Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv5041
Added Files:
emboss.info emboss.patch
Log Message:
completely overhaul package layout, with new lib package-names and
root dir; now with more externalized support libs too!
--- NEW FILE: emboss.patch ---
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/Makefile.am EMBOSS-6.3.1/Makefile.am
--- EMBOSS-6.3.1.orig/Makefile.am 2010-01-11 08:15:41.000000000 -0500
+++ EMBOSS-6.3.1/Makefile.am 2010-08-04 12:15:15.000000000 -0400
@@ -5,7 +5,10 @@
AUTOMAKE_OPTIONS = gnits
-SUBDIRS = plplot ajax nucleus emboss test doc jemboss
+if !ESYSTEMLIBS
+EXTRA_DIRS = plplot
+endif
+SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc jemboss
# AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/Makefile.am
EMBOSS-6.3.1/ajax/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/Makefile.am 2010-06-16 06:26:45.000000000 -0400
+++ EMBOSS-6.3.1/ajax/Makefile.am 2010-08-04 19:07:47.000000000 -0400
@@ -1,6 +1,6 @@
## Process this file with automake to produce Makefile.in
if !ESYSTEMLIBS
-EXTRA_DIRS = expat zlib
+EXTRA_DIRS = pcre expat zlib
endif
-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/acd/Makefile.am
EMBOSS-6.3.1/ajax/acd/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/acd/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/acd/Makefile.am 2010-08-06 04:31:47.000000000 -0400
@@ -13,10 +13,13 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
endif
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core \
-I$(top_srcdir)/ajax/graphics \
@@ -38,3 +41,4 @@
endif
libacd_la_LDFLAGS = $(LINKFLAGS)
+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
../ajaxdb/libajaxdb.la
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/ajaxdb/Makefile.am
EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/ajaxdb/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am 2010-08-06 04:19:18.000000000
-0400
@@ -13,11 +13,12 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
endif
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
@@ -37,3 +38,4 @@
endif
libajaxdb_la_LDFLAGS = $(LINKFLAGS)
+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/core/Makefile.am
EMBOSS-6.3.1/ajax/core/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/core/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/core/Makefile.am 2010-08-06 08:16:54.000000000 -0400
@@ -12,13 +12,18 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_LIBS = -lexpat -lpcre
endif
+EXTRA_DIST = ajax-pcre-config.h.in
+DISTCLEAN = ajax-pcre-config.h
INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
-DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
+$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
AJAXSRC = ajalign.c ajarr.c ajassert.c \
ajbase.c ajcall.c ajcod.c \
@@ -44,7 +49,7 @@
ajmath.h ajmatrices.h ajmem.h ajmess.h \
ajnam.h ajnexus.h ajobo.h \
ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
-ajrange.h ajreg.h ajreport.h ajresource.h \
+ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \
ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h
\
ajsort.h ajsql.h ajstr.h ajsys.h \
ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
@@ -61,3 +66,4 @@
endif
libajax_la_LDFLAGS = $(LINKFLAGS)
+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/core/ajax-pcre-config.h.in
EMBOSS-6.3.1/ajax/core/ajax-pcre-config.h.in
--- EMBOSS-6.3.1.orig/ajax/core/ajax-pcre-config.h.in 1969-12-31
19:00:00.000000000 -0500
+++ EMBOSS-6.3.1/ajax/core/ajax-pcre-config.h.in 2010-08-04
20:21:16.000000000 -0400
@@ -0,0 +1 @@
+...@define_use_system_pcre@ AJAX_USE_SYSTEM_PCRE
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/core/ajreg.h
EMBOSS-6.3.1/ajax/core/ajreg.h
--- EMBOSS-6.3.1.orig/ajax/core/ajreg.h 2010-04-14 03:44:20.000000000 -0400
