Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv26136
Modified Files:
emboss.info emboss.patch
Log Message:
new version (thanks snaggle!)
Index: emboss.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/emboss.patch,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- emboss.patch 2 Nov 2010 15:46:18 -0000 1.6
+++ emboss.patch 2 Jun 2013 19:40:19 -0000 1.7
@@ -1,127 +1,143 @@
-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
+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
--SUBDIRS = plplot ajax nucleus emboss test doc jemboss
+if !ESYSTEMLIBS
+EXTRA_DIRS = plplot
+endif
-+SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc jemboss
-
- # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
+ SUBDIRS = \
+-plplot \
++$(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 )
-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 @@
+ 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
- if !ESYSTEMLIBS
--EXTRA_DIRS = expat zlib
-+EXTRA_DIRS = pcre expat zlib
- endif
-
--SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
-+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
-diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/acd/Makefile.am
EMBOSS-6.3.1/ajax/acd/Makefile.am
---- EMBOSS-6.3.1.orig/ajax/acd/Makefile.am 2010-06-16 07:36:00.000000000
-0400
-+++ EMBOSS-6.3.1/ajax/acd/Makefile.am 2010-08-06 04:31:47.000000000 -0400
-@@ -13,10 +13,13 @@
- endif
+-SUBDIRS = pcre
++SUBDIRS =
if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(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 = $(PLPLOT_CFLAGS)
+-SUBDIRS += expat zlib
++SUBDIRS += pcre expat zlib
endif
+ SUBDIRS += core graphics ensembl ajaxdb acd
+diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/acd/Makefile.am
EMBOSS-6.5.7/ajax/acd/Makefile.am
+--- EMBOSS-6.5.7.orig/ajax/acd/Makefile.am 2012-03-23 16:19:27.000000000
-0400
++++ EMBOSS-6.5.7/ajax/acd/Makefile.am 2013-05-25 19:43:49.000000000 -0400
+@@ -7,12 +7,13 @@
+ libacd_la_CPPFLAGS = -I$(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 += $(JAVA_CPPFLAGS)
--INCLUDES = -I$(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 @@
+ libacd_la_LDFLAGS = -version-info 6:4:0
+@@ -38,6 +39,7 @@
+ libacd_la_LDFLAGS += -lepcre
+ libacd_la_LDFLAGS += -lezlib
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
+ 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) $(JAVA_CFLAGS)
--INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
-+INCLUDES = \
- $(EXTRA_INCLUDES) \
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
+ libajaxdb_la_CPPFLAGS = -I$(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)
-@@ -37,3 +38,4 @@
+@@ -34,6 +34,7 @@
+ libajaxdb_la_LDFLAGS += -lezlib
endif
-
- libajaxdb_la_LDFLAGS = $(LINKFLAGS)
+ libajaxdb_la_LDFLAGS += $(AXIS2C_LDFLAGS)
+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
+ 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
--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
+ 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
-
++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 @@
++
+ 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_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
+
+ 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-6.3.1.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
+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.h"
+#include "ajax-pcre-config.h"
+#ifndef AJAX_USE_SYSTEM_PCRE
#include "pcre_config.h"
@@ -131,82 +147,90 @@
+#include <pcre.h>
+#endif
- #define AJREG_OVECSIZE 30
+ AJ_BEGIN_DECLS
-@@ -41,7 +46,11 @@
-
******************************************************************************/
+@@ -84,7 +88,11 @@
- typedef struct AjSRegexp {
+ typedef struct AjSRegexp
+ {
+#ifndef AJAX_USE_SYSTEM_PCRE
real_pcre *pcre;
+#else
