diff options
Diffstat (limited to 'sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch')
| -rw-r--r-- | sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch | 411 |
1 files changed, 0 insertions, 411 deletions
diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch deleted file mode 100644 index 266bddd95a37..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch +++ /dev/null @@ -1,411 +0,0 @@ - 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 |