* [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-phylipnew/, sci-biology/embassy-phylipnew/files/
@ 2011-03-10 19:00 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2011-03-10 19:00 UTC (permalink / raw
To: gentoo-commits
commit: 223d40267995eaab770c46f3d9e5f15ea66ad658
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 11:28:29 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 11:28:29 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=223d4026
Version Bump, Move to new embassy-ng.eclass
(Portage version: 2.2.0_alpha26/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)
---
sci-biology/embassy-phylipnew/ChangeLog | 63 +++++++++++++
.../embassy-phylipnew-3.69.ebuild | 12 +++
.../files/embassy-phylipnew-3.69.patch | 99 ++++++++++++++++++++
sci-biology/embassy-phylipnew/metadata.xml | 5 +
4 files changed, 179 insertions(+), 0 deletions(-)
diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog
new file mode 100644
index 0000000..246b17b
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/ChangeLog
@@ -0,0 +1,63 @@
+# ChangeLog for sci-biology/embassy-phylipnew
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.12 2010/01/01 22:02:06 fauli Exp $
+
+*embassy-phylipnew-3.69 (10 Mar 2011)
+
+ 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-phylipnew-3.69.ebuild,
+ +files/embassy-phylipnew-3.69.patch, +metadata.xml:
+ Version Bump, Move to new embassy-ng.eclass
+
+ 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org>
+ embassy-phylipnew-3.68.ebuild:
+ Transfer Prefix keywords
+
+ 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+ Giving up maintainership of this package.
+
+*embassy-phylipnew-3.68 (01 Sep 2009)
+
+ 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+ +embassy-phylipnew-3.68.ebuild:
+ Updated version for EMBASSY 6.1.0.
+
+ 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+ embassy-phylipnew-3.67.ebuild:
+ Stabilised on amd64 and x86.
+
+*embassy-phylipnew-3.67 (27 Aug 2008)
+
+ 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org>
+ +embassy-phylipnew-3.67.ebuild:
+ New upstream version/package for EMBASSY 6.0.1.
+
+ 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org>
+ embassy-phylipnew-3.6b.ebuild:
+ Fixed description.
+
+ 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org>
+ embassy-phylipnew-3.6b.ebuild:
+ Adding ~amd64.
+
+ 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-phylipnew-3.6b.ebuild:
+ Stable on ppc wrt bug 153766
+
+ 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org>
+ embassy-phylipnew-3.6b.ebuild:
+ Added ~sparc
+
+ 02 Nov 2006; Fabian Groffen <grobian@gentoo.org>
+ embassy-phylipnew-3.6b.ebuild:
+ Dropped ppc-macos, see you in prefix.
+
+ 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
+ embassy-phylipnew-3.6b.ebuild:
+ Added to x86.
+
+*embassy-phylipnew-3.6b (21 Jul 2006)
+
+ 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+ +embassy-phylipnew-3.6b.ebuild:
+ Initial import. This package will probably replace EMBASSY-PHYLIP in new
+ EMBASSY releases.
+
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild
new file mode 100644
index 0000000..e07308b
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild
@@ -0,0 +1,12 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/embassy-phylipnew-3.68.ebuild,v 1.2 2010/01/01 22:02:06 fauli Exp $
+
+EBOV="6.3.1"
+EBO_DESCRIPTION="PHYLIP - The Phylogeny Inference Package"
+
+inherit embassy-ng
+
+LICENSE="freedist"
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch
new file mode 100644
index 0000000..607b23b
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch
@@ -0,0 +1,99 @@
+diff --git a/Makefile.am b/Makefile.am
+index 14b9f9f..c72b9f3 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,5 +1,6 @@
+ #
+
++ACLOCAL_AMFLAGS = -I m4
+ SUBDIRS = src emboss_acd data emboss_doc
+
+ EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess
+diff --git a/configure.in b/configure.in
+index 0042628..cef7e46 100644
+--- a/configure.in
++++ b/configure.in
+@@ -187,15 +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
+@@ -284,8 +275,8 @@ AX_LIB_POSTGRESQL
+ CFLAGS="$CFLAGS $MYSQL_CFLAGS"
+ LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+
+-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
+-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
+
+
+ dnl "Export" these variables for PCRE
+@@ -422,9 +413,30 @@ AC_ARG_ENABLE(systemlibs,
+ AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
+ if test "${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/src/Makefile.am b/src/Makefile.am