+++ EMBOSS-6.3.1/ajax/core/ajreg.h 2010-08-04 20:29:22.000000000 -0400
@@ -16,9 +16,14 @@
#define ajreg_h
#include "ajax.h"
+#include "ajax-pcre-config.h"
+#ifndef AJAX_USE_SYSTEM_PCRE
#include "pcre_config.h"
#include "pcre_internal.h"
#include "pcreposix.h"
+#else
+#include <pcre.h>
+#endif
#define AJREG_OVECSIZE 30
@@ -41,7 +46,11 @@
******************************************************************************/
typedef struct AjSRegexp {
+#ifndef AJAX_USE_SYSTEM_PCRE
real_pcre *pcre;
+#else
+ pcre *pcre;
+#endif
pcre_extra *extra;
int *ovector;
const char* orig;
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/ensembl/Makefile.am
EMBOSS-6.3.1/ajax/ensembl/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/ensembl/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/ensembl/Makefile.am 2010-08-06 04:16:49.000000000
-0400
@@ -10,12 +10,13 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
endif
-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
+INCLUDES = $(EXTRA_INCLUDES) \
+-I$(top_srcdir)/ajax/core
ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
@@ -56,3 +57,4 @@
endif
libensembl_la_LDFLAGS = $(LINKFLAGS)
+libensembl_la_LIBADD = ../core/libajax.la
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/graphics/Makefile.am
EMBOSS-6.3.1/ajax/graphics/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/graphics/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/graphics/Makefile.am 2010-08-06 04:09:10.000000000
-0400
@@ -10,11 +10,15 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
+EXTRA_LIBS = $(PLPLOT_LIBS)
endif
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
AJAXGSRC = ajgraph.c ajhist.c
@@ -32,3 +36,4 @@
endif
libajaxg_la_LDFLAGS = $(LINKFLAGS)
+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/graphics/ajgraph.c
EMBOSS-6.3.1/ajax/graphics/ajgraph.c
--- EMBOSS-6.3.1.orig/ajax/graphics/ajgraph.c 2010-07-19 07:40:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2010-08-06 04:11:20.000000000
-0400
@@ -1054,8 +1054,18 @@
{
if(!thys->ready)
{
+#ifdef USE_PLXSFNAM_SHIM
+ char *fullname;
+#endif
ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
+#ifdef USE_PLXSFNAM_SHIM
+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
+ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
+ plsfnam(fullname);
+ free(fullname);
+#else
plxsfnam(ajStrGetPtr(txt), ext);
+#endif
ajStrAssignS(&graphBasename, txt);
ajStrAssignC(&graphExtension, ext);
if(ajStrGetCharFirst(graphExtension) == '.')
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/configure.in EMBOSS-6.3.1/configure.in
--- EMBOSS-6.3.1.orig/configure.in 2010-07-19 07:45:34.000000000 -0400
+++ EMBOSS-6.3.1/configure.in 2010-08-06 07:20:07.000000000 -0400
@@ -235,15 +235,6 @@
AC_PROG_LN_S
AC_PROG_MAKE_SET
-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
-if test "${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
# Checks for header files.
#as# AC_PATH_X
@@ -292,9 +283,6 @@
#as# select socket sqrt strchr strcspn strdup strerror strpbrk \
#as# strrchr strspn strstr strtol])
-if test "${with_x}" != "no" ; then
-LF_EMBOSS_PATH_XLIB
-fi
dnl Library checks
AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
@@ -322,8 +310,8 @@
CFLAGS="$CFLAGS $MYSQL_CFLAGS"
LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
dnl Check for 'ant' for packaging Jemboss and export result
@@ -443,13 +431,33 @@
dnl Test if --enable-systemlibs given
have_systemlibs=no
+DEFINE_USE_SYSTEM_PCRE="#undef"
AC_ARG_ENABLE(systemlibs,
AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
if test "${enable_systemlibs}" = "yes" ; then
have_systemlibs=yes
+ DEFINE_USE_SYSTEM_PCRE="#define"
+ PKG_CHECK_MODULES(PLPLOT, [plplotd])
+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 "${with_x}" != "no" ; then
+ LF_EMBOSS_PATH_XLIB
