path: root/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch

 Makefile.am               |  9 +++---
 ajax/Makefile.am          |  4 +--
 ajax/acd/Makefile.am      |  8 +++--
 ajax/ajaxdb/Makefile.am   |  6 ++--
 ajax/core/Makefile.am     |  6 ++--
 ajax/core/ajreg.h         |  7 ++--
 ajax/ensembl/Makefile.am  |  6 ++--
 ajax/graphics/Makefile.am |  8 +++--
 configure.ac              | 82 ++++++++++++++++++++++++++---------------------
 emboss/Makefile.am        | 13 +++++---
 jemboss/lib/Makefile.am   |  2 +-
 m4/idxdbs.m4              | 17 +++-------
 nucleus/Makefile.am       |  8 +++--
 13 files changed, 100 insertions(+), 76 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 177dec5..18dd99a 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -12,8 +12,11 @@ LICENSE \
 ONEWS \
 PROBLEMS
 
-SUBDIRS = \
-plplot \
+SUBDIRS =
+if !ESYSTEMLIBS
+SUBDIRS += plplot
+endif
+SUBDIRS += \
 ajax \
 nucleus \
 emboss \
@@ -33,5 +36,3 @@ dist-hook:
 	tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
 	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 --git a/ajax/Makefile.am b/ajax/Makefile.am
index f27472c..de34e17 100644
--- a/ajax/Makefile.am
+++ b/ajax/Makefile.am
@@ -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 --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
index 9f0f700..3295a1d 100644
--- a/ajax/acd/Makefile.am
+++ b/ajax/acd/Makefile.am
@@ -3,16 +3,20 @@
 lib_LTLIBRARIES = libacd.la
 
 libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
 
 libacd_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ajaxdb
+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
 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/pcre
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
 libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+libacd_la_CFLAGS   += $(PLPLOT_CFLAGS)
+endif
 libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
 libacd_la_LDFLAGS  = -version-info 6:5:0
diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
index c2b0c00..9de14fe 100644
--- a/ajax/ajaxdb/Makefile.am
+++ b/ajax/ajaxdb/Makefile.am
@@ -3,14 +3,16 @@
 lib_LTLIBRARIES = libajaxdb.la
 
 libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
 
 libajaxdb_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ensembl
-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
+endif
 libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
 libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
index 2906837..3189c34 100644
--- a/ajax/core/Makefile.am
+++ b/ajax/core/Makefile.am
@@ -3,13 +3,15 @@
 lib_LTLIBRARIES = libajax.la
 
 libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS)
 
-libajax_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libajax_la_CPPFLAGS  =
 if !ESYSTEMLIBS
+libajax_la_CPPFLAGS += -I$(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)/plplot
+endif
 libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
 libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
index 1623c82..5d928cf 100644
--- a/ajax/core/ajreg.h
+++ b/ajax/core/ajreg.h
@@ -39,9 +39,8 @@
 #include "ajdefine.h"
 #include "ajstr.h"
 
-#include "pcre_config.h"
-#include "pcre_internal.h"
-#include "pcreposix.h"
+#include <pcre.h>
+#include <pcreposix.h>
 
 AJ_BEGIN_DECLS
 
@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS
 
 typedef struct AjSRegexp
 {
-    real_pcre *pcre;
+    struct real_pcre *pcre;
     pcre_extra *extra;
     int *ovector;
     const char* orig;
diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
index 0d1250b..5484c02 100644
--- a/ajax/ensembl/Makefile.am
+++ b/ajax/ensembl/Makefile.am
@@ -3,13 +3,15 @@
 lib_LTLIBRARIES = libensembl.la
 
 libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libensembl_la_LIBADD = ../core/libajax.la
 
-libensembl_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libensembl_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
+endif
 libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
 libensembl_la_LDFLAGS  = -version-info 6:5:0
diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
index a4f202b..1114c2c 100644
--- a/ajax/graphics/Makefile.am
+++ b/ajax/graphics/Makefile.am
@@ -3,12 +3,16 @@
 lib_LTLIBRARIES = libajaxg.la
 
 libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS)
 
-libajaxg_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libajaxg_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
-endif
 libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+libajaxg_la_CFLAGS   += $(PLPLOT_CFLAGS)
+endif
 libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
 libajaxg_la_LDFLAGS  = -version-info 6:5:0
diff --git a/configure.ac b/configure.ac
index a7bd9c6..9ba3121 100644
--- a/configure.ac
+++ b/configure.ac
@@ -629,32 +629,6 @@ AS_CASE([${host_os}],
 
 
 
-
-dnl PCRE library definitions - see the MAJOR and MINOR values
-dnl to see which version's configure.in these lines come from
-
-dnl Provide the current PCRE version information. Do not use numbers
-dnl with leading zeros for the minor version, as they end up in a C
-dnl macro, and may be treated as octal constants. Stick to single
-dnl digits for minor numbers less than 10. There are unlikely to be
-dnl that many releases anyway.
-
-PCRE_MAJOR="7"
-PCRE_MINOR="9"
-PCRE_DATE="11-Apr-2009"
-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
-
-dnl Default values for miscellaneous macros
-
-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
-
-dnl Provide versioning information for libtool shared libraries that
-dnl are built by default on Unix systems.
-
-PCRE_LIB_VERSION="0:1:0"
-PCRE_POSIXLIB_VERSION="0:0:0"
-
-
 dnl Define where the EMBOSS package is located
 AC_SUBST([AJAX_FIXED_ROOT])
 AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL
 