-+ pcre *pcre;
++ 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
+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) $(JAVA_CFLAGS)
--INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
---I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
-+INCLUDES = $(EXTRA_INCLUDES) \
-+-I$(top_srcdir)/ajax/core
+-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)
- ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
- ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
-@@ -56,3 +57,4 @@
+ libensembl_la_LDFLAGS = -version-info 6:4:0
+@@ -27,6 +28,7 @@
+ libensembl_la_LDFLAGS += -leexpat
+ libensembl_la_LDFLAGS += -lepcre
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
+ 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
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ 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
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
++libajaxg_la_CPPFLAGS += $(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
++endif
+ libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
- AJAXGSRC = ajgraph.c ajhist.c
-@@ -32,3 +36,4 @@
+ libajaxg_la_LDFLAGS = -version-info 6:4:0
+@@ -26,6 +27,7 @@
+ libajaxg_la_LDFLAGS += -leexpat
+ libajaxg_la_LDFLAGS += -lepcre
endif
-
- libajaxg_la_LDFLAGS = $(LINKFLAGS)
+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
-diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/graphics/ajgraph.c
EMBOSS-6.3.1/ajax/graphics/ajgraph.c
---- EMBOSS-6.3.1.orig/ajax/graphics/ajgraph.c 2010-07-19 07:40:00.000000000
-0400
-+++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2010-08-06 04:11:20.000000000
-0400
-@@ -1054,8 +1054,18 @@
+
+ libajaxg_la_SOURCES = ajgraph.c ajhist.c
+
+diff -Nurd -x'*~' EMBOSS-6.5.7.orig/ajax/graphics/ajgraph.c
EMBOSS-6.5.7/ajax/graphics/ajgraph.c
+--- EMBOSS-6.5.7.orig/ajax/graphics/ajgraph.c 2011-11-08 10:12:19.000000000
-0500
++++ EMBOSS-6.5.7/ajax/graphics/ajgraph.c 2013-05-25 19:55:59.000000000
-0400
+@@ -963,11 +963,20 @@
{
if(!thys->ready)
{
+#ifdef USE_PLXSFNAM_SHIM
+ char *fullname;
+#endif
+ #if GRAPH_DEBUG
ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
+ #endif
+-
+#ifdef USE_PLXSFNAM_SHIM
+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
+ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
@@ -218,154 +242,101 @@
ajStrAssignS(&graphBasename, txt);
ajStrAssignC(&graphExtension, ext);
if(ajStrGetCharFirst(graphExtension) == '.')
-diff -Nurd -x'*~' EMBOSS-6.3.1.orig/configure.in EMBOSS-6.3.1/configure.in
---- EMBOSS-6.3.1.orig/configure.in 2010-07-19 07:45:34.000000000 -0400
-+++ EMBOSS-6.3.1/configure.in 2010-08-06 07:20:07.000000000 -0400
-@@ -235,15 +235,6 @@
- AC_PROG_LN_S
- AC_PROG_MAKE_SET
-
--dnl Intel MacOSX 10.6 puts X11 in a non-standard place
--if test "${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 "${with_x}" != "no" ; then
--LF_EMBOSS_PATH_XLIB
--fi
+diff -Nurd -x'*~' EMBOSS-6.5.7.orig/configure.in EMBOSS-6.5.7/configure.in
+--- EMBOSS-6.5.7.orig/configure.in 2012-07-24 10:06:02.000000000 -0400
++++ EMBOSS-6.5.7/configure.in 2013-05-25 20:10:04.000000000 -0400
+@@ -707,7 +707,7 @@
- dnl Library checks
- AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
-@@ -322,8 +310,8 @@
- CFLAGS="$CFLAGS $MYSQL_CFLAGS"
- LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+ AC_CHECK_FUNCS([memmove])
--CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
--LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
-+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
-+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
+-AS_IF([test "x${with_x}" != "xno"], [LF_EMBOSS_PATH_XLIB])
++dnl AS_IF([test "x${with_x}" != "xno"], [LF_EMBOSS_PATH_XLIB])
- dnl Check for 'ant' for packaging Jemboss and export result
-@@ -443,13 +431,33 @@
+ # Library checks.