+ fi
fi
AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
AC_SUBST(ESYSTEMLIBS)
+AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
+AC_SUBST(PLPLOT_CFLAGS)
+AC_SUBST(PLPLOT_LIBS)
@@ -683,6 +691,7 @@
AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
+ajax/core/ajax-pcre-config.h
ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
ajax/acd/Makefile
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/emboss/Makefile.am
EMBOSS-6.3.1/emboss/Makefile.am
--- EMBOSS-6.3.1.orig/emboss/Makefile.am 2010-06-16 06:26:45.000000000
-0400
+++ EMBOSS-6.3.1/emboss/Makefile.am 2010-08-06 05:50:53.000000000 -0400
@@ -79,14 +79,17 @@
yank
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
endif
-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
+INCLUDES = -I$(top_srcdir)/nucleus \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
+ -I$(top_srcdir)/ajax/acd
aaindexextract_SOURCES = aaindexextract.c
@@ -319,7 +322,7 @@
treetypedisplay_SOURCES = treetypedisplay.c
if !ESYSTEMLIBS
-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
../plplot/libeplplot.la ../ajax/pcre/libepcre.la
endif
@@ -327,7 +330,6 @@
../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
$(EXTRA_LDS) \
- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
$(XLIB)
pkgdata_DATA = emboss.default.template
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/nucleus/Makefile.am
EMBOSS-6.3.1/nucleus/Makefile.am
--- EMBOSS-6.3.1.orig/nucleus/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/nucleus/Makefile.am 2010-08-06 05:20:16.000000000 -0400
@@ -19,13 +19,16 @@
-lezlib -leplplot
else
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
endif
endif
-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
+INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
+ -I$(top_srcdir)/ajax \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
@@ -55,3 +58,4 @@
endif
libnucleus_la_LDFLAGS = $(LINKFLAGS)
+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la
../ajax/acd/libacd.la
--- NEW FILE: emboss.info ---
Package: emboss
Version: 6.3.1
Revision: 101
Depends: <<
%N-libajax6-shlibs (>= %v-%r),
%N-libnucleus6-shlibs (>= %v-%r),
dpkg-base-files,
expat1-shlibs,
freetype219-shlibs (>= 2.3.12-1),
gd2-shlibs,
libpng14-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
pcre-shlibs,
plplot-shlibs,
plplot-nognome-shlibs,
postgresql84-shlibs,
system-java (>= 1.5.0)
<<
BuildDepends: <<
autoconf2.6,
automake1.11,
fink (>= 0.24.12),
fink-package-precedence,
expat1,
freetype219 (>= 2.3.12-1),
gd2,
libpng14,
libtool2,
mysql-unified-dev,
pcre,
pkgconfig,
plplot-dev,
plplot-nognome-dev,
postgresql84-dev,
system-java-dev (>= 1.5.0)
<<
# plplot's -nognome varianting is a disaster (adding/removing can
# change who if anyone supplies various headers and libs). They claim
# they are co-installable, so just depend on both to make sure.
Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-%v.tar.gz
Source-MD5: 04d1179b6261103a77e396d54f8ac38e
PatchFile: %n.patch
PatchFile-MD5: 714dcd80c41343a1e0c4bc0e90e36718
PatchScript: <<
%{default_script}
find . -name Makefile.am | xargs perl -pi -e 's/(_la_LDFLAGS.*)/\1
-no-undefined/'
<<
ConfigureParams: <<
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home \
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home/include
\
--enable-dependency-tracking --disable-static \
--includedir=%p/lib/EMBOSS/include --libdir=%p/lib/EMBOSS/lib \
--docdir=%p/share/EMBOSS \
--enable-systemlibs --with-postgresql=%p/opt/postgresql-8.4/bin/pg_config
<<
CompileScript: <<
#!/bin/sh -ev
%p/bin/autoreconf -fi
./configure %c
make
fink-package-precedence \
--prohibit-bdep=%N-libajax6-dev,%N-libnucleus6-dev \
--prohibit-bdep=emboss-ajax6-dev,emboss-nucleus6-dev,emboss-plplot3-dev,emboss-plplot6-dev
\
.
