OBJEXT)

diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch
deleted file mode 100644
index 8f87ef9..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch
+++ /dev/null
@@ -1,315 +0,0 @@
---- EMBOSS-6.3.1/configure.in	2013-09-11 03:55:15.510117066 +0200
-+++ configure.in	2013-09-11 03:48:10.410115955 +0200
-@@ -449,7 +447,8 @@
-     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"
-+    CPPFLAGS="$CPPFLAGS -I/usr/X11/include"
-+    LDFLAGS="$LDFLAGS -L/usr/X11/lib"
-     fi
-     fi
-     fi
-@@ -461,7 +460,7 @@
- AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
- AC_SUBST(ESYSTEMLIBS)
- AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
--AC_SUBST(PLPLOT_CFLAGS)
-+AC_SUBST(PLPLOT_CPPFLAGS)
- AC_SUBST(PLPLOT_LIBS)
- 
- 
---- EMBOSS-6.3.1/ajax/graphics/Makefile.am	2013-09-11 03:27:30.110112715 +0200
-+++ ajax/graphics/Makefile.am	2013-09-11 03:58:50.860117628 +0200
-@@ -19,7 +19,7 @@
- 
- 
- INCLUDES = \
--$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
-+$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot
- 
- AJAXGSRC = ajgraph.c ajhist.c
- 
---- EMBOSS-6.3.1/ajax/acd/Makefile.am	2013-09-11 03:27:30.110112715 +0200
-+++ ajax/acd/Makefile.am	2013-09-11 03:59:10.310117679 +0200
-@@ -24,7 +24,8 @@
- -I$(top_srcdir)/ajax/core \
- -I$(top_srcdir)/ajax/graphics \
- -I$(top_srcdir)/ajax/ensembl \
---I$(top_srcdir)/ajax/ajaxdb
-+-I$(top_srcdir)/ajax/ajaxdb \
-+-I$(top_srcdir)/plplot
- 
- ACDSRC = ajacd.c
- 
---- EMBOSS-6.3.1/nucleus/Makefile.am	2013-09-11 03:27:30.110112715 +0200
-+++ nucleus/Makefile.am	2013-09-11 03:59:28.630117727 +0200
-@@ -32,7 +32,7 @@
- 	$(EXTRA_INCLUDES) \
- 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
- 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
--	-I$(top_srcdir)/ajax/acd
-+	-I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
- 
- NUCLSRC =  embaln.c embcom.c embcons.c embdata.c embdbi.c embdmx.c \
- 	embdomain.c embest.c embexit.c embgroup.c embiep.c embindex.c \
---- EMBOSS-6.3.1/emboss/Makefile.am	2013-09-11 03:27:30.110112715 +0200
-+++ emboss/Makefile.am	2013-09-11 03:59:46.340117773 +0200
-@@ -89,7 +89,7 @@
- 	$(EXTRA_INCLUDES) \
- 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
- 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
--	-I$(top_srcdir)/ajax/acd
-+	-I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
- 
- 
- aaindexextract_SOURCES = aaindexextract.c
---- EMBOSS-6.3.1/Makefile.am	2013-09-11 04:19:01.770120791 +0200
-+++ Makefile.am	2013-09-11 04:19:18.460120835 +0200
-@@ -13,8 +13,8 @@
- JEMBOSS_DIR = jemboss
- endif
- 
--SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
--DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
-+SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR)
-+DIST_SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR)
- 
- # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
- 
---- EMBOSS-6.3.1/plplot/Makefile.am	2013-09-11 09:34:44.620170277 +0200
-+++ plplot/Makefile.am	2013-09-11 09:35:35.820170411 +0200
-@@ -10,26 +10,27 @@
- if AMPNG
- 
- if AMPDF
--TESTPDF_CFLAGS = -Wl,-G -lhpdf
-+TESTPDF_LIBS = -Wl,-G -lhpdf
- else
--TESTPDF_CFLAGS = -Wl,-G
-+TESTPDF_LIBS = -Wl,-G
- endif
- 
--TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lgd -lpng -lz -lX11 -lm
-+TESTPNG_LIBS = $(TESTPDF_LIBS) -lgd -lpng -lz -lX11 -lm
- else
--TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lX11
-+TESTPNG_LIBS = $(TESTPDF_LIBS) -lX11
- endif
- endif
- endif
- 
--AM_CFLAGS = $(TESTPNG_CFLAGS)
-+AM_LIBS = $(TESTPNG_LIBS)
- 
- if ISCYGWIN
- CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import
- CYGWIN_LIBS = -lX11 -lgd -lpng -lz
- endif
- 
--INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
-+INCLUDES = -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
-+LIBS = $(AM_LIBS)
- 
- PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \
- plctrl.c plcvt.c pldtik.c plfill.c plhist.c plline.c plmap.c \
