diff -ruN a/configure.ac b/configure.ac --- a/configure.ac 2014-05-02 13:01:56.140478650 +1000 +++ b/configure.ac 2014-10-07 14:42:29.947326449 +1000 @@ -9,11 +9,26 @@ AC_CONFIG_HEADERS([config.h]) AC_CONFIG_SRCDIR(src/alphtype.c) AC_CONFIG_AUX_DIR(config) -AM_INIT_AUTOMAKE([1.9 tar-pax]) +AM_INIT_AUTOMAKE( + m4_esyscmd( + [ + echo 1.9 + echo tar-pax + case `automake --version | head -n 1` in + *1.9*);; + *1.10*);; + *1.11*);; + *) echo subdir-objects;; + esac + ] + ) +) +m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES]) AC_PREFIX_DEFAULT(${HOME}) # Checks for programs. -AM_PROG_CC_C_O +AC_PROG_CC +AC_PROG_CC_C_O AC_PROG_LIBTOOL AC_PROG_INSTALL AC_PROG_MAKE_SET @@ -28,7 +43,7 @@ AC_PATH_PROG(XSLT_CONFIG, xslt-config) AC_PATH_PROG(ANT, ant) -AC_DEFINE_UNQUOTED(HOSTNAME, "`hostname`", [Build host name]) +AC_DEFINE_UNQUOTED(HOSTNAME, "`hostname | head -n 1`", [Build host name]) # Checks for libraries. AC_CHECK_LIB([m], @@ -61,6 +76,26 @@ AC_CHECK_FUNCS([strlcpy], [have_strlcpy=yes], [have_strlcpy=no]) AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no]) +# Check for compiler-specific settings +LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` +if test "${GCC}" = "yes"; then + ac_cc_opt="-O3" + ac_cc_debug_opt="-O0" + ac_cc_warn="-Wall -Wno-unused" + ac_cc_debug="-ggdb" + # Check for OS X llvm (clang) compiler + if `gcc --version |grep llvm >/dev/null`; then + ac_cc_debug="-g" + fi + CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" +else + ac_cc_opt="-O" + ac_cc_debug_opt="" + ac_cc_warn="" + ac_cc_debug="-g" + CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" +fi + # Set up default libxml2 settings # check for installed copy of libxml2 build_libxml2="yes" @@ -157,24 +192,32 @@ # Check for configuration switches #################################### +# Enable optimization by default +OPT_FLAGS="$ac_cc_opt" + # debugging +# if specified then change optimisation to a level approprate to debugging (may be overriden by --enable-opt) AC_ARG_ENABLE( debug, [ --enable-debug Produce an executable with debugging symbols. Default is disabled.], [if test "$enableval" = "yes"; then DEBUG_FLAGS="$ac_cc_debug"; - ac_cc_opt="-O0"; + OPT_FLAGS="$ac_cc_debug_opt"; fi], [DEBUG_FLAGS=""]) # optimization +# if specified we want to override the debugging optimisation flags +# if set to "no" then we don't specifify and let the compiler do its default AC_ARG_ENABLE( opt, - [ --enable-opt Produce an executable with optimization. Default compiler dependent.], + [ --enable-opt Produce an executable with optimization. Default enabled. Must specify no to disable.], [if test "$enableval" = "yes"; then OPT_FLAGS="$ac_cc_opt"; + elif test "$enableval" = "no"; then + OPT_FLAGS=""; fi], - [OPT_FLAGS="$ac_cc_opt"]) + []) # get mpi info, and check if parallel version can be compiled AC_ARG_WITH( @@ -213,24 +256,6 @@ parallel="no"; fi -# Check for compiler-specific settings -LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` -if test "${CC}" = "gcc"; then - ac_cc_opt="-O3" - ac_cc_warn="-Wall -Wno-unused" - ac_cc_debug="-ggdb" - # Check for OS X llvm (clang) compiler - if `gcc --version |grep llvm >/dev/null`; then - ac_cc_debug="-g" - fi - CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" -else - ac_cc_opt="-O" - ac_cc_warn="" - ac_cc_debug="-g" - CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" -fi - # For potentially parallel programs, the correct version (serial or parallel) # is