Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv26207
Added Files:
emboss.info emboss.patch
Log Message:
blindly committing to 10.[78] after testing on 10.6 because hey why not
--- NEW FILE: emboss.patch ---
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/Makefile.am EMBOSS-6.5.7/Makefile.am
--- EMBOSS-6.5.7.orig/Makefile.am 2012-07-22 07:16:46.000000000 -0400
+++ EMBOSS-6.5.7/Makefile.am 2013-05-25 19:37:43.000000000 -0400
@@ -12,8 +12,11 @@
ONEWS \
PROBLEMS
+if !ESYSTEMLIBS
+EXTRA_DIRS = plplot
+endif
SUBDIRS = \
-plplot \
+$(EXTRA_DIRS) \
ajax \
nucleus \
emboss \
@@ -34,4 +37,3 @@
tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS
| xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name
.cvsignore | xargs rm -rf )
install-exec-hook:
- $(bindir)/embossupdate
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/Makefile.am
EMBOSS-6.5.7/ajax/Makefile.am
--- EMBOSS-6.5.7.orig/ajax/Makefile.am 2011-08-25 15:45:55.000000000 -0400
+++ EMBOSS-6.5.7/ajax/Makefile.am 2013-05-25 19:40:09.000000000 -0400
@@ -1,7 +1,7 @@
## Process this file with automake to produce Makefile.in
-SUBDIRS = pcre
+SUBDIRS =
if !ESYSTEMLIBS
-SUBDIRS += expat zlib
+SUBDIRS += pcre expat zlib
endif
SUBDIRS += core graphics ensembl ajaxdb acd
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/acd/Makefile.am
EMBOSS-6.5.7/ajax/acd/Makefile.am
--- EMBOSS-6.5.7.orig/ajax/acd/Makefile.am 2012-03-23 16:19:27.000000000
-0400
+++ EMBOSS-6.5.7/ajax/acd/Makefile.am 2013-05-25 19:43:49.000000000 -0400
@@ -7,12 +7,13 @@
libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
if !ESYSTEMLIBS
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+endif
+libacd_la_CPPFLAGS += $(PLPLOT_CFLAGS)
libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
libacd_la_LDFLAGS = -version-info 6:4:0
@@ -38,6 +39,7 @@
libacd_la_LDFLAGS += -lepcre
libacd_la_LDFLAGS += -lezlib
endif
+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
../ajaxdb/libajaxdb.la
libacd_la_SOURCES = ajacd.c
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/ajaxdb/Makefile.am
EMBOSS-6.5.7/ajax/ajaxdb/Makefile.am
--- EMBOSS-6.5.7.orig/ajax/ajaxdb/Makefile.am 2012-03-23 16:19:27.000000000
-0400
+++ EMBOSS-6.5.7/ajax/ajaxdb/Makefile.am 2013-05-25 19:45:08.000000000
-0400
@@ -5,12 +5,12 @@
libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl
-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
if !ESYSTEMLIBS
libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
+endif
libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS)
@@ -34,6 +34,7 @@
libajaxdb_la_LDFLAGS += -lezlib
endif
libajaxdb_la_LDFLAGS += $(AXIS2C_LDFLAGS)
+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
libajaxdb_la_SOURCES = \
ajassemdb.c \
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/core/Makefile.am
EMBOSS-6.5.7/ajax/core/Makefile.am
--- EMBOSS-6.5.7.orig/ajax/core/Makefile.am 2012-03-23 16:19:27.000000000
-0400
+++ EMBOSS-6.5.7/ajax/core/Makefile.am 2013-05-25 21:34:12.000000000 -0400
@@ -4,12 +4,19 @@
libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
+libajax_la_CPPFLAGS =
if !ESYSTEMLIBS
libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+EXTRA_LIBS = -lexpat -lpcre
+endif
+
+EXTRA_DIST = ajax-pcre-config.h.in
+DISTCLEAN = ajax-pcre-config.h
+
libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
@@ -35,6 +42,7 @@
libajax_la_LDFLAGS += -lepcre
libajax_la_LDFLAGS += -lezlib
endif
+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
libajax_la_SOURCES = \
ajalign.c \
@@ -172,6 +180,7 @@
ajquerydata.h \
ajrange.h \
ajreg.h \
+ajax-pcre-config.h \
ajreport.h \
ajrefseq.h \
ajrefseqdata.h \