---- EMBOSS-6.3.1/m4/pngdriver.m4	2013-09-11 10:39:07.680180369 +0200
-+++ m4/pngdriver.m4	2013-09-11 10:44:16.000181174 +0200
-@@ -63,7 +63,8 @@
- 	  if test "`uname`" = "SunOS"; then
- 	        AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv)
- 	if test $ICCHECK = "1" ; then
--	        LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv"
-+	        LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib"
-+		LIBS="${LIBS} -liconv"
- 	fi
- 	    LDFLAGS="$LDFLAGS -R$ALT_HOME/lib"
-           fi
---- EMBOSS-6.3.1/m4/java.m4	2013-09-11 10:39:03.490180358 +0200
-+++ m4/java.m4	2013-09-11 10:46:08.240181467 +0200
-@@ -180,7 +180,7 @@
- 
- 	  if test "$withval" = "yes" ; then
- 	        CFLAGS="$CFLAGS -D_REENTRANT" 
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- 
-@@ -192,38 +192,38 @@
- 
- 	  if test "$withval" = "linux" ; then
- 	        CFLAGS="$CFLAGS -D_REENTRANT" 
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- 
- 	  if test "$withval" = "solaris" ; then
- 	        CFLAGS="$CFLAGS -D_POSIX_C_SOURCE=199506L" 
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- 	  if test "$withval" = "macos" ; then
- 	        CFLAGS="$CFLAGS"
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- 	  if test "$withval" = "hpux" ; then
- 	        CFLAGS="$CFLAGS -Ae +z -DNATIVE -D_POSIX_C_SOURCE=199506L" 
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- 	  if test "$withval" = "irix" ; then
- 	        CFLAGS="$CFLAGS" 
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- 	  if test "$withval" = "aix" ; then
- 	        CFLAGS="$CFLAGS -D_REENTRANT" 
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- 	  if test "$withval" = "osf" ; then
- 	        CFLAGS="$CFLAGS -D_REENTRANT -D_OSF_SOURCE" 
--		LDFLAGS="$LDFLAGS -lpthread"
-+		LDFLAGS="$LDFLAGS"
- 		LIBS="$LIBS -lpthread"
- 	  fi
- else
---- EMBOSS-6.3.1/m4/mysql.m4	2013-09-11 11:03:07.160184129 +0200
-+++ m4/mysql.m4	2013-09-11 11:04:39.440184370 +0200
-@@ -85,7 +85,6 @@
-             AC_MSG_CHECKING([for MySQL libraries])
- 
- dnl         MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
--            MYSQL_CFLAGS="`$MYSQL_CONFIG --include`"
-             MYSQL_LIBS="`$MYSQL_CONFIG --libs`"
- 
-             MYSQL_VERSION=`$MYSQL_CONFIG --version`
---- EMBOSS-6.3.1/m4/mysql.m4	2013-09-11 11:38:09.330189621 +0200
-+++ m4/mysql.m4	2013-09-11 11:41:02.170190072 +0200
-@@ -170,6 +170,4 @@
-     fi
- 
-     AC_SUBST([MYSQL_VERSION])
--    AC_SUBST([MYSQL_CFLAGS])
--    AC_SUBST([MYSQL_LIBS])
- ])
---- EMBOSS-6.3.1/configure.in	2013-09-11 12:23:17.330196695 +0200
-+++ configure.in	2013-09-11 12:23:21.480196706 +0200
-@@ -8,6 +8,8 @@
- AC_INIT(ajax/core/ajmath.c)
- AM_INIT_AUTOMAKE([EMBOSS],[6.3.1])
- 
-+AC_CONFIG_MACRO_DIR([m4])
-+
- # Make sure CFLAGS is defined to stop LT_INIT adding -g
- CFLAGS="$CFLAGS "
- 
---- EMBOSS-6.3.1/nucleus/Makefile.am	2013-09-11 12:33:14.260198254 +0200
-+++ nucleus/Makefile.am	2013-09-11 12:33:16.650198260 +0200
-@@ -58,4 +58,4 @@
- endif
- 
- libnucleus_la_LDFLAGS =  $(LINKFLAGS)
--libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la
-+libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd
---- EMBOSS-6.3.1/ajax/ensembl/Makefile.am	2013-09-11 12:41:06.340199487 +0200
-+++ ajax/ensembl/Makefile.am	2013-09-11 12:41:40.460199577 +0200
-@@ -56,5 +56,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
- 
--libensembl_la_LDFLAGS = $(LINKFLAGS)
--libensembl_la_LIBADD = ../core/libajax.la
-+libensembl_la_LDFLAGS = $(LINKFLAGS) -L../core
-+libensembl_la_LIBADD = -lajax
---- EMBOSS-6.3.1/ajax/graphics/Makefile.am	2013-09-11 12:42:17.730199674 +0200
-+++ ajax/graphics/Makefile.am	2013-09-11 12:42:47.000199750 +0200
-@@ -35,5 +35,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
- 
--libajaxg_la_LDFLAGS = $(LINKFLAGS)
--libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
-+libajaxg_la_LDFLAGS = $(LINKFLAGS) -L../core/
-+libajaxg_la_LIBADD = -lajax $(EXTRA_LIBS)
