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 +#include 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