Revert quilt changes that should not have been commited (8a2094ea) · Commits · Debian Med / libarb

Makefile

+97 −24

Original line number	Diff line number	Diff line
		@@ -705,7 +705,7 @@ ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
		@echo '$(ARBHOME)/$@:1: has been generated.'
		@echo 'Please edit $@ to configure your system!'
		@echo --------------------------------------------------------------------------------
		# @false
		@false
		else
		@echo '$(ARBHOME)/$<:1: is more recent than'
		@echo '$(ARBHOME)/$@:1:'
		@@ -805,7 +805,7 @@ check_TOOLS:
		"$(LINK_SHARED_LIB)" \


		check_ENVIRONMENT :
		check_ENVIRONMENT : check_PATH check_TOOLS
		@echo "-------------------- Environment [start]"
		@echo "ARBHOME='$(ARBHOME)'"
		@echo "PATH='$(PATH)'"
		@@ -824,7 +824,7 @@ force_tab_check:

		# ---------------------

		check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER
		check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
		@echo Your setup seems to be ok.

		checks: check_setup check_tabs
		@@ -843,16 +843,64 @@ checks: check_setup check_tabs
		# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl

		ARCHS = \
		$(ARCHS_PT_SERVER) \
		AISC/AISC.a \
		AISC_MKPTPS/AISC_MKPTPS.a \
		ARBDB/libARBDB.a \
		CORE/libCORE.a \
		ARB_GDE/ARB_GDE.a \
		AWT/libAWT.a \
		AWTC/AWTC.a \
		AWTI/AWTI.a \
		CONSENSUS_TREE/CONSENSUS_TREE.a \
		CONVERTALN/CONVERTALN.a \
		DBSERVER/DBSERVER.a \
		DIST/DIST.a \
		EDIT4/EDIT4.a \
		EISPACK/EISPACK.a \
		GDE/GDE.a \
		GENOM/GENOM.a \
		GENOM_IMPORT/GENOM_IMPORT.a \
		GL/GL.a \
		ISLAND_HOPPING/ISLAND_HOPPING.a \
		MERGE/MERGE.a \
		MULTI_PROBE/MULTI_PROBE.a \
		NALIGNER/NALIGNER.a \
		NAMES/NAMES.a \
		NAMES_COM/server.a \
		NTREE/NTREE.a \
		PARSIMONY/PARSIMONY.a \
		PERLTOOLS/PERLTOOLS.a \
		PHYLO/PHYLO.a \
		PRIMER_DESIGN/PRIMER_DESIGN.a \
		PROBE_COM/server.a \
		PROBE_DESIGN/PROBE_DESIGN.a \
		PROBE_SET/PROBE_SET.a \
		READSEQ/READSEQ.a \
		RNA3D/RNA3D.a \
		RNACMA/RNACMA.a \
		SECEDIT/SECEDIT.a \
		SEQ_QUALITY/SEQ_QUALITY.a \
		SERVERCNTRL/SERVERCNTRL.a \
		SL/SL.a \
		STAT/STAT.a \
		TOOLS/TOOLS.a \
		TREEGEN/TREEGEN.a \
		UNIT_TESTER/UNIT_TESTER.a \
		WETC/WETC.a \
		WINDOW/libWINDOW.a \
		XML/XML.a \

		# -----------------------
		# library packets

		ARCHS_CLIENT_PROBE = PROBE_COM/client.a PROBE_COM/common.a
		ARCHS_CLIENT_NAMES = NAMES_COM/client.a NAMES_COM/common.a

		ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
		ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)

		ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a

		# communication libs need aisc and aisc_mkpts:

		@@ -1243,8 +1291,9 @@ WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
		# Additional dependencies for subtargets:

		PROBE_COM/PROBE_COM.dummy : comtools
		NAMES_COM/NAMES_COM.dummy : comtools

		com: PROBE_COM/PROBE_COM.dummy
		com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy

		PROBE_COM/server.dummy:
		@echo Unwanted request to make target $<
		@@ -1504,15 +1553,18 @@ genheaders: TEMPLATES/TEMPLATES.dummy
		clrdotdepends:
		-rm PROBE_COM/.depends
		-rm NAMES_COM/.depends
		-rm PERL2ARB/.depends

		comdepends: comtools clrdotdepends
		@echo "$(SEP) Partially build com interface"
		$(MAKE) PROBE_COM/PROBE_COM.depends # NAMES_COM/NAMES_COM.depends
		$(MAKE) PROBE_COM/server.depends # NAMES_COM/server.depends
		$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
		$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends

		depends: genheaders comdepends
		@echo "$(SEP) Updating other dependencies"
		$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
		HELP_SOURCE/HELP_SOURCE.depends \
		SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \

		$(MAKE) libdepends

		@@ -1600,8 +1652,8 @@ tags: $(TAG_SOURCE_LISTS)

		LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links

		links: checks # $(LINKSTAMP) arbmainwrapper
		links_no_checks: # $(LINKSTAMP) arbmainwrapper
		links: checks $(LINKSTAMP) arbmainwrapper
		links_no_checks: $(LINKSTAMP) arbmainwrapper

		forcelinks:
		-rm $(LINKSTAMP)
		@@ -1624,7 +1676,7 @@ redo_links: clean_links
		#********************************************************************************

		header_libs:
		echo "No headerlibs - just create libarb core" # $(MAKE) -C HEADERLIBS all
		$(MAKE) -C HEADERLIBS all

		#********************************************************************************

		@@ -1656,7 +1708,7 @@ endif


		binlink:
		echo "No binaries, build library only" # $(MAKE) -C bin $(BIN_TARGET)
		$(MAKE) -C bin $(BIN_TARGET)

		preplib:
		(cd lib;$(MAKE) all)
		@@ -1676,7 +1728,7 @@ preplib:
		ifeq ($(WITHPERL),1)
		links_non_perl: PERLTOOLS/PERLTOOLS.dummy
		perltools: links_non_perl
		perl:
		perl: realperl
		else
		links_non_perl: links
		perl:
		@@ -1692,14 +1744,27 @@ TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
		endif

		realperl: perltools
		echo "PERL2ARB is not needed for libarb"
		(( \
		echo "$(SEP) Make PERL2ARB" ; \
		$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
		"AUTODEPENDS=1" \
		"dflags=$(dflags)" \
		"cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
		"cross_lflags=$(cross_lflags)" \
		"COMPILER_VERSION=$(COMPILER_VERSION)" \
		all && \
		$(TEST_PERL_SCRIPTS) && \
		echo "$(SEP) Make PERL2ARB [done]" ; \
		) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)

		perl_clean:
		echo "PERL2ARB is not needed for libarb thus nothing to clean"
		@$(MAKE) -C PERL2ARB -r -f Makefile.main \
		"AUTODEPENDS=0" \
		clean

		PERL2ARB/PERL2ARB.clean:
		# $(MAKE) perl_clean
		# $(MAKE) -C PERL_SCRIPTS/test clean
		$(MAKE) perl_clean
		$(MAKE) -C PERL_SCRIPTS/test clean

		# ---------------------------------------- bindings to script languages

		@@ -1745,7 +1810,7 @@ rmbak:
		-exec rm -v {} \;

		bin_reinit:
		#$(MAKE) bin/bin.clean
		$(MAKE) bin/bin.clean
		$(MAKE) -C "bin" all

		clean_directories:
		@@ -1761,14 +1826,19 @@ objclean:

		# bin.clean and HELP_SOURCE.clean interfere
		clean3:
		# $(MAKE) bin/bin.clean
		# $(MAKE) HELP_SOURCE/HELP_SOURCE.clean
		$(MAKE) bin/bin.clean
		$(MAKE) HELP_SOURCE/HELP_SOURCE.clean

		clean2: $(ARCHS:.a=.clean) \
		clean3 \
		rmbak \
		libclean \
		objclean \
		lib/lib.clean \
		GDEHELP/GDEHELP.clean \
		HEADERLIBS/HEADERLIBS.clean \
		SOURCE_TOOLS/SOURCE_TOOLS.clean \
		SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
		UNIT_TESTER/UNIT_TESTER.clean \
		TEMPLATES/TEMPLATES.clean \
		perl_clean \
		@@ -1777,7 +1847,7 @@ clean2: $(ARCHS:.a=.clean) \
		rm -f .last_gcc .last_compiler config.makefile.bak

		# links are needed for cleanup
		clean: redo_links
		clean: redo_links motif_xpm_hack_clean
		$(MAKE) clean2
		$(MAKE) clean_cov_all clean_links

