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Wed, 4 Feb 2015 08:37:07 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1423038494.c6cfc49e81d94445f7053a94f484dbebb00c7342.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-esim4/files/, sci-biology/embassy-esim4/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/embassy-esim4/ChangeLog sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch sci-biology/embassy-esim4/metadata.xml X-VCS-Directories: sci-biology/embassy-esim4/files/ sci-biology/embassy-esim4/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: c6cfc49e81d94445f7053a94f484dbebb00c7342 X-VCS-Branch: master Date: Wed, 4 Feb 2015 08:37:07 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 2f0dcca8-8aa8-4ec7-bc1e-ccbe59ea16cd X-Archives-Hash: 26a51a5fa1550340cb965f6462f8a292 commit: c6cfc49e81d94445f7053a94f484dbebb00c7342 Author: Justin Lecher gentoo org> AuthorDate: Wed Feb 4 08:28:14 2015 +0000 Commit: Justin Lecher gentoo org> CommitDate: Wed Feb 4 08:28:14 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c6cfc49e sci-biology/embassy-esim4: Bump eclass, Drop old Package-Manager: portage-2.2.15 --- sci-biology/embassy-esim4/ChangeLog | 7 +- .../embassy-esim4/embassy-esim4-1.0.0-r7.ebuild | 11 - .../embassy-esim4/embassy-esim4-1.0.0.650.ebuild | 2 +- .../files/embassy-esim4-1.0.0-r7.patch | 345 --------------------- sci-biology/embassy-esim4/metadata.xml | 2 +- 5 files changed, 8 insertions(+), 359 deletions(-) diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog index 5629297..9c25b66 100644 --- a/sci-biology/embassy-esim4/ChangeLog +++ b/sci-biology/embassy-esim4/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-biology/embassy-esim4 -# 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-esim4/ChangeLog,v 1.28 2010/01/01 21:58:14 fauli Exp $ + 04 Feb 2015; Justin Lecher -embassy-esim4-1.0.0-r7.ebuild, + embassy-esim4-1.0.0.650.ebuild, -files/embassy-esim4-1.0.0-r7.patch, + metadata.xml: + Bump eclass, Drop old + 25 Jun 2011; Justin Lecher embassy-esim4-1.0.0-r7.ebuild: Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild deleted file mode 100644 index 96d6fe9..0000000 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="4" - -EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" - -inherit emboss - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild index 93491e9..3085960 100644 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild @@ -6,6 +6,6 @@ EAPI=5 EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" -inherit emboss +inherit emboss-r1 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch deleted file mode 100644 index e2530fd..0000000 --- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch +++ /dev/null @@ -1,345 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index 6bfb6f0..d547b12 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 077c81b..c454696 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 92b3d7c..10e1c9d 100644 ---- a/emboss_doc/html/Makefile.am -+++ b/emboss_doc/html/Makefile.am -@@ -1,4 +1,4 @@ - pkgdata_DATA = index.html \ - esim4.html - --pkgdatadir=$(prefix)/share/EMBOSS/doc/html/embassy/esim4 -+pkgdatadir=$(docdir)/html/embassy/esim4 -diff --git a/emboss_doc/text/Makefile.am b/emboss_doc/text/Makefile.am -index 2ecf830..6945dbb 100644 ---- a/emboss_doc/text/Makefile.am -+++ b/emboss_doc/text/Makefile.am -@@ -1,3 +1,3 @@ - pkgdata_DATA = esim4.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} ${LIBS}" - - AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include - #include "mysql.h"]], -@@ -115,7 +115,7 @@ dnl not be installed - AC_MSG_RESULT([yes]) - else - MYSQL_CFLAGS="" -- MYSQL_LDFLAGS="" -+ MYSQL_LIBS="" - found_mysql="no" - AC_MSG_RESULT([no]) - fi -@@ -172,5 +172,5 @@ dnl not be installed - - AC_SUBST([MYSQL_VERSION]) - AC_SUBST([MYSQL_CFLAGS]) -- AC_SUBST([MYSQL_LDFLAGS]) -+ AC_SUBST([MYSQL_LIBS]) - ]) -diff --git a/m4/pngdriver.m4 b/m4/pngdriver.m4 -index 5934321..de970ae 100644 ---- a/m4/pngdriver.m4 -+++ b/m4/pngdriver.m4 -@@ -44,8 +44,8 @@ ALT_HOME=/usr - # - # Locate png/gd/zlib, if wanted - # --if test -d "${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 e593a9c..6132408 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -18,9 +18,9 @@ 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 -@@ -63,6 +63,6 @@ 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-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml index d464821..f17a827 100644 --- a/sci-biology/embassy-esim4/metadata.xml +++ b/sci-biology/embassy-esim4/metadata.xml @@ -1,5 +1,5 @@ - sci-biology + sci-biology