---- EMBOSS-6.3.1/ajax/acd/Makefile.am	2013-09-11 12:43:11.660199815 +0200
-+++ ajax/acd/Makefile.am	2013-09-11 12:44:01.520199945 +0200
-@@ -41,5 +41,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
- 
--libacd_la_LDFLAGS = $(LINKFLAGS)
--libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
-+libacd_la_LDFLAGS = $(LINKFLAGS) -L../core -L../graphics -L../ajaxdb
-+libacd_la_LIBADD = -lajax -lajaxg -lajaxdb
---- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am	2013-09-11 12:44:10.980199970 +0200
-+++ ajax/ajaxdb/Makefile.am	2013-09-11 12:44:40.040200046 +0200
-@@ -37,5 +37,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
- 
--libajaxdb_la_LDFLAGS = $(LINKFLAGS)
--libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
-+libajaxdb_la_LDFLAGS = $(LINKFLAGS) -L../core -L../ensembl
-+libajaxdb_la_LIBADD = -lajax -lensembl
---- EMBOSS-6.3.1/configure.in	2013-09-11 13:24:39.720206315 +0200
-+++ configure.in	2013-09-11 13:24:58.610206364 +0200
-@@ -319,10 +319,8 @@
- AX_LIB_MYSQL
- AX_LIB_POSTGRESQL
- 
--CFLAGS="$CFLAGS $MYSQL_CFLAGS"
- LIBS="${MYSQL_LIBS} ${LIBS}"
- 
--CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
- LIBS="$POSTGRESQL_LIBS $LIBS"
- 
- 
---- EMBOSS-6.3.1/ajax/core/Makefile.am	2013-09-11 13:47:36.790209912 +0200
-+++ ajax/core/Makefile.am	2013-09-11 13:47:40.550209922 +0200
-@@ -65,5 +65,5 @@
- LINKFLAGS = $(VERS_INF)
- endif
- 
--libajax_la_LDFLAGS = $(LINKFLAGS)
-+libajax_la_LDFLAGS =
- libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS)
---- EMBOSS-6.3.1/nucleus/Makefile.am	2013-09-11 14:03:21.960212381 +0200
-+++ nucleus/Makefile.am	2013-09-11 14:03:58.910212478 +0200
-@@ -22,11 +22,14 @@
- EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
- -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
- else
--EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
-+EXTRA_INCLUDES =
- endif
- endif
- 
- 
-+# zap the crap
-+PLPLOT_CFLAGS =
-+
- INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
- 	-I$(top_srcdir)/ajax \
- 	$(EXTRA_INCLUDES) \
---- EMBOSS-6.3.1/emboss/Makefile.am	2013-09-11 14:23:50.570215591 +0200
-+++ emboss/Makefile.am	2013-09-11 14:24:24.950215680 +0200
-@@ -328,9 +328,7 @@
- 
- LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
- 	../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
--	../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
--	$(EXTRA_LDS) \
--	$(XLIB)
-+	../ajax/graphics/libajaxg.la ../ajax/core/libajax.la
- 
- pkgdata_DATA = emboss.default.template
- pkgdatadir=$(prefix)/share/$(PACKAGE)

diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch
deleted file mode 100644
index ad358e1..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- EMBOSS-6.3.1/m4/libtool.m4	2013-09-11 12:03:45.180193633 +0200
-+++ m4/libtool.m4	2013-09-11 12:04:19.280193722 +0200
-@@ -4768,13 +4768,13 @@
- 	*Sun\ F*)			# Sun Fortran 8.3
- 	  tmp_sharedflag='-G' ;;
- 	esac
--	_LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
-+	_LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname -Wl,--as-needed -o $lib'
- 
-         if test "x$supports_anon_versioning" = xyes; then
-           _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
- 	    cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
- 	    echo "local: *; };" >> $output_objdir/$libname.ver~
--	    $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
-+	    $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -Wl,--as-needed -o $lib'
-         fi
- 
- 	case $cc_basename in

diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch
deleted file mode 100644
index 0f5e592..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c	2012-07-19 23:29:05.000000000 +0200
-+++ /tmp/ajgraph.c	2012-07-19 23:25:00.000000000 +0200
-@@ -1645,14 +1645,14 @@
- ** @return [void]
- ** @@
- ******************************************************************************/
- 
- static void GraphSetPen(ajint colour)
- {
--    ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
