UNIT_TESTER/export2sub

+# -*-Mode: Makefile;-*-
+#
+# --------------------------------------------------------------------------------
+# variables listed here are automatically exported to sub-makefiles
+# documentation for single variables can be found in ../SOURCE_TOOLS/parent_make.txt
+
+export RESTRICT_MODULE
+export RESTRICT_FUN
+export RESTRICT_COVERAGE
+export SORT_COVERAGE
+

debian/copyright

@@ -89,7 +89,6 @@ Files-Excluded: arbsrc*/AISC_COM/C
                 arbsrc*/UNIT_TESTER/valgrind
                 arbsrc*/UNIT_TESTER/TestEnvironment.cxx
                 arbsrc*/UNIT_TESTER/UnitTester*
-                arbsrc*/UNIT_TESTER/export2sub
                 arbsrc*/UNIT_TESTER/gcov2msg.*
                 arbsrc*/UNIT_TESTER/make_symlist.sh
                 arbsrc*/UNIT_TESTER/reporter.pl

debian/patches/fix_main_makefile.patch

@@ -103,7 +103,11 @@
  
  PROBE_COM/server.dummy:
  	@echo Unwanted request to make target $<
-@@ -1557,14 +1508,12 @@ clrdotdepends:
+@@ -1553,18 +1504,15 @@ 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"
@@ -120,7 +124,7 @@
  
  	$(MAKE) libdepends
  
-@@ -1652,8 +1601,8 @@ tags: $(TAG_SOURCE_LISTS)
+@@ -1652,8 +1600,8 @@ tags: $(TAG_SOURCE_LISTS)
  
  LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
  
@@ -131,7 +135,48 @@
  
  forcelinks:
  	-rm $(LINKSTAMP)
-@@ -1810,7 +1759,7 @@ rmbak:
+@@ -1728,7 +1676,7 @@ preplib:
+ ifeq ($(WITHPERL),1)
+ links_non_perl:	PERLTOOLS/PERLTOOLS.dummy
+ perltools:	links_non_perl
+-perl:		realperl
++perl:		
+ else
+ links_non_perl:	links
+ perl:
+@@ -1744,27 +1692,14 @@ TEST_PERL_SCRIPTS=echo "skipping perl sc
+ endif
+ 
+ realperl: perltools
+-	(( \
+-		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)
++	echo "PERL2ARB is not needed for libarb"
+ 
+ perl_clean:
+-	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
+-		"AUTODEPENDS=0" \
+-		clean
++	echo "PERL2ARB is not needed for libarb thus nothing to 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
+ 
+@@ -1810,7 +1745,7 @@ rmbak:
  	        -exec rm -v {} \;
  
  bin_reinit:
@@ -140,7 +185,7 @@
  	$(MAKE) -C "bin" all
  
  clean_directories:
-@@ -1826,19 +1775,14 @@ objclean:
+@@ -1826,19 +1761,14 @@ objclean:
  
  # bin.clean and HELP_SOURCE.clean interfere
  clean3:
@@ -162,7 +207,7 @@
  		UNIT_TESTER/UNIT_TESTER.clean \
  		TEMPLATES/TEMPLATES.clean \
  		perl_clean \
-@@ -1847,7 +1791,7 @@ clean2: $(ARCHS:.a=.clean) \
+@@ -1847,7 +1777,7 @@ clean2: $(ARCHS:.a=.clean) \
  	rm -f *.last_gcc *.last_compiler config.makefile.bak
  
  # links are needed for cleanup
@@ -171,7 +216,7 @@
  	$(MAKE) clean2
  	$(MAKE) clean_cov_all clean_links
  
-@@ -1860,8 +1804,6 @@ reloc_clean: links
+@@ -1860,8 +1790,6 @@ reloc_clean: links
  	$(MAKE) \
  		perl_clean \
  		GDEHELP/GDEHELP.clean \
@@ -180,7 +225,7 @@
  		libclean \
  		objclean
  
-@@ -1896,7 +1838,7 @@ perl4ever: clean
+@@ -1896,7 +1824,7 @@ perl4ever: clean
  rebuild: clean
  	$(MAKE) all
  
@@ -189,7 +234,7 @@
  	$(MAKE) build
  
  tarfile: rebuild
-@@ -1979,9 +1921,9 @@ arbapplications: nt pa e4 wetc pt na nal
+@@ -1979,9 +1907,9 @@ arbapplications: nt pa e4 wetc pt na nal
  
  arb_external: convert tools gde readseq tg pst xmlin
  
@@ -201,7 +246,7 @@
  	$(MAKE) "WITHPERL=1" perl arb_no_perl
  
  motif_xpm_hack:
-@@ -2121,7 +2063,6 @@ UNITS_TESTED = \
+@@ -2121,7 +2049,6 @@ UNITS_TESTED = \
  	SL/FAST_ALIGNER/FAST_ALIGNER.test \
  	SL/PRONUC/PRONUC.test \
  	WINDOW/libWINDOW.test \
@@ -209,12 +254,12 @@
  	CONVERTALN/CONVERTALN.test \
  	SL/SEQIO/SEQIO.test \
  	SL/PTCLEAN/PTCLEAN.test \
-@@ -2312,7 +2253,7 @@ post_commit_check:
+@@ -2312,7 +2239,7 @@ post_commit_check:
  # --------------------------------------------------------------------------------
  
  build: arb
 -	$(MAKE) binlink preplib compile_compatibility
-+	$(MAKE) preplib compile_compatibility
++	$(MAKE) core
  
  all:
  	@echo "Build time" > $(TIMELOG)

debian/patches/ignore_unneeded_stuff.patch

 --- a/SOURCE_TOOLS/generate_all_links.sh
 +++ b/SOURCE_TOOLS/generate_all_links.sh
-@@ -146,64 +146,11 @@ symlink_maybe_no_target GENH/aisc.h
+@@ -126,7 +126,9 @@ makedir lib/help &&
+ (test -z $MOTIF_LIBPATH || symlink_file $MOTIF_LIBPATH lib/libXm.so.3) &&
+ 
+ # Links in bin directory
+-( cd bin ; make all; cd .. ) &&
++if [ -d bin ] ; then
++  ( cd bin ; make all; cd .. ) &&
++fi
+ 
+ # ...COMS
+ 
+@@ -146,64 +148,11 @@ symlink_maybe_no_target GENH/aisc.h
  
  # TEMPLATES directory
  
@@ -153,7 +164,7 @@
  defined $revision || die "expected known revision!";
 --- a/Makefile
 +++ b/Makefile
-@@ -1627,7 +1627,7 @@ redo_links: clean_links
+@@ -1625,7 +1625,7 @@ redo_links: clean_links
  #********************************************************************************
  
  header_libs:
@@ -162,7 +173,7 @@
  
  #********************************************************************************
  
-@@ -1659,7 +1659,7 @@ endif
+@@ -1657,7 +1657,7 @@ endif
  
  
  binlink:
@@ -171,8 +182,8 @@
  
  preplib:
  	(cd lib;$(MAKE) all)
-@@ -1933,7 +1933,7 @@ arb_external: convert tools gde readseq
- arb_no_perl: arbapplications help arb_external
+@@ -1924,7 +1924,7 @@ arb_external: convert tools gde readseq
+ arb_no_perl: arbapplications arb_external
  
  arb: 
 -	$(MAKE) "WITHPERL=1" perl arb_no_perl