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

[Justin Lecher]

commit:     762037714cb5cda109478994a81e21835d313409
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  4 08:29:33 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb  4 08:29:33 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=76203771

sci-biology/embassy-hmmer: Bump eclass, Drop old

Package-Manager: portage-2.2.15

---
 sci-biology/embassy-hmmer/ChangeLog                |   7 +-
 .../embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild    |  13 -
 .../embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild   |   2 +-
 .../files/embassy-hmmer-2.3.2-r4.patch             | 346 ---------------------
 sci-biology/embassy-hmmer/metadata.xml             |   2 +-
 5 files changed, 8 insertions(+), 362 deletions(-)

diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog
index a24cbb0..fa2844c 100644
--- a/sci-biology/embassy-hmmer/ChangeLog
+++ b/sci-biology/embassy-hmmer/ChangeLog
@@ -1,7 +1,12 @@
 # ChangeLog for sci-biology/embassy-hmmer
-# 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-hmmer/ChangeLog,v 1.30 2010/01/01 22:00:05 fauli Exp $
 
+  04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-hmmer-2.3.2-r4.ebuild,
+  embassy-hmmer-2.3.2.650.ebuild, -files/embassy-hmmer-2.3.2-r4.patch,
+  metadata.xml:
+  Bump eclass, Drop old
+
   25 Jun 2011; Justin Lecher <jlec@g.o> embassy-hmmer-2.3.2-r4.ebuild:
   Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
 

diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild
deleted file mode 100644
index 193910a..0000000
--- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r4.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="wrappers for HMMER - Biological sequence analysis with profile HMMs"
-
-inherit emboss
-
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
-
-RDEPEND+=" ~sci-biology/hmmer-${PV}"

diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
index f1a9f29..8f2a68a 100644
--- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile HMMs"
 
-inherit emboss
+inherit emboss-r1
 
 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
 

diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2-r4.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2-r4.patch
deleted file mode 100644
index 87cd5f8..0000000
--- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2-r4.patch
+++ /dev/null
@@ -1,346 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 9172bb3..349b13b 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,5 +1,6 @@
- #
- 
-+ACLOCAL_AMFLAGS = -I m4
- SUBDIRS = src emboss_acd emboss_doc
- 
- EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess
-diff --git a/configure.in b/configure.in
-index 2af5506..e21e5b2 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
-@@ -248,10 +239,10 @@ 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 $LIBS"
- 
- 
- dnl "Export" these variables for PCRE
-@@ -388,9 +379,30 @@ AC_ARG_ENABLE(systemlibs,
-    AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
- if test "${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 de7a4b5..17e272b 100644
---- a/emboss_doc/html/Makefile.am
-+++ b/emboss_doc/html/Makefile.am
-@@ -4,4 +4,4 @@ pkgdata_DATA = index.html \
- 	ehmmemit.html ehmmfetch.html ehmmindex.html \
- 	ehmmpfam.html ehmmsearch.html
- 
--pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/hmmernew
-+pkgdatadir=$(docdir)/html/embassy/hmmernew
-diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am
-index 9f172e4..83e6d59 100644
---- a/emboss_doc/text/Makefile.am
-+++ b/emboss_doc/text/Makefile.am
-@@ -3,4 +3,4 @@ pkgdata_DATA = ehmmalign.txt ehmmbuild.txt \
- 	ehmmemit.txt ehmmfetch.txt ehmmindex.txt \
- 	ehmmpfam.txt ehmmsearch.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 dc3eecc..ad9ab19 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,9 @@ 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
-@@ -66,6 +66,6 @@ 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-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml
index d464821..f17a827 100644
--- a/sci-biology/embassy-hmmer/metadata.xml
+++ b/sci-biology/embassy-hmmer/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>