		@@ -1790,6 +1860,8 @@ reloc_clean: links
		$(MAKE) \
		perl_clean \
		GDEHELP/GDEHELP.clean \
		HELP_SOURCE/genhelp/genhelp.clean \
		bin/bin.clean \
		libclean \
		objclean

		@@ -1824,7 +1896,7 @@ perl4ever: clean
		rebuild: clean
		$(MAKE) all

		relink: libclean
		relink: bin/bin.clean libclean
		$(MAKE) build

		tarfile: rebuild
		@@ -1907,10 +1979,10 @@ arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma

		arb_external: convert tools gde readseq tg pst xmlin

		arb_no_perl: arbapplications arb_external
		arb_no_perl: arbapplications help arb_external

		arb:
		$(MAKE) "WITHPERL=1" perl # arb_no_perl
		arb: motif_xpm_hack
		$(MAKE) "WITHPERL=1" perl arb_no_perl

		motif_xpm_hack:
		$(MAKE) -r -C "lib/motifHack" all
		@@ -2049,6 +2121,7 @@ UNITS_TESTED = \
		SL/FAST_ALIGNER/FAST_ALIGNER.test \
		SL/PRONUC/PRONUC.test \
		WINDOW/libWINDOW.test \
		HELP_SOURCE/arb_help2xml.test \
		CONVERTALN/CONVERTALN.test \
		SL/SEQIO/SEQIO.test \
		SL/PTCLEAN/PTCLEAN.test \
		@@ -2239,7 +2312,7 @@ post_commit_check:
		# --------------------------------------------------------------------------------

		build: arb
		$(MAKE) db core
		$(MAKE) binlink preplib compile_compatibility

		all:
		@echo "Build time" > $(TIMELOG)

PROBE_COM/Makefile

+1 −5

Original line number	Diff line number	Diff line
		@@ -20,11 +20,7 @@ AISC_COMPILER=../AISC/aisc
		AISC_PROTOTYPER=../AISC_MKPTPS/aisc_mkpt
		AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER) $(AISC_PROTOTYPER)

		ifeq (,$(wildcard AISC/export2sub))
		include ../AISC_COM/AISC/export2sub
		else
		include AISC/export2sub
		endif

		$(MAIN): server.a

		@@ -37,7 +33,7 @@ depends:

		clean:
		@rm -f .depends
		#@$(MAKE) -r -f AISC/Makefile clean
		@$(MAKE) -r -f AISC/Makefile clean

		# DO NOT DELETE

SOURCE_TOOLS/build_info.pl

+70 −0

Original line number	Diff line number	Diff line
		@@ -275,6 +275,36 @@ my $in_SVN = (-d $ARBHOME.'/.svn');

		# update revision info?
		my ($revision,$is_tag,$branch) = (undef,undef,undef);
		if ($in_SVN) {
		# in SVN checkout -> update revision info
		$revision = getRevision();
		($is_tag,$branch) = getBranchOrTag();

		# $branch = $RC_BRANCH; # @@@ fake
		# $branch = $STABLE_BRANCH; # @@@ fake
		# $branch = 'gtk_only'; # @@@ fake
		# ($is_tag,$branch) = (1, 'arb-5.20.1'); # @@@ fake
		# ($is_tag,$branch) = (1, 'arb-5.19'); # @@@ fake
		# ($is_tag,$branch) = (1, 'evalSomething'); # @@@ fake
		# ($is_tag,$branch) = (1, 'arb-5.20'); # @@@ fake
		# ($is_tag,$branch) = (1, 'arb-5.20-rc1'); # @@@ fake
		# ($is_tag,$branch) = (1, 'arb-5.20-rc2'); # @@@ fake

		my @svn_revision = (
		'#define ARB_SVN_REVISION "'.$revision.'"',
		'#define ARB_SVN_BRANCH "'.$branch.'"',
		'#define ARB_SVN_BRANCH_IS_TAG '.$is_tag,
		);

		update($svn_revision_h,@svn_revision);
		}
		else {
		if (not -f $svn_revision_h) {
		die "Missing file '$svn_revision_h'";
		}
		# use revision info as in source tarball
		($revision,$is_tag,$branch) = getBranchOrTagFromHeader($svn_revision_h);
		}