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/core/ajax-pcre-config.h.in
EMBOSS-6.5.7/ajax/core/ajax-pcre-config.h.in
--- EMBOSS-6.5.7.orig/ajax/core/ajax-pcre-config.h.in 1969-12-31
19:00:00.000000000 -0500
+++ EMBOSS-6.5.7/ajax/core/ajax-pcre-config.h.in 2013-05-25
19:50:00.000000000 -0400
@@ -0,0 +1 @@
+@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/core/ajreg.h
EMBOSS-6.5.7/ajax/core/ajreg.h
--- EMBOSS-6.5.7.orig/ajax/core/ajreg.h 2011-10-18 10:23:40.000000000 -0400
+++ EMBOSS-6.5.7/ajax/core/ajreg.h 2013-05-25 19:51:43.000000000 -0400
@@ -39,9 +39,14 @@
#include "ajdefine.h"
#include "ajstr.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
AJ_BEGIN_DECLS
@@ -84,7 +88,11 @@
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-6.5.7.orig/ajax/ensembl/Makefile.am
EMBOSS-6.5.7/ajax/ensembl/Makefile.am
--- EMBOSS-6.5.7.orig/ajax/ensembl/Makefile.am 2012-03-23 16:19:27.000000000
-0400
+++ EMBOSS-6.5.7/ajax/ensembl/Makefile.am 2013-05-25 21:34:32.000000000
-0400
@@ -4,12 +4,13 @@
libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
-libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
+libensembl_la_CPPFLAGS =
if !ESYSTEMLIBS
libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+endif
libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
libensembl_la_LDFLAGS = -version-info 6:4:0
@@ -27,6 +28,7 @@
libensembl_la_LDFLAGS += -leexpat
libensembl_la_LDFLAGS += -lepcre
endif
+libensembl_la_LIBADD = ../core/libajax.la
libensembl_la_SOURCES = \
ensalign.c \
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/graphics/Makefile.am
EMBOSS-6.5.7/ajax/graphics/Makefile.am
--- EMBOSS-6.5.7.orig/ajax/graphics/Makefile.am 2012-03-23 16:19:27.000000000
-0400
+++ EMBOSS-6.5.7/ajax/graphics/Makefile.am 2013-05-25 21:35:17.000000000
-0400
@@ -4,11 +4,15 @@
libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
-libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
+libajaxg_la_CPPFLAGS =
if !ESYSTEMLIBS
libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
-endif
+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+libajaxg_la_CPPFLAGS += $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
+EXTRA_LIBS = $(PLPLOT_LIBS)
+endif
libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
libajaxg_la_LDFLAGS = -version-info 6:4:0
@@ -26,6 +27,7 @@
libajaxg_la_LDFLAGS += -leexpat
libajaxg_la_LDFLAGS += -lepcre
endif
+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
libajaxg_la_SOURCES = ajgraph.c ajhist.c
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/graphics/ajgraph.c
EMBOSS-6.5.7/ajax/graphics/ajgraph.c
--- EMBOSS-6.5.7.orig/ajax/graphics/ajgraph.c 2011-11-08 10:12:19.000000000
-0500
+++ EMBOSS-6.5.7/ajax/graphics/ajgraph.c 2013-05-25 19:55:59.000000000
-0400
@@ -963,11 +963,20 @@
{
if(!thys->ready)
{
+#ifdef USE_PLXSFNAM_SHIM
+ char *fullname;
+#endif
#if GRAPH_DEBUG
ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
#endif
-
+#ifdef USE_PLXSFNAM_SHIM
+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
+ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
+ plsfnam(fullname);
+ free(fullname);
+#else
plxsfnam(ajStrGetPtr(txt), ext);
+#endif
ajStrAssignS(&graphBasename, txt);
ajStrAssignC(&graphExtension, ext);
if(ajStrGetCharFirst(graphExtension) == '.')
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/configure.in EMBOSS-6.5.7/configure.in
--- EMBOSS-6.5.7.orig/configure.in 2012-07-24 10:06:02.000000000 -0400
+++ EMBOSS-6.5.7/configure.in 2013-05-25 20:10:04.000000000 -0400
@@ -707,7 +707,7 @@
AC_CHECK_FUNCS([memmove])
-AS_IF([test "x${with_x}" != "xno"], [LF_EMBOSS_PATH_XLIB])
+dnl AS_IF([test "x${with_x}" != "xno"], [LF_EMBOSS_PATH_XLIB])
