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 | 368 |
1 files changed, 368 insertions, 0 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 new file mode 100644 index 000000000000..c831c3ba7e28 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch @@ -0,0 +1,368 @@ +--- EMBOSS-6.6.0/ajax/acd/Makefile.am ++++ EMBOSS-6.6.0/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 +--- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am ++++ EMBOSS-6.6.0/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) + +--- EMBOSS-6.6.0/ajax/core/ajreg.h ++++ EMBOSS-6.6.0/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 @@ + + typedef struct AjSRegexp + { +- real_pcre *pcre; ++ struct real_pcre *pcre; + pcre_extra *extra; + int *ovector; + const char* orig; +--- EMBOSS-6.6.0/ajax/core/Makefile.am ++++ EMBOSS-6.6.0/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) +--- EMBOSS-6.6.0/ajax/ensembl/Makefile.am ++++ EMBOSS-6.6.0/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 +--- EMBOSS-6.6.0/ajax/graphics/Makefile.am ++++ EMBOSS-6.6.0/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 += $(JAVA_CPPFLAGS) + + libajaxg_la_LDFLAGS = -version-info 6:5:0 +--- EMBOSS-6.6.0/ajax/Makefile.am ++++ EMBOSS-6.6.0/ajax/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + +-SUBDIRS = pcre ++SUBDIRS = + if !ESYSTEMLIBS +-SUBDIRS += expat zlib ++SUBDIRS += pcre expat zlib + endif + SUBDIRS += core graphics ensembl ajaxdb acd +--- EMBOSS-6.6.0/configure.ac ++++ EMBOSS-6.6.0/configure.ac +@@ -629,32 +629,6 @@ + + + +- +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- + dnl Define where the EMBOSS package is located + AC_SUBST([AJAX_FIXED_ROOT]) + AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" +@@ -743,17 +717,7 @@ + + + +-dnl "Export" these variables for PCRE + +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) + + + +@@ -849,7 +813,51 @@ + + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + +- ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PCRE], [libpcre]) ++ PKG_CHECK_MODULES([EXPAT], [expat]) ++ PKG_CHECK_MODULES([ZLIB], [zlib]) ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++], ++[ ++dnl using bundled libraries ++ dnl PCRE library definitions - see the MAJOR and MINOR values ++ dnl to see which version's configure.ac these lines come from ++ ++ dnl Provide the current PCRE version information. Do not use numbers ++ dnl with leading zeros for the minor version, as they end up in a C ++ dnl macro, and may be treated as octal constants. Stick to single ++ dnl digits for minor numbers less than 10. There are unlikely to be ++ dnl that many releases anyway. ++ ++ PCRE_MAJOR="7" ++ PCRE_MINOR="9" ++ PCRE_DATE="11-Apr-2009" ++ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" ++ ++ dnl Default values for miscellaneous macros ++ ++ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" ++ ++ dnl Provide versioning information for libtool shared libraries that ++ dnl are built by default on Unix systems. ++ ++ PCRE_LIB_VERSION="0:1:0" ++ PCRE_POSIXLIB_VERSION="0:0:0" ++ ++ dnl "Export" these variables for PCRE ++ AC_SUBST([HAVE_MEMMOVE]) ++ AC_SUBST([HAVE_STRERROR]) ++ AC_SUBST([PCRE_MAJOR]) ++ AC_SUBST([PCRE_MINOR]) ++ AC_SUBST([PCRE_DATE]) ++ AC_SUBST([PCRE_VERSION]) ++ AC_SUBST([PCRE_LIB_VERSION]) ++ AC_SUBST([PCRE_POSIXLIB_VERSION]) ++ AC_SUBST([POSIX_MALLOC_THRESHOLD]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- EMBOSS-6.6.0/emboss/Makefile.am ++++ EMBOSS-6.6.0/emboss/Makefile.am +@@ -28,15 +28,18 @@ + + AM_CPPFLAGS = -I$(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 +-AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + if !ESYSTEMLIBS ++AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat + AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++AM_CPPFLAGS += -I$(top_srcdir)/plplot ++else ++AM_CFLAGS += $(PLPLOT_CFLAGS) + endif + AM_CPPFLAGS += -I$(top_srcdir)/nucleus +-AM_CPPFLAGS += -I$(top_srcdir)/plplot + AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) + AM_CPPFLAGS += $(JAVA_CPPFLAGS) + +@@ -49,9 +52,11 @@ + 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 += $(XLIB) + + #if PURIFY +--- EMBOSS-6.6.0/jemboss/lib/Makefile.am ++++ EMBOSS-6.6.0/jemboss/lib/Makefile.am +@@ -12,7 +12,7 @@ + jalviewApplet.jar \ + jemboss.jar + +-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java ++jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java + if JAVA_BUILD + $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; + endif +--- EMBOSS-6.6.0/m4/idxdbs.m4 ++++ EMBOSS-6.6.0/m4/idxdbs.m4 +@@ -1,17 +1,8 @@ + AC_DEFUN([CHECK_IDXDBS], + [ +-AC_MSG_CHECKING(for EMBOSS pre-indexed databases) ++AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) + +- +-if test -f ./emboss/index/edam.xac; then +-AC_MSG_RESULT(yes) +-else +-AC_MSG_RESULT(no) +-echo "" +-echo "Pre-indexed edam, taxon + drcat databases not found." +-echo "Please download them from within this directory using:" +-echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." +-echo "and then repeat the configure step." +-exit 1 +-fi ++AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], ++ [], ++ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) + ]) +--- EMBOSS-6.6.0/Makefile.am ++++ EMBOSS-6.6.0/Makefile.am +@@ -12,8 +12,11 @@ + ONEWS \ + PROBLEMS + +-SUBDIRS = \ +-plplot \ ++SUBDIRS = ++if !ESYSTEMLIBS ++SUBDIRS += plplot ++endif ++SUBDIRS += \ + ajax \ + nucleus \ + emboss \ +@@ -33,5 +36,3 @@ + 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 +--- EMBOSS-6.6.0/nucleus/Makefile.am ++++ EMBOSS-6.6.0/nucleus/Makefile.am +@@ -3,6 +3,7 @@ + lib_LTLIBRARIES = libnucleus.la + + libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la + + if ISSHARED + if ISAIXIA64 +@@ -10,11 +11,14 @@ + endif + endif + +-libnucleus_la_CPPFLAGS = -I$(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 |