		my $date = `date '+%d.%b.%Y'`;
		chomp($date);
		@@ -365,6 +395,46 @@ my $short_version = undef;
		my $always_show_revision = 1;

		my $orgbranch = $branch; # real branch or branch estimated from tag
		if ($is_tag==1) {
		if ($branch =~ /^arb-[0-9]+\.[0-9]+/o) {
		if ($branch =~ /-rc[0-9]+$/o) { $orgbranch = $RC_BRANCH; }
		else { $orgbranch = $STABLE_BRANCH; }
		}
		else {
		$orgbranch = 'unknown';
		}
		}

		if ($orgbranch eq $STABLE_BRANCH or $orgbranch eq $RC_BRANCH) {
		$always_show_revision = 0;
		$svn_tag = 'arb-'.$version_info{MAJOR}.'.'.$version_info{MINOR};
		if ($orgbranch eq $RC_BRANCH) {
		$svn_tag .= '-rc'.$version_info{CANDIDATE};
		}
		else {
		if ($version_info{PATCHLEVEL} > 0) { $svn_tag .= '.'.$version_info{PATCHLEVEL}; }
		}
		$short_version = $svn_tag;

		if ($is_tag==1) {
		# check real SVN-tag vs generated SVN-tag
		if ($branch ne $svn_tag) {
		die "Version info and SVN-branch-tag mismatch:\n".
		"(version suggests svn-tag = '$svn_tag'\n".
		" real svn-tag = '$branch')";
		}
		}
		print "SVN_URL='$ENV{SVN_URL}'\n";
		print "SVN_REVISION='$ENV{SVN_REVISION}'\n";
		}
		elsif ($is_tag==1) {
		$short_version = 'arb-special-'.$branch; # use custom tag
		}
		else {
		$short_version = 'arb-devel';
		if ($branch ne 'trunk') { $short_version .= '-'.$branch; }
		$short_version .= '-'.$version_info{MAJOR}.'.'.$version_info{MINOR};
		}

		defined $short_version \|\| die "expected known short_version!";
		defined $revision \|\| die "expected known revision!";

SOURCE_TOOLS/generate_all_links.sh

+55 −4

Original line number	Diff line number	Diff line
		#!/bin/bash

		SELF=$ARBHOME/SOURCE_TOOLS/generate_all_links.sh
		READLINK=readlink
		READLINK=${ARBHOME}/SH/arb_readlink


		finderr() {
		@@ -126,9 +126,7 @@ makedir lib/help &&
		(test -z $MOTIF_LIBPATH \|\| symlink_file $MOTIF_LIBPATH lib/libXm.so.3) &&

		# Links in bin directory
		if [ -d bin ] ; then
		( cd bin ; make all; cd .. ) &&
		fi

		# ...COMS

		@@ -148,11 +146,64 @@ symlink_maybe_no_target GENH/aisc.h PROBE_COM/PT_server.h &&

