* [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-vienna/files/, sci-biology/embassy-vienna/
@ 2015-02-04 8:37 Justin Lecher
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From: Justin Lecher @ 2015-02-04 8:37 UTC (permalink / raw
To: gentoo-commits
commit: dbb72cb413214ba571e763ddb927d35056fa54c3
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 4 08:23:53 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 4 08:23:53 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dbb72cb4
sci-biology/embassy-vienna: Bump eclass, drop old
Package-Manager: portage-2.2.15
---
sci-biology/embassy-vienna/ChangeLog | 7 +-
.../embassy-vienna/embassy-vienna-1.7.2-r2.ebuild | 11 -
.../embassy-vienna/embassy-vienna-1.7.2.650.ebuild | 2 +-
.../files/embassy-vienna-1.7.2-r2.patch | 355 ---------------------
sci-biology/embassy-vienna/metadata.xml | 2 +-
5 files changed, 8 insertions(+), 369 deletions(-)
diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog
index 3d15b99..1000b17 100644
--- a/sci-biology/embassy-vienna/ChangeLog
+++ b/sci-biology/embassy-vienna/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-biology/embassy-vienna
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.8 2010/01/15 22:47:16 fauli Exp $
+ 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-vienna-1.7.2-r2.ebuild,
+ embassy-vienna-1.7.2.650.ebuild, -files/embassy-vienna-1.7.2-r2.patch,
+ metadata.xml:
+ Bump eclass, drop old
+
25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild:
Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild
deleted file mode 100644
index bb09be5..0000000
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r2.ebuild
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-EBO_DESCRIPTION="Vienna RNA package - RNA folding"
-
-inherit emboss
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
index b6418c7..e6af9a5 100644
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
@@ -6,6 +6,6 @@ EAPI=5
EBO_DESCRIPTION="Vienna RNA package - RNA folding"
-inherit emboss
+inherit emboss-r1
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2-r2.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2-r2.patch
deleted file mode 100644
index 7bda10b..0000000
--- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2-r2.patch
+++ /dev/null
@@ -1,355 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index ded619f..6a9a5a1 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,5 +1,7 @@
- #
-
-+ACLOCAL_AMFLAGS = -I m4
-+
- SUBDIRS = src emboss_acd emboss_doc
-
- EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess config.h
-diff --git a/configure.in b/configure.in
-index 67f45dc..34df158 100644
---- a/configure.in
-+++ b/configure.in
-@@ -195,15 +195,6 @@ 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
-@@ -256,10 +247,10 @@ 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 $LIBS"
-
-
- dnl "Export" these variables for PCRE
-@@ -397,9 +388,30 @@ AC_ARG_ENABLE(systemlibs,
- AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
- if test "${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 041c2e5..5e4c9ff 100644
---- a/emboss_doc/html/Makefile.am
-+++ b/emboss_doc/html/Makefile.am
-@@ -8,4 +8,4 @@ pkgdata_DATA = index.html \
- vrnalfold.html vrnaplot.html \
- vrnasubopt.html
-
--pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/vienna
-+pkgdatadir=$(docdir)/html/embassy/vienna
-diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am
-index 2b1d8c0..718dde0 100644
---- a/emboss_doc/text/Makefile.am
-+++ b/emboss_doc/text/Makefile.am
-@@ -6,4 +6,4 @@ pkgdata_DATA = vrnaalifold.txt vrnaalifoldpf.txt \
- vrnaheat.txt vrnainverse.txt \
- vrnalfold.txt vrnaplot.txt vrnasubopt.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 995196f..f96e3bb 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -32,9 +32,9 @@ INCLUDES = -I../H -I../../../nucleus -I../../../ajax/pcre \
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- -I../../../ajax/acd -I../../../plplot
- else
--INCLUDES = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \
-- $(NLINCLUDES) \
-- -I${embprefix}/include/epcre
-+INCLUDES = -I../H $(PLPLOT_CFLAGS) \
-+ $(NLINCLUDES) -I${embprefix}/include/emboss \
-+ -I${embprefix}/include/pcre
- endif
-
- if ISSHARED
-@@ -87,6 +87,7 @@ LINKFLAGS = $(VERS_INF)
- endif
-
- libviennarna_la_LDFLAGS = $(LINKFLAGS)
-+libviennarna_la_LIBADD = -lajax
-
- vrnaalifold_SOURCES = vrnaalifold.c
- vrnaalifoldpf_SOURCES = vrnaalifoldpf.c
-@@ -118,6 +119,6 @@ LDADD = libviennarna.la \
- ../../../plplot/libeplplot.la \
- $(XLIB)
- else
--LDADD = libviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
-- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = $(PLPLOT_LIBS) libviennarna.la -lnucleus -lacd -lajaxdb \
-+ -lensembl -lajaxg -lajax -lpcre $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml
index d464821..f17a827 100644
--- a/sci-biology/embassy-vienna/metadata.xml
+++ b/sci-biology/embassy-vienna/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
+ <herd>sci-biology</herd>
</pkgmetadata>
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2015-02-04 8:37 [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-vienna/files/, sci-biology/embassy-vienna/ Justin Lecher
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