AISC_MKPTPS/Makefile

+# for variables passed from parent makefile see ../SOURCE_TOOLS/parent_make.txt
+
+.SUFFIXES: .o .cxx .depend
+
+OBJECTS = mkptypes.o
+BINARY = aisc_mkpt
+
+LOCAL_DEFINES=-DSIMPLE_ARB_ASSERT
+LOCAL_MAKEDEPENDFLAGS=$(MAKEDEPENDFLAGS) $(LOCAL_DEFINES)
+
+$(MAIN): $(BINARY)
+
+$(BINARY): $(OBJECTS) $(use_ARB_main)
+	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(OBJECTS) $(EXECLIBS)
+
+.cxx.o:
+	$(A_CXX) $(cflags) $(cxxflags) $(LOCAL_DEFINES) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
+
+clean:
+	rm -f $(OBJECTS) $(BINARY)
+
+#depends:
+#	@echo "No depends here"
+
+DEPENDS = $(OBJECTS:.o=.depend)
+depends: $(DEPENDS)
+	@cat $(DEPENDS) | grep -v '^#' >>Makefile
+	@rm $(DEPENDS)
+$(DEPENDS): depend.init
+depend.init:
+	$(MAKEDEPEND) $(LOCAL_MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
+.cxx.depend:
+	$(MAKEDEPEND) -f- $(LOCAL_MAKEDEPENDFLAGS) $< 2>/dev/null >$@
+
+
+# DO NOT DELETE THIS LINE -- make depend depends on it.
+
+# Do not add dependencies manually - use 'make depend' in $ARBHOME
+# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from main)
+
+mkptypes.o: $(ARBHOME)/INCLUDE/arb_assert.h
+mkptypes.o: $(ARBHOME)/INCLUDE/arb_early_check.h
+mkptypes.o: $(ARBHOME)/INCLUDE/arb_simple_assert.h
+mkptypes.o: $(ARBHOME)/INCLUDE/arbtools.h
+mkptypes.o: $(ARBHOME)/INCLUDE/attributes.h
+mkptypes.o: $(ARBHOME)/INCLUDE/cxxforward.h
+mkptypes.o: $(ARBHOME)/INCLUDE/dupstr.h
+mkptypes.o: $(ARBHOME)/INCLUDE/gccver.h
+mkptypes.o: $(ARBHOME)/INCLUDE/static_assert.h
+mkptypes.o: $(ARBHOME)/INCLUDE/test_global.h
+mkptypes.o: $(ARBHOME)/INCLUDE/test_unit.h

AISC_MKPTPS/needs_libs.mkptypes_o

+# libraries needed to link against AISC_MKPTPS/mkptypes.o
+
+# none
+

SOURCE_TOOLS/Makefile

+.SUFFIXES: .o .cxx 
+
+SED:=$(ARBHOME)/SH/arb_sed
+
+all:
+		@echo "use make clean"
+
+# --------------------------------------------------------------------------------
+
+OBJECTS=arb_main_cpp.o arb_main_c.o
+
+ARB_MAIN_DEPENDS=Makefile arb_main.h
+
+arb_main_cpp.o: arb_main.cxx $(ARB_MAIN_DEPENDS) 
+	$(A_CXX) $(cflags) $(cxxflags) -c $< -o $@ $(CXX_INCLUDES) $(POST_COMPILE)
+
+arb_main_c.o: arb_main.c $(ARB_MAIN_DEPENDS) arb_main.cxx
+	$(A_CC) $(cflags) -c $< -o $@ $(CC_INCLUDES) $(POST_COMPILE)
+
+mainwrapper: $(OBJECTS)
+
+# --------------------------------------------------------------------------------
+
+clean: 
+		rm -f stamp.* valgrind2grep.lst postcompile.sav $(OBJECTS)
+
+valgrind_update:
+		./arb_valgrind update
+
+# --------------------------------------------------------------------------------
+
+# library dependencies generated here always use dynamic libnames,
+# even if LINK_STATIC=1 defined in ../Makefile@LINK_STATIC
+#
+# The files generated here are not used yet (so the above does not matter)
+# They are intended to be used to link all ARB binaries
+# (instead of using explicit link commands in ../Makefile)
+
+% : %.tmp
+	./mv_if_diff $< $@
+
+CORE_LIB=lib/libCORE.so
+
+TMP=dep.alltargets.tmp.tmp
+
+dep.alltargets.tmp: Makefile needed_libs.pl
+	LINK_STATIC=0;./needed_libs.pl -U -I -F $(CORE_LIB) > $(TMP)
+	$(SED) -e 's/ /\n/g' < $(TMP) > $@
+	rm $(TMP)
+	echo $(CORE_LIB) >>$@
+
+dep.libtargets: dep.alltargets
+	grep -E '\.(a|o|so)' $< > $@ || true
+
+dep.4dummy.tmp: dep.libtargets 
+	./gen_dep.pl dummy <$< >$@
+
+libdepends: dep.4dummy
+
+

