commit: d4a144d5bb641885f2311af3fb3b582b5c68d90d Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Wed Feb 4 08:31:12 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Feb 4 08:31:12 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d4a144d5
sci-biology/embassy-mse: Bump eclass, drop old Package-Manager: portage-2.2.15 --- sci-biology/embassy-mse/ChangeLog | 6 +- .../embassy-mse/embassy-mse-3.0.0.650.ebuild | 4 +- sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild | 23 -- .../embassy-mse/files/embassy-mse-3.0.0.patch | 398 --------------------- sci-biology/embassy-mse/metadata.xml | 2 +- 5 files changed, 8 insertions(+), 425 deletions(-) diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog index 0d60faf..1316099 100644 --- a/sci-biology/embassy-mse/ChangeLog +++ b/sci-biology/embassy-mse/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/embassy-mse -# 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-mse/ChangeLog,v 1.35 2010/01/01 22:05:28 fauli Exp $ + 04 Feb 2015; Justin Lecher <[email protected]> -embassy-mse-3.0.0.ebuild, + embassy-mse-3.0.0.650.ebuild, -files/embassy-mse-3.0.0.patch, metadata.xml: + Bump eclass, drop old + 25 Jun 2011; Justin Lecher <[email protected]> embassy-mse-3.0.0.ebuild: Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild index 1a2ec11..f692c91 100644 --- a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild @@ -7,7 +7,7 @@ EAPI=5 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" EBO_EXTRA_ECONF="$(use_enable ncurses curses)" -inherit emboss +inherit emboss-r1 KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" IUSE+=" ncurses" @@ -15,7 +15,7 @@ IUSE+=" ncurses" RDEPEND+=" ncurses? ( sys-libs/ncurses )" src_install() { - default + emboss-r1_src_install insinto /usr/include/emboss/mse doins h/*.h } diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild deleted file mode 100644 index 312143e..0000000 --- a/sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="4" - -EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" - -inherit emboss - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" - -IUSE+=" ncurses" - -RDEPEND+=" ncurses? ( sys-libs/ncurses )" - -EBO_EXTRA_ECONF="$(use_with ncurses curses)" - -src_install() { - default - insinto /usr/include/emboss/mse - doins h/*.h -} diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch deleted file mode 100644 index 54c3690..0000000 --- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch +++ /dev/null @@ -1,398 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index 3e3dcb3..6fcfdc0 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -1,5 +1,6 @@ - # - -+ACLOCAL_AMFLAGS = -I m4 - SUBDIRS = ckit src h emboss_acd emboss_doc - - EXTRA_DIST = LICENSE depcomp ltmain.sh install-sh config.sub config.guess -diff --git a/ckit/datafiles.c b/ckit/datafiles.c -index d9e0f11..4ef70a4 100644 ---- a/ckit/datafiles.c -+++ b/ckit/datafiles.c -@@ -211,7 +211,7 @@ void ShowGCGEnzymes(char *enzFName,Boolean doSchiz,int *where) - #define PERLINE 8 - #define PERSCREEN 21 - --char line[256]; -+char line[512]; - int i,j; - - char *cPos; -diff --git a/ckit/gcg.c b/ckit/gcg.c -index a1e63a6..c6347f1 100644 ---- a/ckit/gcg.c -+++ b/ckit/gcg.c -@@ -165,7 +165,7 @@ char errMsg[80]; - static char *NextGCGCode(void) - { - static Boolean initialized = 0; --static char code[20]; -+static char code[64]; - - if (!initialized) { - initialized = 1; -diff --git a/ckit/readentry.c b/ckit/readentry.c -index a01b1c0..86fae27 100644 ---- a/ckit/readentry.c -+++ b/ckit/readentry.c -@@ -343,7 +343,7 @@ static Boolean FindSeqSpec( SeqSpec *spec, SeqEntry *seq) - { - char line[512]; - static char name[256] = ""; --static char title[256] = ""; -+static char title[512] = ""; - char errMsg[80]; - char *cPos; - -diff --git a/configure.in b/configure.in -index 445e48b..995c414 100644 ---- a/configure.in -+++ b/configure.in -@@ -187,15 +187,6 @@ AC_PROG_INSTALL - AC_PROG_LN_S - AC_PROG_MAKE_SET - --dnl Intel MacOSX 10.6 puts X11 in a non-standard place --if test "${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) - - - -@@ -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 -+++ b/src/Makefile.am -@@ -18,9 +18,9 @@ INCLUDES = -I../h \ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --INCLUDES = -I../h -I${embprefix}/include \ -- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ -- $(NLINCLUDES) -+INCLUDES = -I../h -I${embprefix}/include $(PLPLOT_CFLAGS) \ -+ $(NLINCLUDES) -I${embprefix}/include/emboss \ -+ -I${embprefix}/include/pcre - endif - - if ISSHARED -@@ -59,6 +59,6 @@ LDADD = ../ckit/libckit.la \ - ../../../plplot/libeplplot.la \ - $(XLIB) - else --LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ -- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+LDADD = ../ckit/libckit.la -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -+ -lajax -lpcre $(NLADD) $(PLPLOT_LIBS) $(XLIB) - endif diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml index d464821..f17a827 100644 --- a/sci-biology/embassy-mse/metadata.xml +++ b/sci-biology/embassy-mse/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>