+index 9d3b413..894b8a6 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -16,9 +16,9 @@ INCLUDES = -I../include -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-INCLUDES = -I../include -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++INCLUDES = -I../include -I${embprefix}/include $(PLPLOT_CFLAGS) \
++ $(NLINCLUDES) -I${embprefix}/include/emboss \
++ -I${embprefix}/include/pcre
+ endif
+
+ if ISSHARED
+@@ -118,6 +118,6 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ ../../../ajax/pcre/libepcre.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-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml
new file mode 100644
index 0000000..d464821
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-phylipnew/, sci-biology/embassy-phylipnew/files/
@ 2011-03-20 16:28 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2011-03-20 16:28 UTC (permalink / raw
To: gentoo-commits
commit: c93800671b5eac3d76cee27ec51020924c66ca22
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 20 12:59:38 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 20 12:59:38 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c9380067
Fixed for reviewed eclass
(Portage version: 2.2.0_alpha28/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)
---
sci-biology/embassy-phylipnew/ChangeLog | 4 +
.../embassy-phylipnew-3.69.ebuild | 6 +-
.../files/embassy-phylipnew-3.69.patch | 255 +++++++++++++++++++-
3 files changed, 259 insertions(+), 6 deletions(-)
diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog
index bc0c18f..048d0bd 100644
--- a/sci-biology/embassy-phylipnew/ChangeLog
+++ b/sci-biology/embassy-phylipnew/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.12 2010/01/01 22:02:06 fauli Exp $
+ 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild,
+ files/embassy-phylipnew-3.69.patch:
+ Fixed for reviewed eclass
+
15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild:
Naming of eclass changed
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild
index 8b3d916..6767ae7 100644
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild
@@ -2,10 +2,12 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/embassy-phylipnew-3.68.ebuild,v 1.2 2010/01/01 22:02:06 fauli Exp $
-EBO_DESCRIPTION="PHYLIP - The Phylogeny Inference Package"
+EAPI="4"
+
+EBO_DESCRIPTION="the Phylogeny Inference Package"
inherit emboss
-LICENSE="freedist"
+LICENSE+=" freedist"
KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch
index 607b23b..cb43d1b 100644
--- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch
@@ -10,7 +10,7 @@ index 14b9f9f..c72b9f3 100644
EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess
diff --git a/configure.in b/configure.in
-index 0042628..cef7e46 100644
+index 0042628..6d7d0a5 100644
--- a/configure.in
+++ b/configure.in
@@ -187,15 +187,6 @@ AC_PROG_INSTALL
@@ -29,14 +29,17 @@ index 0042628..cef7e46 100644
dnl Check for header files
AC_PATH_XTRA
-@@ -284,8 +275,8 @@ AX_LIB_POSTGRESQL
+@@ -282,10 +273,10 @@ AX_LIB_MYSQL
+ AX_LIB_POSTGRESQL
+
CFLAGS="$CFLAGS $MYSQL_CFLAGS"
- LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+-LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
++LIBS="${MYSQL_LIBS} ${LIBS}"
-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
-+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
++LIBS="$POSTGRESQL_LIBS $LIBS"
dnl "Export" these variables for PCRE
@@ -71,6 +74,250 @@ index 0042628..cef7e46 100644
+diff --git a/emboss_doc/html/Makefile.am b/emboss_doc/html/Makefile.am
+index 34c3ecd..847fe37 100644
+--- a/emboss_doc/html/Makefile.am
++++ b/emboss_doc/html/Makefile.am
+@@ -14,4 +14,4 @@ pkgdata_DATA = index.html \
+ fseqboot.html fseqbootall.html \
+ ftreedist.html ftreedistpair.html
+
+-pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/phylipnew
++pkgdatadir=$(docdir)/html/embassy/phylipnew
+diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am
+index f3186b4..6134acc 100644
+--- a/emboss_doc/text/Makefile.am
++++ b/emboss_doc/text/Makefile.am
+@@ -13,4 +13,4 @@ pkgdata_DATA = fclique.txt \
+ fseqboot.txt fseqbootall.txt \
+ ftreedist.txt ftreedistpair.txt
+
+-pkgdatadir=$(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 9d3b413..894b8a6 100644
--- a/src/Makefile.am
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-phylipnew/, sci-biology/embassy-phylipnew/files/
@ 2015-02-04 8:37 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-02-04 8:37 UTC (permalink / raw
To: gentoo-commits
commit: 606bfa7e2085e8f87846703de86577b3eea846cd
