From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Q1LVi-0004x3-O0 for garchives@archives.gentoo.org; Sun, 20 Mar 2011 16:29:47 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 0FE73E05A4; Sun, 20 Mar 2011 16:28:29 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id C0F35E05A4 for ; Sun, 20 Mar 2011 16:28:29 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 71F251B4108 for ; Sun, 20 Mar 2011 16:28:29 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id DEE9A80073 for ; Sun, 20 Mar 2011 16:28:28 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-iprscan/files/, sci-biology/embassy-iprscan/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/embassy-iprscan/ChangeLog sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r2.ebuild sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1-r2.patch X-VCS-Directories: sci-biology/embassy-iprscan/files/ sci-biology/embassy-iprscan/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: bef2e14378ad5dbb994ba21d13b4de49f76a7dce Date: Sun, 20 Mar 2011 16:28:28 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: 12ac6435945b1b4534b3090d51915ece commit: bef2e14378ad5dbb994ba21d13b4de49f76a7dce Author: Justin Lecher gentoo org> AuthorDate: Sun Mar 20 12:34:05 2011 +0000 Commit: Justin Lecher gentoo org> CommitDate: Sun Mar 20 12:34:05 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Dbef2e143 Fixed for reviewed eclass (Portage version: 2.2.0_alpha28/git/Linux x86_64, RepoMan options: --forc= e, 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 + 20 Mar 2011; Justin Lecher embassy-iprscan-4.3.1-r2.= ebuild, + files/embassy-iprscan-4.3.1-r2.patch: + Fixed for reviewed eclass + 15 Mar 2011; Justin Lecher embassy-iprscan-4.3.1-r2.= ebuild: Naming of eclass changed =20 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-i= prscan-4.3.1-r1.ebuild,v 1.2 2010/01/15 22:45:28 fauli Exp $ =20 +EAPI=3D"4" + EBO_DESCRIPTION=3D"InterProScan motif detection add-on package" =20 inherit emboss diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1-r2.p= atch 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 $(distdir); tar xBf - ; cd emboss_acd; rm = -rf CVS) diff --git a/configure.in b/configure.in -index 3c69e1b..b936c25 100644 +index 3c69e1b..d78c862 100644 --- a/configure.in +++ b/configure.in @@ -187,15 +187,6 @@ AC_PROG_INSTALL @@ -33,14 +33,17 @@ index 3c69e1b..b936c25 100644 =20 dnl Check for header files AC_PATH_XTRA -@@ -250,8 +241,8 @@ AX_LIB_POSTGRESQL +@@ -248,10 +239,10 @@ AX_LIB_MYSQL + AX_LIB_POSTGRESQL +=20 CFLAGS=3D"$CFLAGS $MYSQL_CFLAGS" - LDFLAGS=3D"$LDFLAGS $MYSQL_LDFLAGS" +-LDFLAGS=3D"$LDFLAGS $MYSQL_LDFLAGS" ++LIBS=3D"${MYSQL_LIBS} ${LIBS}" =20 -CFLAGS=3D"$CFLAGS $POSTGRESQL_CFLAGS" -LDFLAGS=3D"$LDFLAGS $POSTGRESQL_LDFLAGS" +CFLAGS=3D"$POSTGRESQL_CFLAGS $CFLAGS" -+LDFLAGS=3D"$POSTGRESQL_LDFLAGS $LDFLAGS" ++LIBS=3D"$POSTGRESQL_LIBS $LIBS" =20 =20 dnl "Export" these variables for PCRE @@ -75,6 +78,249 @@ index 3c69e1b..b936c25 100644 =20 =20 =20 +diff --git a/emboss_doc/html/Makefile.am