[med-svn] [Git][med-team/libarb][master] Revert quilt changes that should not have been commited
Andreas Tille
gitlab at salsa.debian.org
Fri Jun 7 07:21:36 BST 2019
Andreas Tille pushed to branch master at Debian Med / libarb
Commits:
8a2094ea by Andreas Tille at 2019-06-07T06:20:37Z
Revert quilt changes that should not have been commited
- - - - -
4 changed files:
- Makefile
- PROBE_COM/Makefile
- SOURCE_TOOLS/build_info.pl
- SOURCE_TOOLS/generate_all_links.sh
Changes:
=====================================
Makefile
=====================================
@@ -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 . at 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
=====================================
@@ -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
=====================================
@@ -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, at 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 $revision || die "expected known revision!";
=====================================
SOURCE_TOOLS/generate_all_links.sh
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
SELF=$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
+( cd bin ; make all; cd .. ) &&
# ...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 &&
View it on GitLab: https://salsa.debian.org/med-team/libarb/commit/8a2094ea1d412cdda44297478128b66c9a39146b
--
View it on GitLab: https://salsa.debian.org/med-team/libarb/commit/8a2094ea1d412cdda44297478128b66c9a39146b
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