+@@ -846,9 +846,14 @@
- dnl Test if --enable-systemlibs given
- have_systemlibs=no
+ AC_ARG_ENABLE([systemlibs],
+ [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
+DEFINE_USE_SYSTEM_PCRE="#undef"
- AC_ARG_ENABLE(systemlibs,
- AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
- if test "${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)
+
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+-
++DEFINE_USE_SYSTEM_PCRE="#define"
++PKG_CHECK_MODULES(PLPLOT, [plplotd])
+AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
+AC_SUBST(PLPLOT_CFLAGS)
+AC_SUBST(PLPLOT_LIBS)
-@@ -683,6 +691,7 @@
-
-
- AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
-+ajax/core/ajax-pcre-config.h
- ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
- ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
- ajax/acd/Makefile
-diff -Nurd -x'*~' EMBOSS-6.3.1.orig/emboss/Makefile.am
EMBOSS-6.3.1/emboss/Makefile.am
---- EMBOSS-6.3.1.orig/emboss/Makefile.am 2010-06-16 06:26:45.000000000
-0400
-+++ EMBOSS-6.3.1/emboss/Makefile.am 2010-08-06 05:50:53.000000000 -0400
-@@ -79,14 +79,17 @@
- yank
-
+@@ -988,6 +991,7 @@
+ ajax/acd/Makefile
+ ajax/ajaxdb/Makefile
+ ajax/core/Makefile
++ ajax/core/ajax-pcre-config.h
+ ajax/ensembl/Makefile
+ ajax/expat/Makefile
+ ajax/graphics/Makefile
+diff -Nurd -x'*~' EMBOSS-6.5.7.orig/emboss/Makefile.am
EMBOSS-6.5.7/emboss/Makefile.am
+--- EMBOSS-6.5.7.orig/emboss/Makefile.am 2012-07-14 12:46:15.000000000
-0400
++++ EMBOSS-6.5.7/emboss/Makefile.am 2013-05-25 20:13:39.000000000 -0400
+@@ -30,13 +30,14 @@
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
+-AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(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 = $(PLPLOT_CFLAGS)
+ AM_CPPFLAGS += -I$(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 += $(JAVA_CPPFLAGS)
--INCLUDES = -I$(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
-
+@@ -49,9 +50,9 @@
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
-
+ 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)
-@@ -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 \
- $(XLIB)
+ #if PURIFY
+diff -Nurd -x'*~' EMBOSS-6.5.7.orig/nucleus/Makefile.am
EMBOSS-6.5.7/nucleus/Makefile.am
+--- EMBOSS-6.5.7.orig/nucleus/Makefile.am 2011-08-25 17:18:40.000000000
-0400
++++ EMBOSS-6.5.7/nucleus/Makefile.am 2013-05-25 21:35:32.000000000 -0400
+@@ -10,12 +10,16 @@
+ endif
+ endif
- pkgdata_DATA = emboss.default.template
-diff -Nurd -x'*~' EMBOSS-6.3.1.orig/nucleus/Makefile.am
EMBOSS-6.3.1/nucleus/Makefile.am
---- EMBOSS-6.3.1.orig/nucleus/Makefile.am 2010-06-16 07:36:00.000000000
-0400
-+++ EMBOSS-6.3.1/nucleus/Makefile.am 2010-08-06 05:20:16.000000000 -0400
-@@ -19,13 +19,16 @@
- -lezlib -leplplot
- else
+-libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot
+-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
++libnucleus_la_CPPFLAGS =
if !ESYSTEMLIBS
--EXTRA_INCLUDES = -I$(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$(top_srcdir)/ajax/pcre
+ libnucleus_la_CPPFLAGS += -I$(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
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
