Fixed for reviewed eclass

(Portage version: 2.2.0_alpha28/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

4 files changed, 287 insertions, 9 deletions

diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog
index 795a50b66..986307764 100644
--- a/sci-biology/embassy-mse/ChangeLog
+++ b/sci-biology/embassy-mse/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.35 2010/01/01 22:05:28 fauli Exp $
 
+  20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild,
+  files/embassy-mse-3.0.0.patch:
+  Fixed for reviewed eclass
+
   15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild:
   Naming of eclass changed
 
diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
index 56983aeee..ae991627e 100644
--- a/sci-biology/embassy-mse/Manifest
+++ b/sci-biology/embassy-mse/Manifest
@@ -1,5 +1,15 @@
-AUX embassy-mse-3.0.0.patch 3953 RMD160 e8670a0fe9e802b2637f0881f96f68e9bc37ef1c SHA1 bee37894f52d9f5c85906dc2891cd1015021bb1d SHA256 6213066d66a635b78eab2db1d7fe2564ab93d8f85b1bc528c0baf9a001cb2f75
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX embassy-mse-3.0.0.patch 10900 RMD160 171a943e032522e6de380e699c9a917c634d7fc7 SHA1 28d39621f0b0924bf4c5982a5b50376453d6410f SHA256 1d900f8fb9d6d45f160a33faeb41ba5dc10413c5034d0ee0dcb020a5414bb5ce
 DIST embassy-mse-3.0.0.tar.gz 435315 RMD160 9e94bdc1cbff5b684a6d7f33a7a95de33c1b910e SHA1 bae84ef0154f444037653df322fb605d013dca0c SHA256 f3bb205b197d4cc4ad7d6ee8e3696eb59d84a8b60a8369d4a645871d0c9619c3
-EBUILD embassy-mse-3.0.0.ebuild 514 RMD160 91ffe385475f6739fac163a81d0716a248451500 SHA1 16ed2e92c69f34c57939d22ad31c5138dcc8c8a4 SHA256 0648c35ef2d4c519733869d11f5511c32e77de95da92239d4a85c6440145558b
-MISC ChangeLog 5463 RMD160 1d00e619dfe9ce30eae17f24b6882bae8950131e SHA1 33d7d5331cfcd07e73926cfe15762b67478e8810 SHA256 941c398528450b626e48734ddfab50e0a1bc752407c25bebd5729c2452d5a560
+EBUILD embassy-mse-3.0.0.ebuild 547 RMD160 5949b0db7f8addc9dafca3b3f08b5eda51824e18 SHA1 da9045e9c1c5cf5a0d5e805613c2a0243cb99bc8 SHA256 236230400b07988f6a06de2c73e4913612fc6934339120a79d9fad1cf18ee4b9
+MISC ChangeLog 5598 RMD160 cd7c8a60b5413e0bbb0b12a2f80b8f70082ea099 SHA1 f4076a406c8e947ce68f53a751b5d3dede0da448 SHA256 b27312004ed0af85916da8c9708b3174da48f0a0055d23c493b533f423477932
 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk2F+L4ACgkQgAnW8HDreRYFjQCdHmwyYJP/PHR0fJ1l1YZvvsrh
+gtEAn3p6LUF1syBnnokCmBkqPPU0HYiy
+=BiI2
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild
index c02479aec..dd6a473f0 100644
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild
@@ -2,6 +2,8 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-1.0.0-r7.ebuild,v 1.2 2010/01/01 22:05:28 fauli Exp $
 
+EAPI="4"
+
 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
 
 inherit emboss
@@ -10,10 +12,12 @@ KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
 
 IUSE+=" ncurses"
 
-EBO_ECONF="$(use_with ncurses curses ${EPREFIX}/usr)"
+RDEPEND+=" ncurses? ( sys-libs/ncurses )"
+
+EBO_EXTRA_ECONF="$(use_with ncurses curses)"
 
 src_install() {
-	emboss_src_install
+	default
 	insinto /usr/include/emboss/mse
 	doins h/*.h
 }
diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch
index e7cf4dd55..54c3690a0 100644
--- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch
+++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch
@@ -49,7 +49,7 @@ index a01b1c0..86fae27 100644
  char *cPos;
  
 diff --git a/configure.in b/configure.in
-index 445e48b..d48c1b8 100644
+index 445e48b..995c414 100644
 --- a/configure.in
 +++ b/configure.in
 @@ -187,15 +187,6 @@ AC_PROG_INSTALL
@@ -68,14 +68,17 @@ index 445e48b..d48c1b8 100644
  
  dnl Check for header files
  AC_PATH_XTRA
-@@ -250,8 +241,8 @@ AX_LIB_POSTGRESQL
+@@ -248,10 +239,10 @@ 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
@@ -110,6 +113,263 @@ index 445e48b..d48c1b8 100644
  
  
  
+@@ -423,10 +435,10 @@ AC_ARG_WITH(curses,
+ [ --with-curses	   curses (or ncurses)])
+ if test "${with_curses}" ; then
+ AC_MSG_CHECKING(for with_curses)
+-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
+-LDFLAGS="$LDFLAGS -L${with_curses}/lib"
++AC_CHECK_PROG([CURSES_CONFIG],[ncurses5-config])
++CPPFLAGS="$CPPFLAGS -I`ncurses5-config --includedir`"
+ fi
+-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses")
++AC_CHECK_LIB(ncurses, main, LIBS="$LIBS `ncurses5-config --libs`", LIBS="$LIBS `ncurses5-config --libs`")
+ 
+ 
+ 
+diff --git a/emboss_doc/html/Makefile.am b/emboss_doc/html/Makefile.am
+index 4f85547..33a1b81 100644
+--- a/emboss_doc/html/Makefile.am
++++ b/emboss_doc/html/Makefile.am
+@@ -1,4 +1,4 @@
+ pkgdata_DATA = index.html \
+ 	mse.html
+ 
+-pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/mse
++pkgdatadir=$(docdir)/html/embassy/mse
+diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am
+index 5c50f75..3d2b446 100644
+--- a/emboss_doc/text/Makefile.am
++++ b/emboss_doc/text/Makefile.am
+@@ -1,3 +1,3 @@
+ pkgdata_DATA =  mse.txt
+ 
+-pkgdatadir=$(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 f52d4ec..a3c08ef 100644
 --- a/src/Makefile.am