 
 
-dnl "Export" these variables for PCRE
 
-AC_SUBST([HAVE_MEMMOVE])
-AC_SUBST([HAVE_STRERROR])
-AC_SUBST([PCRE_MAJOR])
-AC_SUBST([PCRE_MINOR])
-AC_SUBST([PCRE_DATE])
-AC_SUBST([PCRE_VERSION])
-AC_SUBST([PCRE_LIB_VERSION])
-AC_SUBST([PCRE_POSIXLIB_VERSION])
-AC_SUBST([POSIX_MALLOC_THRESHOLD])
 
 
 
@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs],
 
 AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
 
+AS_IF([test "x${enable_systemlibs}" = "xyes"],
+[
+dnl using system libraries
+  PKG_CHECK_MODULES([PCRE], [libpcre])
+  PKG_CHECK_MODULES([EXPAT], [expat])
+  PKG_CHECK_MODULES([ZLIB], [zlib])
+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
+    [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
+    )
+],
+[
+dnl using bundled libraries
+  dnl PCRE library definitions - see the MAJOR and MINOR values
+  dnl to see which version's configure.ac these lines come from
 
+  dnl Provide the current PCRE version information. Do not use numbers
+  dnl with leading zeros for the minor version, as they end up in a C
+  dnl macro, and may be treated as octal constants. Stick to single
+  dnl digits for minor numbers less than 10. There are unlikely to be
+  dnl that many releases anyway.
+
+  PCRE_MAJOR="7"
+  PCRE_MINOR="9"
+  PCRE_DATE="11-Apr-2009"
+  PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+
+  dnl Default values for miscellaneous macros
+
+  POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+
+  dnl Provide versioning information for libtool shared libraries that
+  dnl are built by default on Unix systems.
+
+  PCRE_LIB_VERSION="0:1:0"
+  PCRE_POSIXLIB_VERSION="0:0:0"
+
+  dnl "Export" these variables for PCRE
+  AC_SUBST([HAVE_MEMMOVE])
+  AC_SUBST([HAVE_STRERROR])
+  AC_SUBST([PCRE_MAJOR])
+  AC_SUBST([PCRE_MINOR])
+  AC_SUBST([PCRE_DATE])
+  AC_SUBST([PCRE_VERSION])
+  AC_SUBST([PCRE_LIB_VERSION])
+  AC_SUBST([PCRE_POSIXLIB_VERSION])
+  AC_SUBST([POSIX_MALLOC_THRESHOLD])
+])
 
 
 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
diff --git a/emboss/Makefile.am b/emboss/Makefile.am
index 89ada78..f987d40 100644
--- a/emboss/Makefile.am
+++ b/emboss/Makefile.am
@@ -28,15 +28,18 @@ endif
 
 AM_CPPFLAGS  = -I$(top_srcdir)/ajax/acd
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
+if !ESYSTEMLIBS
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
-if !ESYSTEMLIBS
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
-AM_CPPFLAGS += -I$(top_srcdir)/nucleus
 AM_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+AM_CFLAGS   += $(PLPLOT_CFLAGS)
+endif
+AM_CPPFLAGS += -I$(top_srcdir)/nucleus
 AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
 AM_CPPFLAGS += $(JAVA_CPPFLAGS)
 
@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la
 if !ESYSTEMLIBS
 LDADD += ../ajax/zlib/libezlib.la
 LDADD += ../ajax/expat/libeexpat.la
-endif
 LDADD += ../ajax/pcre/libepcre.la
 LDADD += ../plplot/libeplplot.la
+else
+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS)
+endif
 LDADD += $(XLIB)
 
 #if PURIFY
diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am
index 5f7e21e..8b45ce2 100644
--- a/jemboss/lib/Makefile.am
+++ b/jemboss/lib/Makefile.am
@@ -12,7 +12,7 @@ mail.jar \
 jalviewApplet.jar \
 jemboss.jar
 
-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java
+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java
 if JAVA_BUILD
 	$(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes;
 endif
diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4
index 0ca7ea9..9b54f2a 100644
--- a/m4/idxdbs.m4
+++ b/m4/idxdbs.m4
@@ -1,17 +1,8 @@
 AC_DEFUN([CHECK_IDXDBS],
 [
-AC_MSG_CHECKING(for EMBOSS pre-indexed databases)
+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases)
 
-
-if test -f ./emboss/index/edam.xac; then
-AC_MSG_RESULT(yes)
-else
-AC_MSG_RESULT(no)
-echo ""
-echo "Pre-indexed edam, taxon + drcat databases not found."
-echo "Please download them from within this directory using:"
-echo "    rsync -av rsync://emboss.open-bio.org/EMBOSS/ ."
-echo "and then repeat the configure step."
-exit 1
-fi
+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac],
+	[],
+	[AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])])
 ])
diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
index 37b8543..5819c89 100644
--- a/nucleus/Makefile.am
+++ b/nucleus/Makefile.am
@@ -3,6 +3,7 @@
 lib_LTLIBRARIES = libnucleus.la
 
 libnucleus_la_CFLAGS  = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libnucleus_la_LIBADD  = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
 
 if ISSHARED
 if ISAIXIA64
@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm
 endif
 endif
 
-libnucleus_la_CPPFLAGS  = -I$(top_srcdir)/plplot
-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+libnucleus_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+else
+libnucleus_la_CFLAGS   += $(PLPLOT_CFLAGS)
 endif
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl