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

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

commit:     bef2e14378ad5dbb994ba21d13b4de49f76a7dce
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 20 12:34:05 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 20 12:34:05 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bef2e143

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-iprscan/ChangeLog              |    4 +
 .../embassy-iprscan-4.3.1-r2.ebuild                |    2 +
 .../files/embassy-iprscan-4.3.1-r2.patch           |  254 +++++++++++++++++++-
 3 files changed, 256 insertions(+), 4 deletions(-)

diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog
index 8ab4f2a..5a00be3 100644
--- a/sci-biology/embassy-iprscan/ChangeLog
+++ b/sci-biology/embassy-iprscan/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.5 2010/01/15 22:45:28 fauli Exp $
 
+  20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild,
+  files/embassy-iprscan-4.3.1-r2.patch:
+  Fixed for reviewed eclass
+
   15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild:
   Naming of eclass changed
 

diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild
index 8cde03f..c69c125 100644
--- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild
@@ -2,6 +2,8 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r1.ebuild,v 1.2 2010/01/15 22:45:28 fauli Exp $
 
+EAPI="4"
+
 EBO_DESCRIPTION="InterProScan motif detection add-on package"
 
 inherit emboss

diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1-r2.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1-r2.patch
index 0e2b04f..a22f062 100644
--- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1-r2.patch
+++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1-r2.patch
@@ -14,7 +14,7 @@ index 12686b3..d547b12 100644
  dist-hook:
  	tar cBf - emboss_acd | ( cd $(distdir); tar xBf - ; cd emboss_acd; rm -rf CVS)
 diff --git a/configure.in b/configure.in
-index 3c69e1b..b936c25 100644
+index 3c69e1b..d78c862 100644
 --- a/configure.in
 +++ b/configure.in
 @@ -187,15 +187,6 @@ AC_PROG_INSTALL
@@ -33,14 +33,17 @@ index 3c69e1b..b936c25 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
@@ -75,6 +78,249 @@ index 3c69e1b..b936c25 100644
  
  
  
+diff --git a/emboss_doc/html/Makefile.am b/emboss_doc/html/Makefile.am
+index eb337f3..ea58a27 100644
+--- a/emboss_doc/html/Makefile.am
++++ b/emboss_doc/html/Makefile.am
+@@ -1,4 +1,4 @@
+ pkgdata_DATA = index.html \
+ 	eiprscan.html
+ 
+-pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/iprscan
++pkgdatadir=$(docdir)/html/embassy/iprscan
+diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am
+index 5af1309..8110248 100644
+--- a/emboss_doc/text/Makefile.am
++++ b/emboss_doc/text/Makefile.am
+@@ -1,3 +1,3 @@
+ pkgdata_DATA =  eiprscan.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 e6ba236..fae5c0f 100644
 --- a/src/Makefile.am