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 4 08:29:39 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 4 08:29:39 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=606bfa7e
sci-biology/embassy-phylipnew: Bump eclass, drop old
Package-Manager: portage-2.2.15
---
sci-biology/embassy-phylipnew/ChangeLog | 7 +-
.../embassy-phylipnew-3.69.650.ebuild | 2 +-
.../embassy-phylipnew-3.69.ebuild | 13 -
.../files/embassy-phylipnew-3.69.patch | 346 ---------------------
sci-biology/embassy-phylipnew/metadata.xml | 2 +-
5 files changed, 8 insertions(+), 362 deletions(-)
diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog
index 4053bf0..7c9443a 100644
--- a/sci-biology/embassy-phylipnew/ChangeLog
+++ b/sci-biology/embassy-phylipnew/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-biology/embassy-phylipnew
-# 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-phylipnew/ChangeLog,v 1.12 2010/01/01 22:02:06 fauli Exp $
+ 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-phylipnew-3.69.ebuild,
+ embassy-phylipnew-3.69.650.ebuild, -files/embassy-phylipnew-3.69.patch,
+ metadata.xml:
+ Bump eclass, drop old
+
25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild:
Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
index b451603..602bec9 100644
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
@@ -6,7 +6,7 @@ EAPI=5
EBO_DESCRIPTION="the Phylogeny Inference Package"
-inherit emboss
+inherit emboss-r1
LICENSE+=" freedist"
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild
deleted file mode 100644
index 2a17906..0000000
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.ebuild
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-EBO_DESCRIPTION="the Phylogeny Inference Package"
-
-inherit emboss
-
-LICENSE+=" freedist"
-
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch
deleted file mode 100644
index cb43d1b..0000000
--- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch
+++ /dev/null
@@ -1,346 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 14b9f9f..c72b9f3 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,5 +1,6 @@
- #
-
-+ACLOCAL_AMFLAGS = -I m4
- SUBDIRS = src emboss_acd data emboss_doc
-
- EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess
-diff --git a/configure.in b/configure.in
-index 0042628..6d7d0a5 100644
---- a/configure.in
-+++ b/configure.in
-@@ -187,15 +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
-@@ -282,10 +273,10 @@ 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 $LIBS"
-
-
- dnl "Export" these variables for PCRE
-@@ -422,9 +413,30 @@ AC_ARG_ENABLE(systemlibs,
- AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
- if test "${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 34c3ecd..847fe37 100644
---- a/emboss_doc/html/Makefile.am
-+++ b/emboss_doc/html/Makefile.am
-@@ -14,4 +14,4 @@ pkgdata_DATA = index.html \
- fseqboot.html fseqbootall.html \
- ftreedist.html ftreedistpair.html
-
--pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/phylipnew
-+pkgdatadir=$(docdir)/html/embassy/phylipnew
-diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am
-index f3186b4..6134acc 100644
---- a/emboss_doc/text/Makefile.am
-+++ b/emboss_doc/text/Makefile.am
-@@ -13,4 +13,4 @@ pkgdata_DATA = fclique.txt \
- fseqboot.txt fseqbootall.txt \
- ftreedist.txt ftreedistpair.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 9d3b413..894b8a6 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -16,9 +16,9 @@ INCLUDES = -I../include -I../../../nucleus -I../../../ajax/pcre \
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- -I../../../ajax/acd -I../../../plplot
- else
--INCLUDES = -I../include -I${embprefix}/include -I${embprefix}/include/eplplot \
-- $(NLINCLUDES) \
-- -I${embprefix}/include/epcre
-+INCLUDES = -I../include -I${embprefix}/include $(PLPLOT_CFLAGS) \
-+ $(NLINCLUDES) -I${embprefix}/include/emboss \
-+ -I${embprefix}/include/pcre
- endif
-
- if ISSHARED
-@@ -118,6 +118,6 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
- ../../../ajax/pcre/libepcre.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-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml
index d464821..f17a827 100644
--- a/sci-biology/embassy-phylipnew/metadata.xml
+++ b/sci-biology/embassy-phylipnew/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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2011-03-20 16:28 [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-phylipnew/, sci-biology/embassy-phylipnew/files/ Justin Lecher
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2015-02-04 8:37 Justin Lecher
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