built in the /parallel directory. That is why MPICC is set to CC below. if test "$parallel" = "yes"; then @@ -278,11 +303,11 @@ OPAL_URL="http://nbcr-222.ucsd.edu/opal2/services" AC_MSG_WARN(Opal URL not specified with --enable-web option! Defaulting to http://nbcr-222.ucsd.edu/opal2/services) else - OPAL_URL=$enableval + OPAL_URL="$enableval" fi - ],OPAL_URL=no) -AM_CONDITIONAL(WEBSITE, test ["$OPAL_URL" != no]) -AM_CONDITIONAL(WEBEITHER, test ["" != "$OPAL_DEPLOY" || "$OPAL_URL" != no]) + ],OPAL_URL="no") +AM_CONDITIONAL(WEBSITE, test ["x$OPAL_URL" != "xno"]) +AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"]) # enable building of included libxml2 AC_ARG_ENABLE( @@ -523,17 +548,17 @@ tests/web/Makefile]) AC_OUTPUT -# Raise warning if convert utility can't be found. -if test -z "$CONVERT" -o ! -e "$CONVERT" +# Raise warning if a EPS to PNG conversion utility can't be found. +if test "(" -z "$GHOSTSCRIPT" -o ! -e "$GHOSTSCRIPT" ")" -a "(" -z "$CONVERT" -o ! -e "$CONVERT" ")" then AC_MSG_WARN( \ - [The 'convert' utility can''t be found.] \ + [Neither Ghostscript or convert utilities were found. Png images won''t be generated from encapsulated postscript.] \ ) fi # Check for required Perl Modules MISSING_PERL_MODULES="`$PERL $srcdir/scripts/dependencies.pl`" -if test "`echo "$MISSING_PERL_MODULES" | wc -l`" -ne 2 +if test "`echo "$MISSING_PERL_MODULES" | wc -l`" -ne 4 then AC_MSG_WARN( \ [$MISSING_PERL_MODULES] \ diff -ruN a/aclocal.m4 b/aclocal.m4 --- a/aclocal.m4 2014-05-21 10:36:40.540537855 +1000 +++ b/aclocal.m4 2014-10-07 17:37:04.183255386 +1000 @@ -9242,38 +9242,6 @@ rm -f confinc confmf ]) -# Copyright (C) 1999-2013 Free Software Foundation, Inc. -# -# This file is free software; the Free Software Foundation -# gives unlimited permission to copy and/or distribute it, -# with or without modifications, as long as this notice is preserved. - -# AM_PROG_CC_C_O -# -------------- -# Like AC_PROG_CC_C_O, but changed for automake. -AC_DEFUN([AM_PROG_CC_C_O], -[AC_REQUIRE([AC_PROG_CC_C_O])dnl -AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl -AC_REQUIRE_AUX_FILE([compile])dnl -# FIXME: we rely on the cache variable name because -# there is no other way. -set dummy $CC -am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']` -eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o -if test "$am_t" != yes; then - # Losing compiler, so override with the script. - # FIXME: It is wrong to rewrite CC. - # But if we don't then we get into trouble of one sort or another. - # A longer-term fix would be to have automake use am__CC in this case, - # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)" - CC="$am_aux_dir/compile $CC" -fi -dnl Make sure AC_PROG_CC is never called again, or it will override our -dnl setting of CC. -m4_define([AC_PROG_CC], - [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])]) -]) - # Fake the existence of programs that GNU maintainers use. -*- Autoconf -*- # Copyright (C) 1997-2013 Free Software Foundation, Inc. diff -ruN a/configure b/configure --- a/configure 2014-05-21 10:36:44.968537908 +1000 +++ b/configure 2014-10-07 17:37:08.107255360 +1000 @@ -1487,7 +1487,7 @@ optimize for fast installation [default=yes] --disable-libtool-lock avoid locking (might break parallel builds) --enable-debug Produce an executable with debugging symbols. Default is disabled. - --enable-opt Produce an executable with optimization. Default compiler dependent. + --enable-opt