b/emboss_doc/html/Makefile.am +index eb337f3..ea58a27 100644 +--- a/emboss_doc/html/Makefile.am ++++ b/emboss_doc/html/Makefile.am +@@ -1,4 +1,4 @@ + pkgdata_DATA =3D index.html \ + eiprscan.html +=20 +-pkgdatadir=3D$(prefix)/share/EMBOSS/doc/html/embassy/iprscan ++pkgdatadir=3D$(docdir)/html/embassy/iprscan +diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am +index 5af1309..8110248 100644 +--- a/emboss_doc/text/Makefile.am ++++ b/emboss_doc/text/Makefile.am +@@ -1,3 +1,3 @@ + pkgdata_DATA =3D eiprscan.txt +=20 +-pkgdatadir=3D$(prefix)/share/EMBOSS/doc/programs/text ++pkgdatadir=3D$(docdir)/programs/text +diff --git a/m4/hpdf.m4 b/m4/hpdf.m4 +index a37940f..80b329c 100644 +--- a/m4/hpdf.m4 ++++ b/m4/hpdf.m4 +@@ -33,8 +33,8 @@ ALT_HOME=3D/usr + # + # Locate hpdf + # +-if test -d "${ALT_HOME}" +-then ++#if test -d "${ALT_HOME}" ++#then +=20 + # + # Keep a copy if it fails +@@ -45,13 +45,13 @@ then + # + # Set=20 + # +- LDFLAGS=3D"${LDFLAGS} -L${ALT_HOME}/lib" +- CPPFLAGS=3D"$CPPFLAGS -I$ALT_HOME/include" ++# LDFLAGS=3D"${LDFLAGS} -L${ALT_HOME}/lib" ++# CPPFLAGS=3D"$CPPFLAGS -I$ALT_HOME/include" +=20 + # + # Check for libharu in ALT_HOME + # +- AC_CHECK_LIB(hpdf, HPDF_New, CHECK=3D1, CHECK=3D0, -L${ALT_HOME= }/lib) ++ AC_CHECK_LIB(hpdf, HPDF_New, CHECK=3D1, CHECK=3D0) + # + # + # If everything found okay then proceed to include png driver in config= . +@@ -80,10 +80,4 @@ then + echo "No pdf support (libhpdf) found." + fi +=20 +-else +- if test $withval !=3D "no"; then +- echo "Directory $ALT_HOME does not exist" +- exit 0 +- fi +-fi + ]) +diff --git a/m4/mysql.m4 b/m4/mysql.m4 +index 12f8fe9..5cd8b90 100644 +--- a/m4/mysql.m4 ++++ b/m4/mysql.m4 +@@ -26,7 +26,7 @@ + # This macro calls: + # + # AC_SUBST(MYSQL_CFLAGS) +-# AC_SUBST(MYSQL_LDFLAGS) ++# AC_SUBST(MYSQL_LIBS) + # AC_SUBST(MYSQL_VERSION) + # + # And sets: +@@ -68,7 +68,7 @@ AC_DEFUN([AX_LIB_MYSQL], + ) +=20 + MYSQL_CFLAGS=3D"" +- MYSQL_LDFLAGS=3D"" ++ MYSQL_LIBS=3D"" + MYSQL_VERSION=3D"" +=20 + dnl +@@ -86,7 +86,7 @@ AC_DEFUN([AX_LIB_MYSQL], +=20 + dnl MYSQL_CFLAGS=3D"`$MYSQL_CONFIG --cflags`" + MYSQL_CFLAGS=3D"`$MYSQL_CONFIG --include`" +- MYSQL_LDFLAGS=3D"`$MYSQL_CONFIG --libs`" ++ MYSQL_LIBS=3D"`$MYSQL_CONFIG --libs`" +=20 + MYSQL_VERSION=3D`$MYSQL_CONFIG --version` +=20 +@@ -97,7 +97,7 @@ dnl not be installed + EMBCFLAGS=3D$CFLAGS + EMBLDFLAGS=3D$LDFLAGS + CFLAGS=3D"$MYSQL_CFLAGS $EMBCFLAGS" +- LDFLAGS=3D"$MYSQL_LDFLAGS $EMBLDFLAGS" ++ LIBS=3D"${MYSQL_LIBS} ${LIBS}" +=20 + AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include + #include "mysql.h"]], +@@ -115,7 +115,7 @@ dnl not be installed + AC_MSG_RESULT([yes]) + else + MYSQL_CFLAGS=3D"" +- MYSQL_LDFLAGS=3D"" ++ MYSQL_LIBS=3D"" + found_mysql=3D"no" + AC_MSG_RESULT([no]) + fi +@@ -172,5 +172,5 @@ dnl not be installed +=20 + AC_SUBST([MYSQL_VERSION]) + AC_SUBST([MYSQL_CFLAGS]) +- AC_SUBST([MYSQL_LDFLAGS]) ++ AC_SUBST([MYSQL_LIBS]) + ]) +diff --git a/m4/pngdriver.m4 b/m4/pngdriver.m4 +index 5934321..de970ae 100644 +--- a/m4/pngdriver.m4 ++++ b/m4/pngdriver.m4 +@@ -44,8 +44,8 @@ ALT_HOME=3D/usr + # + # Locate png/gd/zlib, if wanted + # +-if test -d "${ALT_HOME}" +-then ++#if test -d "${ALT_HOME}" ++#then +=20 + # + # Keep a copy if it fails +@@ -69,20 +69,26 @@ then + fi +=20 +=20 ++PKG_CHECK_MODULES([PNG], [libpng]) ++PKG_CHECK_MODULES([ZLIB], [zlib]) ++AC_CHECK_PROG(GD_LIBS, [gdlib-config]) ++GD_LIBS=3D"`gdlib-config --libs` -lgd" ++GD_CFLAGS=3D"`gdlib-config --cflags`" ++ +=20 +=20 +=20 + # + # Check for zlib in ALT_HOME + # +- AC_CHECK_LIB(z, inflateEnd, CHECK=3D1, CHECK=3D0, -L${ALT_HOME}= /lib -lz) ++ AC_CHECK_LIB(z, inflateEnd, CHECK=3D1, CHECK=3D0, ${ZLIB_LIBS}) + # +=20 + # + # Check for png + # + if test $CHECK =3D "1" ; then +- AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=3D1, CHECK=3D0 , -L= ${ALT_HOME}/lib -lz) ++ AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=3D1, CHECK=3D0 , ${= ZLIB_LIBS}) + fi + =09 +=20 +@@ -92,7 +98,7 @@ then + # Check for gd + # + if test $CHECK =3D "1"; then +- AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=3D1, CHECK=3D0 , -L${AL= T_HOME}/lib -lgd -lpng -lz -lm) ++ AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=3D1, CHECK=3D0 , ${PNG_= LIBS} ${ZLIB_LIBS} ${GD_LIBS}) + if test $CHECK =3D "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 $CHECK =3D "1" ; then +- LIBS=3D"$LIBS -lgd -lpng -lz -lm" ++ LIBS=3D"$LIBS ${PNG_LIBS} ${ZLIB_LIBS} ${GD_LIBS}" +=20 + if test $ICCHECK =3D "1" ; then + LIBS=3D"$LIBS -liconv" +@@ -114,10 +120,11 @@ then + AC_DEFINE(PLD_png) + AM_CONDITIONAL(AMPNG, true) + echo PNG libraries found +- if test $ALT_HOME =3D "/usr" ; then ++# if test $ALT_HOME =3D "/usr" ; then + LDFLAGS=3D"$ALT_LDFLAGS" + CPPFLAGS=3D"$ALT_CPPFLAGS" +- fi ++ CFLAGS=3D"${CFLAGS} ${PNG_CFLAGS} ${ZLIB_CFLAGS} ${GD_CFLAGS}" ++# fi + else + # + # If not okay then reset FLAGS. +@@ -134,10 +141,4 @@ then + # echo CPPFLAGS =3D $CPPFLAGS +=20 +=20 +-else +- if test $withval !=3D "no"; then +- echo "Directory $ALT_HOME does not exist" +- exit 0 +- fi +-fi + ]) +diff --git a/m4/postgresql.m4 b/m4/postgresql.m4 +index e6a804d..ef4d49c 100644 +--- a/m4/postgresql.m4 ++++ b/m4/postgresql.m4 +@@ -26,7 +26,7 @@ + # This macro calls: + # + # AC_SUBST(POSTGRESQL_CFLAGS) +-# AC_SUBST(POSTGRESQL_LDFLAGS) ++# AC_SUBST(POSTGRESQL_LIBS) + # AC_SUBST(POSTGRESQL_VERSION) + # + # And sets: +@@ -65,7 +65,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL], + ) +=20 + POSTGRESQL_CFLAGS=3D"" +- POSTGRESQL_LDFLAGS=3D"" ++ POSTGRESQL_LIBS=3D"" + POSTGRESQL_POSTGRESQL=3D"" +=20 + dnl +@@ -82,7 +82,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL], + AC_MSG_CHECKING([for PostgreSQL libraries]) +=20 + POSTGRESQL_CFLAGS=3D"-I`$PG_CONFIG --includedir`" +- POSTGRESQL_LDFLAGS=3D"-L`$PG_CONFIG --libdir` -lpq" ++ POSTGRESQL_LIBS=3D"-L`$PG_CONFIG --libdir` `$PG_CONFIG --li= bs`" +=20 + POSTGRESQL_VERSION=3D`$PG_CONFIG --version | sed -e 's#Post= greSQL ##'` +=20 +@@ -144,5 +144,5 @@ AC_DEFUN([AX_LIB_POSTGRESQL], +=20 + 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