<<
Installscript: <<
make install DESTDIR=%d
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS LICENSE NEWS
ONEWS PROBLEMS README THANKS
RunTimeVars: <<
# EMBOSS_ROOT: %p/share/EMBOSS
EMBOSS_DATA: %p/share/EMBOSS/data
<<
SplitOff10: <<
Package: %N-libajax6-shlibs
Depends: <<
expat1-shlibs,
freetype219-shlibs (>= 2.3.12-1),
gd2-shlibs,
libpng14-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
pcre-shlibs,
plplot-shlibs,
plplot-nognome-shlibs,
postgresql84-shlibs
<<
Files: <<
lib/EMBOSS/lib/libacd.6*.dylib
lib/EMBOSS/lib/libajax.6*.dylib
lib/EMBOSS/lib/libajaxdb.6*.dylib
lib/EMBOSS/lib/libajaxg.6*.dylib
lib/EMBOSS/lib/libensembl.6*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/lib/libacd.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libajax.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libajaxdb.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libajaxg.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libensembl.6.dylib 7.0.0 %n (>= 6.3.1-101)
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
SplitOff11: <<
Package: %N-libajax6-dev
Depends: %N-libajax6-shlibs (= %v-%r)
BuildDependsOnly: True
Files: <<
lib/EMBOSS/lib/libacd.*
lib/EMBOSS/lib/libajax.*
lib/EMBOSS/lib/libajaxdb.*
lib/EMBOSS/lib/libajaxg.*
lib/EMBOSS/lib/libensembl.*
lib/EMBOSS/include/aj*.h
lib/EMBOSS/include/ens*.h
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
SplitOff20: <<
Package: %N-libnucleus6-shlibs
Depends: <<
%N-libajax6-shlibs (>= %v-%r),
expat1-shlibs,
freetype219-shlibs (>= 2.3.12-1),
gd2-shlibs,
libpng14-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
pcre-shlibs,
plplot-shlibs,
plplot-nognome-shlibs,
postgresql84-shlibs
<<
Files: <<
lib/EMBOSS/lib/libnucleus.6*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/lib/libnucleus.6.dylib 7.0.0 %n (>= 6.3.1-101)
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
SplitOff21: <<
Package: %N-libnucleus6-dev
Depends: %N-libnucleus6-shlibs (= %v-%r)
BuildDependsOnly: True
Files: <<
lib/EMBOSS/lib/libnucleus.*
lib/EMBOSS/include/em*.h
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
Description: Molecular Biology Open Software Suite
DescDetail: <<
EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety of
formats and even allows transparent retrieval of sequence data from the
web. Also, as extensive libraries are provided with the package, it is a
platform to allow other scientists to develop and release software in
true open source spirit. EMBOSS also integrates a range of currently
available packages and tools for sequence analysis into a seamless
whole.
<<
DescUsage: <<
See the README file for other environment variables you may need to
configure. See http://emboss.sourceforge.net/Jemboss/ for
information on using the Jemboss GUI for EMBOSS. To prevent conflicts,
the headers are located in %p/lib/EMBOSS/include instead of %p/include.
Install kemboss-qt4-mac or kemboss-qt4-x11 for a GUI that works either
in Aqua or X11 respectively or emboss-kaptain for a different X11 GUI.
<<
DescPort: <<
Add explicit linking to libs that supply symbols used by the
shared libraries here. This prevents things that link against
the shared libraries from having to know to pass additional
flags when the linker requires all symbols be defined.
Home-grown hack mis-passes things and isn't portable. But we
don't need it because we're using system plplot so omit rather
than fix.
Fink plplot doesn't have plxsfnam(), which takes separate
filename and extension, so hack ajgraph.c to use plfnam(),
which takes single filename.
<<
DescPackaging: <<
Former Maintainer: Koen van der Drift <[email protected]>
There have been a ton of Shlibs Policy problems. As of
6.3.1-101, making clean break with new library package-names
and install_names (via never-before-used --libdir and parallel
--includedir) and no attempt to retain symlinks for -dev or
-shlibs since old pkgs are not necessarily compatible with
these new ones.
Hack configure and Makefiles to consider external plplot and
expat library as other systemlibs.
Make sure pg flags get passed early so specific-version buried
-I and -L supercede unpredictably-versioned ones in default
locations.
<<
Maintainer: Daniel Macks <[email protected]>
Homepage: http://emboss.sourceforge.net
License: GPL
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