		# TEMPLATES directory

		symlink_file ../TEMPLATES/arb_algo.h INCLUDE/arb_algo.h &&
		symlink_file ../TEMPLATES/arb_backtrace.h INCLUDE/arb_backtrace.h &&
		symlink_file ../TEMPLATES/arb_debug.h INCLUDE/arb_debug.h &&
		symlink_file ../TEMPLATES/arb_defs.h INCLUDE/arb_defs.h &&
		symlink_file ../TEMPLATES/arb_early_check.h INCLUDE/arb_early_check.h &&
		symlink_file ../TEMPLATES/arb_error.h INCLUDE/arb_error.h &&
		symlink_file ../TEMPLATES/arb_forward_list.h INCLUDE/arb_forward_list.h &&
		symlink_file ../TEMPLATES/arb_global_defs.h INCLUDE/arb_global_defs.h &&
		symlink_file ../TEMPLATES/arb_simple_assert.h INCLUDE/arb_simple_assert.h &&
		symlink_file ../TEMPLATES/arb_sleep.h INCLUDE/arb_sleep.h &&
		symlink_file ../TEMPLATES/arb_stdstr.h INCLUDE/arb_stdstr.h &&
		symlink_file ../TEMPLATES/arb_str.h INCLUDE/arb_str.h &&
		symlink_file ../TEMPLATES/arb_unit_test.h INCLUDE/arb_unit_test.h &&
		symlink_file ../TEMPLATES/arb_unordered_map.h INCLUDE/arb_unordered_map.h &&
		symlink_file ../TEMPLATES/arb_version.h INCLUDE/arb_version.h &&
		symlink_file ../TEMPLATES/arbtools.h INCLUDE/arbtools.h &&
		symlink_file ../TEMPLATES/attributes.h INCLUDE/attributes.h &&
		symlink_file ../TEMPLATES/bytestring.h INCLUDE/bytestring.h &&
		symlink_file ../TEMPLATES/cache.h INCLUDE/cache.h &&
		symlink_file ../TEMPLATES/ChecksumCollector.h INCLUDE/ChecksumCollector.h &&
		symlink_file ../TEMPLATES/command_output.h INCLUDE/command_output.h &&
		symlink_file ../TEMPLATES/config_parser.h INCLUDE/config_parser.h &&
		symlink_file ../TEMPLATES/cxxforward.h INCLUDE/cxxforward.h &&
		symlink_file ../TEMPLATES/downcast.h INCLUDE/downcast.h &&
		symlink_file ../TEMPLATES/dupstr.h INCLUDE/dupstr.h &&
		symlink_file ../TEMPLATES/gccver.h INCLUDE/gccver.h &&
		symlink_file ../TEMPLATES/malloc.h INCLUDE/malloc.h &&
		symlink_file ../TEMPLATES/mode_text.h INCLUDE/mode_text.h &&
		symlink_file ../TEMPLATES/output.h INCLUDE/output.h &&
		symlink_file ../TEMPLATES/perf_timer.h INCLUDE/perf_timer.h &&
		symlink_file ../TEMPLATES/SigHandler.h INCLUDE/SigHandler.h &&
		symlink_file ../TEMPLATES/smartptr.h INCLUDE/smartptr.h &&
		symlink_file ../TEMPLATES/static_assert.h INCLUDE/static_assert.h &&
		symlink_file ../TEMPLATES/SuppressOutput.h INCLUDE/SuppressOutput.h &&
		symlink_file ../TEMPLATES/ttypes.h INCLUDE/ttypes.h &&
		symlink_file ../TEMPLATES/ut_valgrinded.h INCLUDE/ut_valgrinded.h &&
		symlink_file ../TEMPLATES/valgrind.h INCLUDE/valgrind.h &&

		symlink_maybe_no_target ../TEMPLATES/arb_build.h INCLUDE/arb_build.h &&
		symlink_maybe_no_target ../TEMPLATES/svn_revision.h INCLUDE/svn_revision.h &&

		# INCLUDE directory

		symlink_maybe_no_target ../NAMES_COM/names_client.h INCLUDE/names_client.h &&
		symlink_maybe_no_target ../NAMES_COM/names_prototypes.h INCLUDE/names_prototypes.h &&
		symlink_maybe_no_target ../NAMES_COM/names_server.h INCLUDE/names_server.h &&

		symlink_maybe_no_target ../PROBE_COM/PT_com.h INCLUDE/PT_com.h &&
		symlink_maybe_no_target ../PROBE_COM/PT_server.h INCLUDE/PT_server.h &&
		symlink_maybe_no_target ../PROBE_COM/PT_server_prototypes.h INCLUDE/PT_server_prototypes.h &&

		symlink_file ../AISC_COM/C/aisc_func_types.h INCLUDE/aisc_func_types.h &&
		symlink_file ../AISC_COM/C/aisc_global.h INCLUDE/aisc_global.h &&
		symlink_file ../AISC_COM/C/client.h INCLUDE/client.h &&
		symlink_file ../AISC_COM/C/client_types.h INCLUDE/client_types.h &&
		symlink_file ../AISC_COM/C/client_privat.h INCLUDE/client_privat.h &&
		symlink_file ../AISC_COM/C/server.h INCLUDE/server.h &&
		symlink_file ../AISC_COM/C/struct_man.h INCLUDE/struct_man.h &&
		symlink_file ../ARBDB/ad_cb.h INCLUDE/ad_cb.h &&
		symlink_file ../ARBDB/ad_cb_prot.h INCLUDE/ad_cb_prot.h &&
		symlink_file ../ARBDB/ad_config.h INCLUDE/ad_config.h &&