--    plcol((PLINT)colour);
-+    ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
-+    plcol0((PLINT)colour);
- 
-     return;
- }
- 
- 
- 
---- EMBOSS-6.3.1/plplot/plcore.c	2007-10-24 15:14:43.000000000 +0200
-+++ /tmp/plcore.c	2012-07-19 23:25:00.000000000 +0200
-@@ -1709,13 +1709,13 @@
-     if (plsc->zdigmax == 0)
- 	plsc->zdigmax = 3;
- 
- /* Switch to graphics mode and set color and arrow style*/
- 
-     plgra();
--    plcol(1);
-+    plcol0(1);
- 
-     plstyl(0, &mk, &sp);
-     plpat(1, &inc, &del);
- 
-     plsvect(def_arrow_x, def_arrow_y, 6, 0);
- 
---- EMBOSS-6.3.1/plplot/plstripc.c	2007-05-08 11:09:37.000000000 +0200
-+++ /tmp/plstripc.c	2012-07-19 23:25:00.000000000 +0200
-@@ -153,17 +153,17 @@
- 
-     plgchr(&sc, &dy);
-     sc = dy = dy/100;
-     plwind(-0.01, 1.01, -0.01, 1.01);
-     for (i=0; i<PEN; i++) {
- 	if (mystripc->npts[i] || first) {
--	    plcol(mystripc->colline[i]);
-+	    plcol0(mystripc->colline[i]);
- 	    pllsty(mystripc->styline[i]);
- 	    pljoin(mystripc->xlpos, mystripc->ylpos - sc,
- 		   mystripc->xlpos + 0.1, mystripc->ylpos - sc);
--	    plcol(mystripc->collab);
-+	    plcol0(mystripc->collab);
- 	    plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc,
- 		   0., 0., 0, mystripc->legline[i]);
- 	    sc += dy;
- 	}
-     }
-     plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax);
-@@ -184,34 +184,34 @@
-     PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.};
- 
- /* Set up window */
- 
-     plvpor(0,1,0,1);
-     plwind(0,1,0,1);
--    plcol(0);plpsty(0);
-+    plcol0(0);plpsty(0);
-     plfill(4, &x[0], &y[0]);
-     plvsta();
- 
- /* Draw box and same window dimensions */
-     mystrip->wxmin=mystrip->xmin;
-     mystrip->wxmax=mystrip->xmax;
-     mystrip->wymin=mystrip->ymin;
-     mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */
- 
-     plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax);
- 
-     pllsty(1);
--    plcol(mystrip->colbox);
-+    plcol0(mystrip->colbox);
-     plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0);
- 
--    plcol(mystrip->collab);
-+    plcol0(mystrip->collab);
-     pllab(mystrip->labx, mystrip->laby, mystrip->labtop);
- 
-     for (i=0; i<PEN; i++) {
-         if (mystrip->npts[i] > 0) {
--            plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]);
-+            plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]);
-             plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]);
-         }
-     }
- 
-     plstrip_legend(mystrip,0);
- }
-@@ -269,13 +269,13 @@
-         if (stripc->xmax - stripc->xmin < stripc->xlen) {
-             if( yasc == 0) {
- 
-             /* If user has changed subwindow, make shure we have the correct one */
-                 plvsta();
-                 plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */
--		plcol(stripc->colline[p]); pllsty(stripc->styline[p]);
-+		plcol0(stripc->colline[p]); pllsty(stripc->styline[p]);
- 		if ((stripc->npts[p]-2) < 0)
- 		  plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
- 		else
- 		  plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]);
- 		plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
- 		plflush();

diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
deleted file mode 100644
index e66a696..0000000
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c.ori	2014-07-04 18:25:18.000000000 +0200
-+++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c	2014-07-04 18:25:32.000000000 +0200
-@@ -1329,8 +1329,8 @@
- 
- void ajGraphicsSetPenwidth(float penwidth)
- {
--    ajDebug("=g= plwid(%.2f) [width]\n", penwidth);
--    plwid((PLINT)penwidth);
-+    ajDebug("=g= plwidth(%.2f) [width]\n", penwidth);
-+    plwidth((PLINT)penwidth);
- 
-     return;
- }

diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2
deleted file mode 100644
index 72fa366..0000000
--- a/sci-biology/emboss/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