# Library checks.
@@ -846,9 +846,14 @@
AC_ARG_ENABLE([systemlibs],
[AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
+DEFINE_USE_SYSTEM_PCRE="#undef"
AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
-
+DEFINE_USE_SYSTEM_PCRE="#define"
+PKG_CHECK_MODULES(PLPLOT, [plplotd])
+AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
+AC_SUBST(PLPLOT_CFLAGS)
+AC_SUBST(PLPLOT_LIBS)
@@ -988,6 +991,7 @@
ajax/acd/Makefile
ajax/ajaxdb/Makefile
ajax/core/Makefile
+ ajax/core/ajax-pcre-config.h
ajax/ensembl/Makefile
ajax/expat/Makefile
ajax/graphics/Makefile
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/emboss/Makefile.am
EMBOSS-6.5.7/emboss/Makefile.am
--- EMBOSS-6.5.7.orig/emboss/Makefile.am 2012-07-14 12:46:15.000000000
-0400
+++ EMBOSS-6.5.7/emboss/Makefile.am 2013-05-25 20:13:39.000000000 -0400
@@ -30,13 +30,14 @@
AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
-AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
if !ESYSTEMLIBS
AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+AM_CPPFLAGS += -I$(top_srcdir)/plplot
endif
+AM_CPPFLAGS += $(PLPLOT_CFLAGS)
AM_CPPFLAGS += -I$(top_srcdir)/nucleus
-AM_CPPFLAGS += -I$(top_srcdir)/plplot
AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
AM_CPPFLAGS += $(JAVA_CPPFLAGS)
@@ -49,9 +50,9 @@
if !ESYSTEMLIBS
LDADD += ../ajax/zlib/libezlib.la
LDADD += ../ajax/expat/libeexpat.la
-endif
-LDADD += ../ajax/pcre/libepcre.la
LDADD += ../plplot/libeplplot.la
+LDADD += ../ajax/pcre/libepcre.la
+endif
LDADD += $(XLIB)
#if PURIFY
diff -Nurd -x'*~' EMBOSS-6.5.7.orig/nucleus/Makefile.am
EMBOSS-6.5.7/nucleus/Makefile.am
--- EMBOSS-6.5.7.orig/nucleus/Makefile.am 2011-08-25 17:18:40.000000000
-0400
+++ EMBOSS-6.5.7/nucleus/Makefile.am 2013-05-25 21:35:32.000000000 -0400
@@ -10,12 +10,16 @@
endif
endif
-libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot
-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+libnucleus_la_CPPFLAGS =
if !ESYSTEMLIBS
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+else
+libnucleus_la_CPPFLAGS += $(PLPLOT_CFLAGS)
endif
+
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
@@ -48,6 +52,7 @@
libnucleus_la_LDFLAGS += -lezlib
libnucleus_la_LDFLAGS += -leplplot
endif
+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la
../ajax/acd/libacd.la
libnucleus_la_SOURCES = \
embaln.c \
--- NEW FILE: emboss.info ---
Package: emboss
Version: 6.5.7
Revision: 104
Depends: <<
%N-libajax6-shlibs (>= %v-%r),
%N-libnucleus6-shlibs (>= %v-%r),
dpkg-base-files,
expat1-shlibs,
gd2-shlibs,
libharu2.2.1-shlibs,
libpcre1-shlibs,
libplplot10-shlibs,
libpng15-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
postgresql92-shlibs,
system-java (>= 1.5.0)
<<
BuildDepends: <<
autoconf2.6,
automake1.12,
fink-package-precedence,
expat1,
freetype219 (>= 2.4.11-1),
gd2,
libharu2.2.1-dev,
libpcre1,
libplplot10-dev,
libpng15,
libtool2,
mysql-unified-dev,
pkgconfig,
postgresql92-dev (>= 1:0-0),
system-java-dev (>= 1.5.0)
<<
Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-%v.tar.gz
Source-MD5: 6a2cb3f93d5e9415c74ab0f6b1ede5f0
PatchFile: %n.patch
PatchFile-MD5: 60b721bf71919a7357f952b017a2ae7f
PatchScript: <<
%{default_script}
find . -name Makefile.am | xargs perl -pi -e 's/(_la_LDFLAGS.*)/\1
-no-undefined/'
<<
ConfigureParams: <<
--with-java=${java_home} \
--with-javaos=${java_includes} \
--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-9.2/bin/pg_config
<<
CompileScript: <<
#!/bin/sh -ev
if [ -x /usr/libexec/java_home ]; then
export java_home=`/usr/libexec/java_home`
else
export
java_home=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home
fi
# 10.7+ doesn't have 'include' under $java_home, but has the Headers in
JavaVM.framework
if [ -d ${java_home}/include ]; then
export java_includes=${java_home}/include
else
ln -s /System/Library/Frameworks/JavaVM.framework/Headers
%b/java_include
export java_includes=%b/java_include
fi
%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
\
.
<<
InfoTest: <<
TestScript: <<
make check || exit 2
<<
<<
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,
gd2-shlibs,
libharu2.2.1-shlibs,
libpcre1-shlibs,
libplplot10-shlibs,
libpng15-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
postgresql92-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,
gd2-shlibs,
libharu2.2.1-shlibs,
libpcre1-shlibs,
libplplot10-shlibs,
libpng15-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
postgresql92-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 <drift...@users.sourceforge.net>
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 <dma...@netspace.org>
Homepage: http://emboss.sourceforge.net
License: GPL
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