- endif
++libnucleus_la_CPPFLAGS += $(PLPLOT_CFLAGS)
endif
-
-
--INCLUDES = -I$(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$(top_srcdir)/ajax/ajaxdb \
-@@ -55,3 +58,4 @@
++
+ libnucleus_la_CPPFLAGS += -I$(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_LDFLAGS = $(LINKFLAGS)
+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la
../ajax/acd/libacd.la
+
+ libnucleus_la_SOURCES = \
+ embaln.c \
Index: emboss.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- emboss.info 15 Jan 2013 16:56:49 -0000 1.17
+++ emboss.info 2 Jun 2013 19:40:19 -0000 1.18
@@ -1,52 +1,51 @@
Package: emboss
-Version: 6.3.1
+Version: 6.5.7
Revision: 104
Depends: <<
%N-libajax6-shlibs (>= %v-%r),
%N-libnucleus6-shlibs (>= %v-%r),
dpkg-base-files,
expat1-shlibs,
- freetype219-shlibs (>= 2.4.11-1),
gd2-shlibs,
+ libharu2.2.1-shlibs,
+ libpcre1-shlibs,
+ libplplot10-shlibs,
libpng15-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
- libpcre1-shlibs,
- libplplot10-shlibs,
postgresql92-shlibs,
system-java (>= 1.5.0)
<<
BuildDepends: <<
autoconf2.6,
- automake1.11,
- fink (>= 0.24.12),
+ automake1.12,
fink-package-precedence,
expat1,
freetype219 (>= 2.4.11-1),
gd2,
+ libharu2.2.1-dev,
+ libpcre1,
+ libplplot10-dev,
libpng15,
libtool2,
mysql-unified-dev,
- libpcre1,
pkgconfig,
- libplplot10-dev,
postgresql92-dev (>= 1:0-0),
system-java-dev (>= 1.5.0)
<<
Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-%v.tar.gz
-Source-MD5: 04d1179b6261103a77e396d54f8ac38e
+Source-MD5: 6a2cb3f93d5e9415c74ab0f6b1ede5f0
PatchFile: %n.patch
-PatchFile-MD5: 714dcd80c41343a1e0c4bc0e90e36718
+PatchFile-MD5: 60b721bf71919a7357f952b017a2ae7f
PatchScript: <<
%{default_script}
find . -name Makefile.am | xargs perl -pi -e 's/(_la_LDFLAGS.*)/\1
-no-undefined/'
<<
-
ConfigureParams: <<
--with-java=${java_home} \
- --with-javaos=${java_home}/include \
+ --with-javaos=${java_includes} \
--enable-dependency-tracking --disable-static \
--includedir=%p/lib/EMBOSS/include --libdir=%p/lib/EMBOSS/lib \
--docdir=%p/share/EMBOSS \
@@ -54,12 +53,19 @@
<<
CompileScript: <<
#!/bin/sh -ev
- %p/bin/autoreconf -fi
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
+ 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 \
@@ -68,6 +74,11 @@
.
<<
+InfoTest: <<
+ TestScript: <<
+ make check || exit 2
+ <<
+<<
Installscript: <<
make install DESTDIR=%d
<<
@@ -81,13 +92,13 @@
Package: %N-libajax6-shlibs
Depends: <<
expat1-shlibs,
- freetype219-shlibs (>= 2.4.11-1),
gd2-shlibs,
+ libharu2.2.1-shlibs,
+ libpcre1-shlibs,
+ libplplot10-shlibs,
libpng15-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
- libpcre1-shlibs,
- libplplot10-shlibs,
postgresql92-shlibs
<<
Files: <<
@@ -126,13 +137,13 @@
Depends: <<
%N-libajax6-shlibs (>= %v-%r),
expat1-shlibs,
- freetype219-shlibs (>= 2.4.11-1),
gd2-shlibs,
+ libharu2.2.1-shlibs,
+ libpcre1-shlibs,
+ libplplot10-shlibs,
libpng15-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
- libpcre1-shlibs,
- libplplot10-shlibs,
postgresql92-shlibs
<<
Files: <<
------------------------------------------------------------------------------
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