SOURCE_TOOLS/Makefile.commitbuild

+
+MAIN_MAKE=$(MAKE) -C $(ARBHOME)
+
+REV_CHECK=$(ARBHOME)/SOURCE_TOOLS/rev_check.sh
+
+SUCCEEDED_REVISION:=$(shell $(REV_CHECK) last_succeeded)
+CURRENT_REVISION:=$(shell $(REV_CHECK) current)
+
+ifeq ($(SUCCEEDED_REVISION),$(CURRENT_REVISION))
+UPTODATE=1
+else
+UPTODATE=0
+endif
+
+
+build_CTARGET:
+ifeq ($(CTARGET),)
+	@echo "Error: You have to pass CTARGET to Makefile"
+	false
+else
+	@echo "Last success: '$(SUCCEEDED_REVISION)'"
+	@echo "Current rev:  '$(CURRENT_REVISION)'"
+#	@echo "Uptodate:     '$(UPTODATE)'"
+ifeq ($(UPTODATE),0)
+	@echo "Need to make '$(CTARGET)'"
+	+$(MAIN_MAKE) $(CTARGET)
+	$(REV_CHECK) set_succeeded
+else
+	@echo "Already did a successful '$(CTARGET)' for [$(SUCCEEDED_REVISION)]"
+endif
+endif
+
+reset:
+	$(REV_CHECK) reset

SOURCE_TOOLS/arb_main.c

+#include "arb_main.cxx"

SOURCE_TOOLS/arb_main.cxx

+// main-wrapper
+
+#include <arb_main.h>
+
+int ARB_main(int argc, char *argv[]);
+int main(int argc, char **argv) {
+    // this is the only main() we like in production code
+    // other main()'s occur in test-code
+    start_of_main();
+    return ARB_main(argc, argv);
+}

SOURCE_TOOLS/arb_main.h

+// ================================================================ //
+//                                                                  //
+//   File      : arb_main.h                                         //
+//   Purpose   : code executed at start of main()                   //
+//                                                                  //
+//   Coded by Ralf Westram (coder@reallysoft.de) in February 2014   //
+//   http://www.arb-home.de/                                        //
+//                                                                  //
+// ================================================================ //
+
+#ifndef ARB_MAIN_H
+#define ARB_MAIN_H
+
+#include <locale.h>
+
+static void start_of_main() {
+    // const char *USER_LOCALE = ""; // -> use user-defined locale
+    // const char *USER_LOCALE = "de_DE.UTF-8"; // use german locale
+
+
+    // gtk apparently calls 'setlocale(LC_ALL, "");'
+    // @@@ we should already call it here, to make ARB-motif-version behave samesame.
+
+    // --------------------------------------------------------------------------------
+    // Fails-counts mentioned below were determined under ubuntu 13.10/64bit.
+    // Make sure only one section is enabled!
+
+#if 1
+    // enabling this section does not fail any unit test
+    setlocale(LC_ALL,  "C");
+    // overwritten as soon as gtk-GUI starts (causing wrong behavior throughout ARB)
+#endif
+
+#if 0
+    // enabling this section does not fail any unit test
+    setlocale(LC_ALL,     USER_LOCALE);
+    setlocale(LC_NUMERIC, "C");
+#endif
+
+#if 0
+    // enabling this section does not fail any unit test
+    setlocale(LC_ALL,      "C");
+    setlocale(LC_COLLATE,  USER_LOCALE);
+    setlocale(LC_CTYPE,    USER_LOCALE);
+    setlocale(LC_MESSAGES, USER_LOCALE);
+    setlocale(LC_MONETARY, USER_LOCALE);
+    setlocale(LC_TIME,     USER_LOCALE);
+#endif
+
+
+#if 0
+    // enabling this section fails 57 unit tests (for german USER_LOCALE)
+    setlocale(LC_ALL, USER_LOCALE);
+#endif
+
+#if 0
+    // enabling this section fails 57 unit tests (for german USER_LOCALE)
+    setlocale(LC_COLLATE,  "C");
+    setlocale(LC_CTYPE,    "C");
+    setlocale(LC_MESSAGES, "C");
+    setlocale(LC_MONETARY, "C");
+    setlocale(LC_NUMERIC,  USER_LOCALE);
+    setlocale(LC_TIME,     "C");
+#endif
+
+#if 0
+    // enabling this section fails 57 unit tests (for german USER_LOCALE)
+    // (fails 57 unit tests under ubuntu 13.10, centos 5 and 6)
+    setlocale(LC_ALL,     "C");
+    setlocale(LC_NUMERIC, USER_LOCALE);
+#endif
+}
+
+#else
+#error arb_main.h included twice
+#endif // ARB_MAIN_H