Produce an executable with optimization. Default enabled. Must specify no to disable. --enable-serial Produce only serial executables. Default parallel and serial. --enable-webservice=deploy_dir Deploy the MEME service on an existing Opal 2.5+ installation --enable-web=opal_url Build website applications. Default is disabled. Specify the Opal URL for the service to communicate with. @@ -3018,72 +3018,48 @@ +# Check whether --enable-silent-rules was given. +if test "${enable_silent_rules+set}" = set; then : + enableval=$enable_silent_rules; +fi - -# Checks for programs. -DEPDIR="${am__leading_dot}deps" - -ac_config_commands="$ac_config_commands depfiles" - - +case $enable_silent_rules in # ((( + yes) AM_DEFAULT_VERBOSITY=0;; + no) AM_DEFAULT_VERBOSITY=1;; + *) AM_DEFAULT_VERBOSITY=1;; +esac am_make=${MAKE-make} -cat > confinc << 'END' +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5 +$as_echo_n "checking whether $am_make supports nested variables... " >&6; } +if ${am_cv_make_support_nested_variables+:} false; then : + $as_echo_n "(cached) " >&6 +else + if $as_echo 'TRUE=$(BAR$(V)) +BAR0=false +BAR1=true +V=1 am__doit: - @echo this is the am__doit target -.PHONY: am__doit -END -# If we don't find an include directive, just comment out the code. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5 -$as_echo_n "checking for style of include used by $am_make... " >&6; } -am__include="#" -am__quote= -_am_result=none -# First try GNU make style include. -echo "include confinc" > confmf -# Ignore all kinds of additional output from 'make'. -case `$am_make -s -f confmf 2> /dev/null` in #( -*the\ am__doit\ target*) - am__include=include - am__quote= - _am_result=GNU - ;; -esac -# Now try BSD make style include. -if test "$am__include" = "#"; then - echo '.include "confinc"' > confmf - case `$am_make -s -f confmf 2> /dev/null` in #( - *the\ am__doit\ target*) - am__include=.include - am__quote="\"" - _am_result=BSD - ;; - esac -fi - - -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5 -$as_echo "$_am_result" >&6; } -rm -f confinc confmf - -# Check whether --enable-dependency-tracking was given. -if test "${enable_dependency_tracking+set}" = set; then : - enableval=$enable_dependency_tracking; + @$(TRUE) +.PHONY: am__doit' | $am_make -f - >/dev/null 2>&1; then + am_cv_make_support_nested_variables=yes +else + am_cv_make_support_nested_variables=no fi - -if test "x$enable_dependency_tracking" != xno; then - am_depcomp="$ac_aux_dir/depcomp" - AMDEPBACKSLASH='\' - am__nodep='_no' fi - if test "x$enable_dependency_tracking" != xno; then - AMDEP_TRUE= - AMDEP_FALSE='#' +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_make_support_nested_variables" >&5 +$as_echo "$am_cv_make_support_nested_variables" >&6; } +if test $am_cv_make_support_nested_variables = yes; then + AM_V='$(V)' + AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' else - AMDEP_TRUE='#' - AMDEP_FALSE= + AM_V=$AM_DEFAULT_VERBOSITY + AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY fi +AM_BACKSLASH='\' + +# Checks for programs. ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' @@ -3872,6 +3848,69 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu +DEPDIR="${am__leading_dot}deps" + +ac_config_commands="$ac_config_commands depfiles" + + +am_make=${MAKE-make} +cat > confinc << 'END' +am__doit: + @echo this is the am__doit target +.PHONY: am__doit +END +# If we don't find an include directive, just comment out the code. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5 +$as_echo_n "checking for style of include used by $am_make... " >&6; } +am__include="#" +am__quote= +_am_result=none +# First try GNU make style include. +echo "include confinc" > confmf +# Ignore all kinds of additional output from 'make'. +case `$am_make -s -f confmf 2> /dev/null` in #( +*the\ am__doit\ target*) + am__include=include + am__quote= + _am_result=GNU + ;; +esac +# Now try BSD make style include. +if test "$am__include" = "#"; then + echo '.include "confinc"' > confmf + case `$am_make -s -f confmf 2> /dev/null` in #( + *the\ am__doit\ target*) + am__include=.include + am__quote="\"" + _am_result=BSD + ;; + esac +fi + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5 +$as_echo "$_am_result" >&6; } +rm -f confinc confmf + +# Check whether --enable-dependency-tracking was given. +if test "${enable_dependency_tracking+set}" = set; then : + enableval=$enable_dependency_tracking; +fi + +if test "x$enable_dependency_tracking" != xno; then + am_depcomp="$ac_aux_dir/depcomp" + AMDEPBACKSLASH='\' + am__nodep='_no' +fi + if test "x$enable_dependency_tracking" != xno; then + AMDEP_TRUE= + AMDEP_FALSE='#' +else + AMDEP_TRUE='#' + AMDEP_FALSE= +fi + + depcc="$CC" am_compiler_list= @@ -4112,21 +4151,6 @@ fi -# FIXME: we rely on the cache variable name because -# there is no other way. -set dummy $CC -am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'` -eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o -if test "$am_t" != yes; then - # Losing compiler, so override with the script. - # FIXME: It is wrong to rewrite CC. - # But if we don't then we get into trouble of one sort or another. - # A longer-term fix would be to have automake use am__CC in this case, - # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)" - CC="$am_aux_dir/compile $CC" -fi - - case `pwd` in *\ * | *\ *) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5 @@ -12151,7 +12175,7 @@ cat >>confdefs.h <<_ACEOF -#define HOSTNAME "`hostname`" +#define HOSTNAME "`hostname | head -n 1`" _ACEOF @@ -13142,6 +13166,26 @@ fi +# Check for compiler-specific settings +LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` +if test "${GCC}" = "yes"; then + ac_cc_opt="-O3" + ac_cc_debug_opt="-O0" + ac_cc_warn="-Wall -Wno-unused" + ac_cc_debug="-ggdb" + # Check for OS X llvm (clang) compiler + if `gcc --version |grep llvm >/dev/null`; then + ac_cc_debug="-g" + fi + CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" +else + ac_cc_opt="-O" + ac_cc_debug_opt="" + ac_cc_warn="" + ac_cc_debug="-g" + CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" +fi + # Set up default libxml2 settings # check for installed copy of libxml2 build_libxml2="yes" @@ -13346,12 +13390,16 @@ # Check for configuration switches #################################### +# Enable optimization by default +OPT_FLAGS="$ac_cc_opt" + # debugging +# if specified then change optimisation to a level approprate to debugging (may be overriden by --enable-opt) # Check whether --enable-debug was given. if test "${enable_debug+set}" = set; then : enableval=$enable_debug; if test "$enableval" = "yes"; then DEBUG_FLAGS="$ac_cc_debug"; - ac_cc_opt="-O0"; + OPT_FLAGS="$ac_cc_debug_opt"; fi else DEBUG_FLAGS="" @@ -13359,13 +13407,15 @@ # optimization +# if specified we want to override the debugging optimisation flags +# if set to "no" then we don't specifify and let the compiler do its default # Check whether --enable-opt was given. if test "${enable_opt+set}" = set; then : enableval=$enable_opt; if test "$enableval" = "yes"; then OPT_FLAGS="$ac_cc_opt"; + elif test "$enableval" = "no"; then + OPT_FLAGS=""; fi -else - OPT_FLAGS="$ac_cc_opt" fi @@ -13676,24 +13726,6 @@ parallel="no"; fi -# Check for compiler-specific settings -LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` -if test "${CC}" = "gcc"; then - ac_cc_opt="-O3" - ac_cc_warn="-Wall -Wno-unused" - ac_cc_debug="-ggdb" - # Check for OS X llvm (clang) compiler - if `gcc --version |grep llvm >/dev/null`; then - ac_cc_debug="-g" - fi - CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" -else - ac_cc_opt="-O" - ac_cc_warn="" - ac_cc_debug="-g" - CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" -fi - # For potentially parallel programs, the correct version (serial or parallel) # is built in the /parallel directory. That is why MPICC is set to CC below. if test "$parallel" = "yes"; then @@ -13765,14 +13797,14 @@ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Opal URL not specified with --enable-web option! Defaulting to http://nbcr-222.ucsd.edu/opal2/services" >&5 $as_echo "$as_me: WARNING: Opal URL not specified with --enable-web option! Defaulting to http://nbcr-222.ucsd.edu/opal2/services" >&2;} else - OPAL_URL=$enableval + OPAL_URL="$enableval" fi else - OPAL_URL=no + OPAL_URL="no" fi - if test "$OPAL_URL" != no; then + if test "x$OPAL_URL" != "xno"; then WEBSITE_TRUE= WEBSITE_FALSE='#' else @@ -13780,7 +13812,7 @@ WEBSITE_FALSE= fi - if test "" != "$OPAL_DEPLOY" || "$OPAL_URL" != no; then + if test "x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"; then WEBEITHER_TRUE= WEBEITHER_FALSE='#' else @@ -16672,20 +16704,20 @@ fi -# Raise warning if convert utility can't be found. -if test -z "$CONVERT" -o ! -e "$CONVERT" +# Raise warning if a EPS to PNG conversion utility can't be found. +if test "(" -z "$GHOSTSCRIPT" -o ! -e "$GHOSTSCRIPT" ")" -a "(" -z "$CONVERT" -o ! -e "$CONVERT" ")" then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \ - The 'convert' utility can''t be found. \ + Neither Ghostscript or convert utilities were found. Png images won''t be generated from encapsulated postscript. \ " >&5 $as_echo "$as_me: WARNING: \ - The 'convert' utility can''t be found. \ + Neither Ghostscript or convert utilities were found. Png images won''t be generated from encapsulated postscript. \ " >&2;} fi # Check for required Perl Modules MISSING_PERL_MODULES="`$PERL $srcdir/scripts/dependencies.pl`" -if test "`echo "$MISSING_PERL_MODULES" | wc -l`" -ne 2 +if test "`echo "$MISSING_PERL_MODULES" | wc -l`" -ne 4 then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \ $MISSING_PERL_MODULES \ diff -ruN a/doc/examples/ame_example_output_files/ame.html b/doc/examples/ame_example_output_files/ame.html --- a/doc/examples/ame_example_output_files/ame.html 2014-05-13 08:24:28.000000000 +1000 +++ b/doc/examples/ame_example_output_files/ame.html 2014-10-07 16:13:42.000000000 +1000 @@ -7,8 +7,8 @@ //@JSON_VAR data var data = { "version": "4.10.0", - "revision": "4f3599b86c7ee1597e34ec256e25771bc545b1dd", - "release": "Tue May 06 16:46:04 2014 +1000", + "revision": "994f5bf522b6536cb8e2324fa497ed91a1404a20", + "release": "Wed May 21 10:35:36 2014 +1000", "cmd": [ "ame", "-oc", "ame_example_output_files", "-control", "lex0.s", "-bgformat", "0", "-scoring", "avg", "-method", "ranksum", "crp0.s", @@ -93,7 +93,7 @@ };
-