TEMPLATES/arb_early_check.h

+// ================================================================ //
+//                                                                  //
+//   File      : arb_early_check.h                                  //
+//   Purpose   : early check for 32/64bit mismatch                  //
+//                                                                  //
+//   Coded by Ralf Westram (coder@reallysoft.de) in December 2012   //
+//   Institute of Microbiology (Technical University Munich)        //
+//   http://www.arb-home.de/                                        //
+//                                                                  //
+// ================================================================ //
+
+#ifndef ARB_EARLY_CHECK_H
+#define ARB_EARLY_CHECK_H
+
+#ifndef STATIC_ASSERT_H
+#include "static_assert.h"
+#endif
+
+// --------------------------------------------------------------------------------
+// if any of the assertions below fails, then ...
+// 
+// - edit ../config.makefile and correct ARB_64 to match your machine
+// - make clean
+// - make all
+
+#if defined(ARB_64)
+STATIC_ASSERT_ANNOTATED(sizeof(void*) == 8, "You cannot compile a 64bit-ARB on a 32bit-machine");
+#else // !defined(ARB_64)
+STATIC_ASSERT_ANNOTATED(sizeof(void*) == 4, "You cannot compile a 32bit-ARB on a 64bit-machine");
+#endif
+
+
+#else
+#error arb_early_check.h included twice
+#endif // ARB_EARLY_CHECK_H

TEMPLATES/arb_simple_assert.h

+// ============================================================ //
+//                                                              //
+//   File      : arb_simple_assert.h                            //
+//   Purpose   : simple assert (independent from libCORE)       //
+//                                                              //
+//   Coded by Ralf Westram (coder@reallysoft.de) in June 2013   //
+//   Institute of Microbiology (Technical University Munich)    //
+//   http://www.arb-home.de/                                    //
+//                                                              //
+// ============================================================ //
+
+#ifndef ARB_SIMPLE_ASSERT_H
+#define ARB_SIMPLE_ASSERT_H
+
+#if !defined(SIMPLE_ARB_ASSERT)
+#error you have to define SIMPLE_ARB_ASSERT in Makefile and pass it to compiler and makedepend
+// please DO NOT define SIMPLE_ARB_ASSERT in code
+#endif
+
+#ifndef ARB_ASSERT_H
+#include <arb_assert.h>
+#else
+#error included arb_simple_assert.h too late (arb_assert.h already has been included)
+#endif
+
+#else
+#error arb_simple_assert.h included twice
+#endif // ARB_SIMPLE_ASSERT_H

debian/copyright

@@ -9,7 +9,6 @@ Files-Excluded: arbsrc*/AISC_COM/C
                 arbsrc*/AISC_COM/AISC/aisc*
                 arbsrc*/AISC_COM/AISC/keys.README
                 arbsrc*/AISC_COM/AISC/magic.lst
-                arbsrc*/AISC_MKPTPS
                 arbsrc*/ARB_GDE
                 arbsrc*/AW*
                 arbsrc*/BINDEP
@@ -52,12 +51,10 @@ Files-Excluded: arbsrc*/AISC_COM/C
                 arbsrc*/SL/TREE_*
                 arbsrc*/SOURCE_TOOLS/COMPILE_COMPAT
                 arbsrc*/SOURCE_TOOLS/docs
-                arbsrc*/SOURCE_TOOLS/Makefile*
                 arbsrc*/SOURCE_TOOLS/arb.cloc.*
                 arbsrc*/SOURCE_TOOLS/arb_DEBUG.txt
                 arbsrc*/SOURCE_TOOLS/arb_cleanup_patches.pl
                 arbsrc*/SOURCE_TOOLS/arb_create_patch.sh
-                arbsrc*/SOURCE_TOOLS/arb_main*
                 arbsrc*/SOURCE_TOOLS/arb_valgrind*
                 arbsrc*/SOURCE_TOOLS/binuptodate.pl
                 arbsrc*/SOURCE_TOOLS/c*
@@ -77,9 +74,7 @@ Files-Excluded: arbsrc*/AISC_COM/C
                 arbsrc*/ST*
                 arbsrc*/TEMPLATES/C*
                 arbsrc*/TEMPLATES/arb_debug.h
-                arbsrc*/TEMPLATES/arb_early_check.h
                 arbsrc*/TEMPLATES/arb_forward_list.h
-                arbsrc*/TEMPLATES/arb_simple_assert.h
                 arbsrc*/TEMPLATES/arb_stdstr.h
                 arbsrc*/TEMPLATES/arb_unordered_map.h
                 arbsrc*/TEMPLATES/arb_version.h

debian/patches/fix_main_makefile.patch

@@ -315,7 +315,7 @@ Description: Strip everything from ARB Makefiles that's not contained in the
  
  build: arb
 -	$(MAKE) binlink preplib compile_compatibility
-+	$(MAKE) core db SL/HELIX/HELIX.dummy SL/PTCLEAN/PTCLEAN.dummy
++	$(MAKE) core db SL/HELIX/HELIX.dummy SL/PTCLEAN/PTCLEAN.dummy PROBE_COM/PROBE_COM.dummy
  
  all:
  	@echo "Build time" > $(TIMELOG)